Sending build context to Docker daemon 2.936GB Step 1/5 : FROM hugheylab/hugheyverse latest: Pulling from hugheylab/hugheyverse ae79f2514705: Pulling fs layer 5ad56d5fc149: Pulling fs layer 170e558760e8: Pulling fs layer 395460e233f5: Pulling fs layer 6f01dc62e444: Pulling fs layer 504db34ffd53: Pulling fs layer 470d81b2bd82: Pulling fs layer 4ec917438280: Pulling fs layer 8c431f001d99: Pulling fs layer 504db34ffd53: Waiting 470d81b2bd82: Waiting 395460e233f5: Waiting 6f01dc62e444: Waiting 4ec917438280: Waiting 8c431f001d99: Waiting 170e558760e8: Download complete 5ad56d5fc149: Verifying Checksum 5ad56d5fc149: Download complete 6f01dc62e444: Verifying Checksum 6f01dc62e444: Download complete 395460e233f5: Verifying Checksum 395460e233f5: Download complete 504db34ffd53: Verifying Checksum 504db34ffd53: Download complete 4ec917438280: Download complete ae79f2514705: Verifying Checksum ae79f2514705: Download complete ae79f2514705: Pull complete 5ad56d5fc149: Pull complete 170e558760e8: Pull complete 395460e233f5: Pull complete 6f01dc62e444: Pull complete 504db34ffd53: Pull complete 8c431f001d99: Verifying Checksum 8c431f001d99: Download complete 470d81b2bd82: Verifying Checksum 470d81b2bd82: Download complete 470d81b2bd82: Pull complete 4ec917438280: Pull complete 8c431f001d99: Pull complete Digest: sha256:e2692a9bb5a63e65c16ae46add2ad80f9bb4557d62d25136b2b56dcec0ed0928 Status: Downloaded newer image for hugheylab/hugheyverse:latest ---> 16f0c9501b24 Step 2/5 : MAINTAINER "Jake Hughey" jakejhughey@gmail.com ---> Running in 83018eb9db71 ---> 11dfd57bd01f Removing intermediate container 83018eb9db71 Step 3/5 : COPY analysis /analysis ---> fd696f7a845d Step 4/5 : WORKDIR /analysis ---> 4220a803c841 Removing intermediate container fdda4ec3855f Step 5/5 : RUN Rscript install_packages.R && rm -rf /tmp/downloaded_packages/ /tmp/*.rds && ./analyze_all.sh ---> Running in 2333050b8389 Bioconductor version 3.6 (BiocInstaller 1.28.0), ?biocLite for help BioC_mirror: https://bioconductor.org Using Bioconductor 3.6 (BiocInstaller 1.28.0), R 3.4.2 (2017-09-28). Installing package(s) 'GO.db', 'impute' trying URL 'https://bioconductor.org/packages/3.6/data/annotation/src/contrib/GO.db_3.5.0.tar.gz' Content type 'application/x-gzip' length 31663705 bytes (30.2 MB) ================================================== downloaded 30.2 MB trying URL 'https://bioconductor.org/packages/3.6/bioc/src/contrib/impute_1.52.0.tar.gz' Content type 'application/x-gzip' length 641451 bytes (626 KB) ================================================== downloaded 626 KB * installing *source* package 'GO.db' ... ** R ** inst ** preparing package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded * DONE (GO.db) * installing *source* package 'impute' ... ** libs gfortran -fpic -g -O2 -fstack-protector-strong -c knnimpute.f -o knnimpute.o gcc -std=gnu99 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o impute.so knnimpute.o -lgfortran -lm -lquadmath -L/usr/lib/R/lib -lR installing to /usr/local/lib/R/site-library/impute/libs ** R ** data ** preparing package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded * DONE (impute)  The downloaded source packages are in '/tmp/RtmpxNJ6sA/downloaded_packages' Updating packages 'GEOquery', 'RCurl', 'Rcpp', 'backports', 'curl', 'dbplyr', 'digest', 'foreach', 'git2r', 'hms', 'iterators', 'knitr', 'limma', 'openssl', 'proxy', 'registry', 'reshape2', 'rlang', 'rprojroot', 'stringi', 'tibble', 'tidyselect', 'withr', 'yaml', 'XML', 'bitops', 'littler', 'MASS', 'Matrix', 'codetools', 'lattice', 'spatial' also installing the dependencies 'utf8', 'pillar' trying URL 'https://cran.rstudio.com/src/contrib/utf8_1.1.3.tar.gz' Content type 'application/x-gzip' length 217735 bytes (212 KB) ================================================== downloaded 212 KB trying URL 'https://cran.rstudio.com/src/contrib/pillar_1.0.1.tar.gz' Content type 'application/x-gzip' length 69210 bytes (67 KB) ================================================== downloaded 67 KB trying URL 'https://bioconductor.org/packages/3.6/bioc/src/contrib/GEOquery_2.46.13.tar.gz' Content type 'application/x-gzip' length 13745245 bytes (13.1 MB) ================================================== downloaded 13.1 MB trying URL 'https://cran.rstudio.com/src/contrib/RCurl_1.95-4.9.tar.gz' Content type 'application/x-gzip' length 917039 bytes (895 KB) ================================================== downloaded 895 KB trying URL 'https://cran.rstudio.com/src/contrib/Rcpp_0.12.14.tar.gz' Content type 'application/x-gzip' length 3756532 bytes (3.6 MB) ================================================== downloaded 3.6 MB trying URL 'https://cran.rstudio.com/src/contrib/backports_1.1.2.tar.gz' Content type 'application/x-gzip' length 10900 bytes (10 KB) ================================================== downloaded 10 KB trying URL 'https://cran.rstudio.com/src/contrib/curl_3.1.tar.gz' Content type 'application/x-gzip' length 366086 bytes (357 KB) ================================================== downloaded 357 KB trying URL 'https://cran.rstudio.com/src/contrib/dbplyr_1.2.0.tar.gz' Content type 'application/x-gzip' length 263521 bytes (257 KB) ================================================== downloaded 257 KB trying URL 'https://cran.rstudio.com/src/contrib/digest_0.6.13.tar.gz' Content type 'application/x-gzip' length 121202 bytes (118 KB) ================================================== downloaded 118 KB trying URL 'https://cran.rstudio.com/src/contrib/foreach_1.4.4.tar.gz' Content type 'application/x-gzip' length 360705 bytes (352 KB) ================================================== downloaded 352 KB trying URL 'https://cran.rstudio.com/src/contrib/git2r_0.20.0.tar.gz' Content type 'application/x-gzip' length 1161747 bytes (1.1 MB) ================================================== downloaded 1.1 MB trying URL 'https://cran.rstudio.com/src/contrib/hms_0.4.0.tar.gz' Content type 'application/x-gzip' length 12506 bytes (12 KB) ================================================== downloaded 12 KB trying URL 'https://cran.rstudio.com/src/contrib/iterators_1.0.9.tar.gz' Content type 'application/x-gzip' length 290634 bytes (283 KB) ================================================== downloaded 283 KB trying URL 'https://cran.rstudio.com/src/contrib/knitr_1.18.tar.gz' Content type 'application/x-gzip' length 649748 bytes (634 KB) ================================================== downloaded 634 KB trying URL 'https://bioconductor.org/packages/3.6/bioc/src/contrib/limma_3.34.5.tar.gz' Content type 'application/x-gzip' length 1473189 bytes (1.4 MB) ================================================== downloaded 1.4 MB trying URL 'https://cran.rstudio.com/src/contrib/openssl_0.9.9.tar.gz' Content type 'application/x-gzip' length 1112927 bytes (1.1 MB) ================================================== downloaded 1.1 MB trying URL 'https://cran.rstudio.com/src/contrib/proxy_0.4-20.tar.gz' Content type 'application/x-gzip' length 115783 bytes (113 KB) ================================================== downloaded 113 KB trying URL 'https://cran.rstudio.com/src/contrib/registry_0.5.tar.gz' Content type 'application/x-gzip' length 182463 bytes (178 KB) ================================================== downloaded 178 KB trying URL 'https://cran.rstudio.com/src/contrib/reshape2_1.4.3.tar.gz' Content type 'application/x-gzip' length 36405 bytes (35 KB) ================================================== downloaded 35 KB trying URL 'https://cran.rstudio.com/src/contrib/rlang_0.1.6.tar.gz' Content type 'application/x-gzip' length 202290 bytes (197 KB) ================================================== downloaded 197 KB trying URL 'https://cran.rstudio.com/src/contrib/rprojroot_1.3-1.tar.gz' Content type 'application/x-gzip' length 50302 bytes (49 KB) ================================================== downloaded 49 KB trying URL 'https://cran.rstudio.com/src/contrib/stringi_1.1.6.tar.gz' Content type 'application/x-gzip' length 3647049 bytes (3.5 MB) ================================================== downloaded 3.5 MB trying URL 'https://cran.rstudio.com/src/contrib/tibble_1.4.1.tar.gz' Content type 'application/x-gzip' length 108604 bytes (106 KB) ================================================== downloaded 106 KB trying URL 'https://cran.rstudio.com/src/contrib/tidyselect_0.2.3.tar.gz' Content type 'application/x-gzip' length 21704 bytes (21 KB) ================================================== downloaded 21 KB trying URL 'https://cran.rstudio.com/src/contrib/withr_2.1.1.tar.gz' Content type 'application/x-gzip' length 52603 bytes (51 KB) ================================================== downloaded 51 KB trying URL 'https://cran.rstudio.com/src/contrib/yaml_2.1.16.tar.gz' Content type 'application/x-gzip' length 85275 bytes (83 KB) ================================================== downloaded 83 KB * installing *source* package 'utf8' ... ** package 'utf8' successfully unpacked and MD5 sums checked ** libs gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -Iutf8lite/src -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c as_utf8.c -o as_utf8.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -Iutf8lite/src -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c bytes.c -o bytes.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -Iutf8lite/src -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c context.c -o context.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -Iutf8lite/src -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c init.c -o init.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -Iutf8lite/src -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c render.c -o render.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -Iutf8lite/src -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c render_table.c -o render_table.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -Iutf8lite/src -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c string.c -o string.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -Iutf8lite/src -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c text.c -o text.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -Iutf8lite/src -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c utf8_encode.c -o utf8_encode.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -Iutf8lite/src -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c utf8_format.c -o utf8_format.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -Iutf8lite/src -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c utf8_normalize.c -o utf8_normalize.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -Iutf8lite/src -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c utf8_valid.c -o utf8_valid.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -Iutf8lite/src -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c utf8_width.c -o utf8_width.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -Iutf8lite/src -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c util.c -o util.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -Iutf8lite/src -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c utf8lite/src/array.c -o utf8lite/src/array.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -Iutf8lite/src -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c utf8lite/src/char.c -o utf8lite/src/char.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -Iutf8lite/src -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c utf8lite/src/encode.c -o utf8lite/src/encode.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -Iutf8lite/src -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c utf8lite/src/error.c -o utf8lite/src/error.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -Iutf8lite/src -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c utf8lite/src/escape.c -o utf8lite/src/escape.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -Iutf8lite/src -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c utf8lite/src/graph.c -o utf8lite/src/graph.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -Iutf8lite/src -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c utf8lite/src/graphscan.c -o utf8lite/src/graphscan.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -Iutf8lite/src -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c utf8lite/src/normalize.c -o utf8lite/src/normalize.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -Iutf8lite/src -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c utf8lite/src/render.c -o utf8lite/src/render.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -Iutf8lite/src -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c utf8lite/src/text.c -o utf8lite/src/text.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -Iutf8lite/src -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c utf8lite/src/textassign.c -o utf8lite/src/textassign.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -Iutf8lite/src -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c utf8lite/src/textiter.c -o utf8lite/src/textiter.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -Iutf8lite/src -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c utf8lite/src/textmap.c -o utf8lite/src/textmap.o ar rcs libcutf8lite.a utf8lite/src/array.o utf8lite/src/char.o utf8lite/src/encode.o utf8lite/src/error.o utf8lite/src/escape.o utf8lite/src/graph.o utf8lite/src/graphscan.o utf8lite/src/normalize.o utf8lite/src/render.o utf8lite/src/text.o utf8lite/src/textassign.o utf8lite/src/textiter.o utf8lite/src/textmap.o ranlib libcutf8lite.a gcc -std=gnu99 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o utf8.so as_utf8.o bytes.o context.o init.o render.o render_table.o string.o text.o utf8_encode.o utf8_format.o utf8_normalize.o utf8_valid.o utf8_width.o util.o -L. -lcutf8lite -L/usr/lib/R/lib -lR installing to /usr/local/lib/R/site-library/utf8/libs ** R ** inst ** preparing package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded * DONE (utf8) * installing *source* package 'RCurl' ... ** package 'RCurl' successfully unpacked and MD5 sums checked checking for curl-config... /usr/bin/curl-config checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking how to run the C preprocessor... gcc -E Version has a libidn field Version has CURLOPT_URL Version has CURLINFO_EFFECTIVE_URL Version has CURLINFO_RESPONSE_CODE Version has CURLINFO_TOTAL_TIME Version has CURLINFO_NAMELOOKUP_TIME Version has CURLINFO_CONNECT_TIME Version has CURLINFO_PRETRANSFER_TIME Version has CURLINFO_SIZE_UPLOAD Version has CURLINFO_SIZE_DOWNLOAD Version has CURLINFO_SPEED_DOWNLOAD Version has CURLINFO_SPEED_UPLOAD Version has CURLINFO_HEADER_SIZE Version has CURLINFO_REQUEST_SIZE Version has CURLINFO_SSL_VERIFYRESULT Version has CURLINFO_FILETIME Version has CURLINFO_CONTENT_LENGTH_DOWNLOAD Version has CURLINFO_CONTENT_LENGTH_UPLOAD Version has CURLINFO_STARTTRANSFER_TIME Version has CURLINFO_CONTENT_TYPE Version has CURLINFO_REDIRECT_TIME Version has CURLINFO_REDIRECT_COUNT Version has CURLINFO_PRIVATE Version has CURLINFO_HTTP_CONNECTCODE Version has CURLINFO_HTTPAUTH_AVAIL Version has CURLINFO_PROXYAUTH_AVAIL Version has CURLINFO_OS_ERRNO Version has CURLINFO_NUM_CONNECTS Version has CURLINFO_SSL_ENGINES Version has CURLINFO_COOKIELIST Version has CURLINFO_LASTSOCKET Version has CURLINFO_FTP_ENTRY_PATH Version has CURLINFO_REDIRECT_URL Version has CURLINFO_PRIMARY_IP Version has CURLINFO_APPCONNECT_TIME Version has CURLINFO_CERTINFO Version has CURLINFO_CONDITION_UNMET Version has CURLOPT_WRITEDATA Version has CURLOPT_KEYPASSWD Version has CURLOPT_DIRLISTONLY Version has CURLOPT_APPEND Version has CURLOPT_KRBLEVEL Version has CURLOPT_USE_SSL Version has CURLOPT_TIMEOUT_MS Version has CURLOPT_CONNECTTIMEOUT_MS Version has CURLOPT_HTTP_TRANSFER_DECODING Version has CURLOPT_HTTP_CONTENT_DECODING Version has CURLOPT_NEW_FILE_PERMS Version has CURLOPT_NEW_DIRECTORY_PERMS Version has CURLOPT_POSTREDIR Version has CURLOPT_OPENSOCKETFUNCTION Version has CURLOPT_OPENSOCKETDATA Version has CURLOPT_COPYPOSTFIELDS Version has CURLOPT_PROXY_TRANSFER_MODE Version has CURLOPT_SEEKFUNCTION Version has CURLOPT_SEEKDATA Version has CURLOPT_CRLFILE Version has CURLOPT_ISSUERCERT Version has CURLOPT_ADDRESS_SCOPE Version has CURLOPT_CERTINFO Version has CURLOPT_USERNAME Version has CURLOPT_PASSWORD Version has CURLOPT_PROXYUSERNAME Version has CURLOPT_PROXYPASSWORD Version has CURLOPT_SSH_HOST_PUBLIC_KEY_MD5 Version has CURLOPT_NOPROXY Version has CURLOPT_TFTP_BLKSIZE Version has CURLOPT_SOCKS5_GSSAPI_SERVICE Version has CURLOPT_SOCKS5_GSSAPI_NEC Version has CURLOPT_PROTOCOLS Version has CURLOPT_REDIR_PROTOCOLS Version has CURLOPT_SSH_AUTH_TYPES Version has CURLOPT_SSH_PUBLIC_KEYFILE Version has CURLOPT_SSH_PRIVATE_KEYFILE Version has CURLOPT_FTP_SSL_CCC Version has CURLOPT_COOKIELIST Version has CURLOPT_IGNORE_CONTENT_LENGTH Version has CURLOPT_FTP_SKIP_PASV_IP Version has CURLOPT_FTP_FILEMETHOD Version has CURLOPT_LOCALPORT Version has CURLOPT_LOCALPORTRANGE Version has CURLOPT_CONNECT_ONLY Version has CURLOPT_CONV_FROM_NETWORK_FUNCTION Version has CURLOPT_CONV_TO_NETWORK_FUNCTION Version has CURLOPT_CONV_FROM_UTF8_FUNCTION Version has CURLOPT_MAX_SEND_SPEED_LARGE Version has CURLOPT_MAX_RECV_SPEED_LARGE Version has CURLOPT_FTP_ALTERNATIVE_TO_USER Version has CURLOPT_SOCKOPTFUNCTION Version has CURLOPT_SOCKOPTDATA Version has CURLOPT_SSL_SESSIONID_CACHE libcurl version: libcurl 7.47.0 configure: creating ./config.status config.status: creating src/Makevars ** libs gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DHAVE_LIBIDN_FIELD=1 -DHAVE_CURLOPT_URL=1 -DHAVE_CURLINFO_EFFECTIVE_URL=1 -DHAVE_CURLINFO_RESPONSE_CODE=1 -DHAVE_CURLINFO_TOTAL_TIME=1 -DHAVE_CURLINFO_NAMELOOKUP_TIME=1 -DHAVE_CURLINFO_CONNECT_TIME=1 -DHAVE_CURLINFO_PRETRANSFER_TIME=1 -DHAVE_CURLINFO_SIZE_UPLOAD=1 -DHAVE_CURLINFO_SIZE_DOWNLOAD=1 -DHAVE_CURLINFO_SPEED_DOWNLOAD=1 -DHAVE_CURLINFO_SPEED_UPLOAD=1 -DHAVE_CURLINFO_HEADER_SIZE=1 -DHAVE_CURLINFO_REQUEST_SIZE=1 -DHAVE_CURLINFO_SSL_VERIFYRESULT=1 -DHAVE_CURLINFO_FILETIME=1 -DHAVE_CURLINFO_CONTENT_LENGTH_DOWNLOAD=1 -DHAVE_CURLINFO_CONTENT_LENGTH_UPLOAD=1 -DHAVE_CURLINFO_STARTTRANSFER_TIME=1 -DHAVE_CURLINFO_CONTENT_TYPE=1 -DHAVE_CURLINFO_REDIRECT_TIME=1 -DHAVE_CURLINFO_REDIRECT_COUNT=1 -DHAVE_CURLINFO_PRIVATE=1 -DHAVE_CURLINFO_HTTP_CONNECTCODE=1 -DHAVE_CURLINFO_HTTPAUTH_AVAIL=1 -DHAVE_CURLINFO_PROXYAUTH_AVAIL=1 -DHAVE_CURLINFO_OS_ERRNO=1 -DHAVE_CURLINFO_NUM_CONNECTS=1 -DHAVE_CURLINFO_SSL_ENGINES=1 -DHAVE_CURLINFO_COOKIELIST=1 -DHAVE_CURLINFO_LASTSOCKET=1 -DHAVE_CURLINFO_FTP_ENTRY_PATH=1 -DHAVE_CURLINFO_REDIRECT_URL=1 -DHAVE_CURLINFO_PRIMARY_IP=1 -DHAVE_CURLINFO_APPCONNECT_TIME=1 -DHAVE_CURLINFO_CERTINFO=1 -DHAVE_CURLINFO_CONDITION_UNMET=1 -DHAVE_CURLOPT_WRITEDATA=1 -DHAVE_CURLOPT_KEYPASSWD=1 -DHAVE_CURLOPT_DIRLISTONLY=1 -DHAVE_CURLOPT_APPEND=1 -DHAVE_CURLOPT_KRBLEVEL=1 -DHAVE_CURLOPT_USE_SSL=1 -DHAVE_CURLOPT_TIMEOUT_MS=1 -DHAVE_CURLOPT_CONNECTTIMEOUT_MS=1 -DHAVE_CURLOPT_HTTP_TRANSFER_DECODING=1 -DHAVE_CURLOPT_HTTP_CONTENT_DECODING=1 -DHAVE_CURLOPT_NEW_FILE_PERMS=1 -DHAVE_CURLOPT_NEW_DIRECTORY_PERMS=1 -DHAVE_CURLOPT_POSTREDIR=1 -DHAVE_CURLOPT_OPENSOCKETFUNCTION=1 -DHAVE_CURLOPT_OPENSOCKETDATA=1 -DHAVE_CURLOPT_COPYPOSTFIELDS=1 -DHAVE_CURLOPT_PROXY_TRANSFER_MODE=1 -DHAVE_CURLOPT_SEEKFUNCTION=1 -DHAVE_CURLOPT_SEEKDATA=1 -DHAVE_CURLOPT_CRLFILE=1 -DHAVE_CURLOPT_ISSUERCERT=1 -DHAVE_CURLOPT_ADDRESS_SCOPE=1 -DHAVE_CURLOPT_CERTINFO=1 -DHAVE_CURLOPT_USERNAME=1 -DHAVE_CURLOPT_PASSWORD=1 -DHAVE_CURLOPT_PROXYUSERNAME=1 -DHAVE_CURLOPT_PROXYPASSWORD=1 -DHAVE_CURLOPT_SSH_HOST_PUBLIC_KEY_MD5=1 -DHAVE_CURLOPT_NOPROXY=1 -DHAVE_CURLOPT_TFTP_BLKSIZE=1 -DHAVE_CURLOPT_SOCKS5_GSSAPI_SERVICE=1 -DHAVE_CURLOPT_SOCKS5_GSSAPI_NEC=1 -DHAVE_CURLOPT_PROTOCOLS=1 -DHAVE_CURLOPT_REDIR_PROTOCOLS=1 -DHAVE_CURLOPT_SSH_AUTH_TYPES=1 -DHAVE_CURLOPT_SSH_PUBLIC_KEYFILE=1 -DHAVE_CURLOPT_SSH_PRIVATE_KEYFILE=1 -DHAVE_CURLOPT_FTP_SSL_CCC=1 -DHAVE_CURLOPT_COOKIELIST=1 -DHAVE_CURLOPT_IGNORE_CONTENT_LENGTH=1 -DHAVE_CURLOPT_FTP_SKIP_PASV_IP=1 -DHAVE_CURLOPT_FTP_FILEMETHOD=1 -DHAVE_CURLOPT_LOCALPORT=1 -DHAVE_CURLOPT_LOCALPORTRANGE=1 -DHAVE_CURLOPT_CONNECT_ONLY=1 -DHAVE_CURLOPT_CONV_FROM_NETWORK_FUNCTION=1 -DHAVE_CURLOPT_CONV_TO_NETWORK_FUNCTION=1 -DHAVE_CURLOPT_CONV_FROM_UTF8_FUNCTION=1 -DHAVE_CURLOPT_MAX_SEND_SPEED_LARGE=1 -DHAVE_CURLOPT_MAX_RECV_SPEED_LARGE=1 -DHAVE_CURLOPT_FTP_ALTERNATIVE_TO_USER=1 -DHAVE_CURLOPT_SOCKOPTFUNCTION=1 -DHAVE_CURLOPT_SOCKOPTDATA=1 -DHAVE_CURLOPT_SSL_SESSIONID_CACHE=1 -I/usr/include/libxml2 -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c base64.c -o base64.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DHAVE_LIBIDN_FIELD=1 -DHAVE_CURLOPT_URL=1 -DHAVE_CURLINFO_EFFECTIVE_URL=1 -DHAVE_CURLINFO_RESPONSE_CODE=1 -DHAVE_CURLINFO_TOTAL_TIME=1 -DHAVE_CURLINFO_NAMELOOKUP_TIME=1 -DHAVE_CURLINFO_CONNECT_TIME=1 -DHAVE_CURLINFO_PRETRANSFER_TIME=1 -DHAVE_CURLINFO_SIZE_UPLOAD=1 -DHAVE_CURLINFO_SIZE_DOWNLOAD=1 -DHAVE_CURLINFO_SPEED_DOWNLOAD=1 -DHAVE_CURLINFO_SPEED_UPLOAD=1 -DHAVE_CURLINFO_HEADER_SIZE=1 -DHAVE_CURLINFO_REQUEST_SIZE=1 -DHAVE_CURLINFO_SSL_VERIFYRESULT=1 -DHAVE_CURLINFO_FILETIME=1 -DHAVE_CURLINFO_CONTENT_LENGTH_DOWNLOAD=1 -DHAVE_CURLINFO_CONTENT_LENGTH_UPLOAD=1 -DHAVE_CURLINFO_STARTTRANSFER_TIME=1 -DHAVE_CURLINFO_CONTENT_TYPE=1 -DHAVE_CURLINFO_REDIRECT_TIME=1 -DHAVE_CURLINFO_REDIRECT_COUNT=1 -DHAVE_CURLINFO_PRIVATE=1 -DHAVE_CURLINFO_HTTP_CONNECTCODE=1 -DHAVE_CURLINFO_HTTPAUTH_AVAIL=1 -DHAVE_CURLINFO_PROXYAUTH_AVAIL=1 -DHAVE_CURLINFO_OS_ERRNO=1 -DHAVE_CURLINFO_NUM_CONNECTS=1 -DHAVE_CURLINFO_SSL_ENGINES=1 -DHAVE_CURLINFO_COOKIELIST=1 -DHAVE_CURLINFO_LASTSOCKET=1 -DHAVE_CURLINFO_FTP_ENTRY_PATH=1 -DHAVE_CURLINFO_REDIRECT_URL=1 -DHAVE_CURLINFO_PRIMARY_IP=1 -DHAVE_CURLINFO_APPCONNECT_TIME=1 -DHAVE_CURLINFO_CERTINFO=1 -DHAVE_CURLINFO_CONDITION_UNMET=1 -DHAVE_CURLOPT_WRITEDATA=1 -DHAVE_CURLOPT_KEYPASSWD=1 -DHAVE_CURLOPT_DIRLISTONLY=1 -DHAVE_CURLOPT_APPEND=1 -DHAVE_CURLOPT_KRBLEVEL=1 -DHAVE_CURLOPT_USE_SSL=1 -DHAVE_CURLOPT_TIMEOUT_MS=1 -DHAVE_CURLOPT_CONNECTTIMEOUT_MS=1 -DHAVE_CURLOPT_HTTP_TRANSFER_DECODING=1 -DHAVE_CURLOPT_HTTP_CONTENT_DECODING=1 -DHAVE_CURLOPT_NEW_FILE_PERMS=1 -DHAVE_CURLOPT_NEW_DIRECTORY_PERMS=1 -DHAVE_CURLOPT_POSTREDIR=1 -DHAVE_CURLOPT_OPENSOCKETFUNCTION=1 -DHAVE_CURLOPT_OPENSOCKETDATA=1 -DHAVE_CURLOPT_COPYPOSTFIELDS=1 -DHAVE_CURLOPT_PROXY_TRANSFER_MODE=1 -DHAVE_CURLOPT_SEEKFUNCTION=1 -DHAVE_CURLOPT_SEEKDATA=1 -DHAVE_CURLOPT_CRLFILE=1 -DHAVE_CURLOPT_ISSUERCERT=1 -DHAVE_CURLOPT_ADDRESS_SCOPE=1 -DHAVE_CURLOPT_CERTINFO=1 -DHAVE_CURLOPT_USERNAME=1 -DHAVE_CURLOPT_PASSWORD=1 -DHAVE_CURLOPT_PROXYUSERNAME=1 -DHAVE_CURLOPT_PROXYPASSWORD=1 -DHAVE_CURLOPT_SSH_HOST_PUBLIC_KEY_MD5=1 -DHAVE_CURLOPT_NOPROXY=1 -DHAVE_CURLOPT_TFTP_BLKSIZE=1 -DHAVE_CURLOPT_SOCKS5_GSSAPI_SERVICE=1 -DHAVE_CURLOPT_SOCKS5_GSSAPI_NEC=1 -DHAVE_CURLOPT_PROTOCOLS=1 -DHAVE_CURLOPT_REDIR_PROTOCOLS=1 -DHAVE_CURLOPT_SSH_AUTH_TYPES=1 -DHAVE_CURLOPT_SSH_PUBLIC_KEYFILE=1 -DHAVE_CURLOPT_SSH_PRIVATE_KEYFILE=1 -DHAVE_CURLOPT_FTP_SSL_CCC=1 -DHAVE_CURLOPT_COOKIELIST=1 -DHAVE_CURLOPT_IGNORE_CONTENT_LENGTH=1 -DHAVE_CURLOPT_FTP_SKIP_PASV_IP=1 -DHAVE_CURLOPT_FTP_FILEMETHOD=1 -DHAVE_CURLOPT_LOCALPORT=1 -DHAVE_CURLOPT_LOCALPORTRANGE=1 -DHAVE_CURLOPT_CONNECT_ONLY=1 -DHAVE_CURLOPT_CONV_FROM_NETWORK_FUNCTION=1 -DHAVE_CURLOPT_CONV_TO_NETWORK_FUNCTION=1 -DHAVE_CURLOPT_CONV_FROM_UTF8_FUNCTION=1 -DHAVE_CURLOPT_MAX_SEND_SPEED_LARGE=1 -DHAVE_CURLOPT_MAX_RECV_SPEED_LARGE=1 -DHAVE_CURLOPT_FTP_ALTERNATIVE_TO_USER=1 -DHAVE_CURLOPT_SOCKOPTFUNCTION=1 -DHAVE_CURLOPT_SOCKOPTDATA=1 -DHAVE_CURLOPT_SSL_SESSIONID_CACHE=1 -I/usr/include/libxml2 -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c curl.c -o curl.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DHAVE_LIBIDN_FIELD=1 -DHAVE_CURLOPT_URL=1 -DHAVE_CURLINFO_EFFECTIVE_URL=1 -DHAVE_CURLINFO_RESPONSE_CODE=1 -DHAVE_CURLINFO_TOTAL_TIME=1 -DHAVE_CURLINFO_NAMELOOKUP_TIME=1 -DHAVE_CURLINFO_CONNECT_TIME=1 -DHAVE_CURLINFO_PRETRANSFER_TIME=1 -DHAVE_CURLINFO_SIZE_UPLOAD=1 -DHAVE_CURLINFO_SIZE_DOWNLOAD=1 -DHAVE_CURLINFO_SPEED_DOWNLOAD=1 -DHAVE_CURLINFO_SPEED_UPLOAD=1 -DHAVE_CURLINFO_HEADER_SIZE=1 -DHAVE_CURLINFO_REQUEST_SIZE=1 -DHAVE_CURLINFO_SSL_VERIFYRESULT=1 -DHAVE_CURLINFO_FILETIME=1 -DHAVE_CURLINFO_CONTENT_LENGTH_DOWNLOAD=1 -DHAVE_CURLINFO_CONTENT_LENGTH_UPLOAD=1 -DHAVE_CURLINFO_STARTTRANSFER_TIME=1 -DHAVE_CURLINFO_CONTENT_TYPE=1 -DHAVE_CURLINFO_REDIRECT_TIME=1 -DHAVE_CURLINFO_REDIRECT_COUNT=1 -DHAVE_CURLINFO_PRIVATE=1 -DHAVE_CURLINFO_HTTP_CONNECTCODE=1 -DHAVE_CURLINFO_HTTPAUTH_AVAIL=1 -DHAVE_CURLINFO_PROXYAUTH_AVAIL=1 -DHAVE_CURLINFO_OS_ERRNO=1 -DHAVE_CURLINFO_NUM_CONNECTS=1 -DHAVE_CURLINFO_SSL_ENGINES=1 -DHAVE_CURLINFO_COOKIELIST=1 -DHAVE_CURLINFO_LASTSOCKET=1 -DHAVE_CURLINFO_FTP_ENTRY_PATH=1 -DHAVE_CURLINFO_REDIRECT_URL=1 -DHAVE_CURLINFO_PRIMARY_IP=1 -DHAVE_CURLINFO_APPCONNECT_TIME=1 -DHAVE_CURLINFO_CERTINFO=1 -DHAVE_CURLINFO_CONDITION_UNMET=1 -DHAVE_CURLOPT_WRITEDATA=1 -DHAVE_CURLOPT_KEYPASSWD=1 -DHAVE_CURLOPT_DIRLISTONLY=1 -DHAVE_CURLOPT_APPEND=1 -DHAVE_CURLOPT_KRBLEVEL=1 -DHAVE_CURLOPT_USE_SSL=1 -DHAVE_CURLOPT_TIMEOUT_MS=1 -DHAVE_CURLOPT_CONNECTTIMEOUT_MS=1 -DHAVE_CURLOPT_HTTP_TRANSFER_DECODING=1 -DHAVE_CURLOPT_HTTP_CONTENT_DECODING=1 -DHAVE_CURLOPT_NEW_FILE_PERMS=1 -DHAVE_CURLOPT_NEW_DIRECTORY_PERMS=1 -DHAVE_CURLOPT_POSTREDIR=1 -DHAVE_CURLOPT_OPENSOCKETFUNCTION=1 -DHAVE_CURLOPT_OPENSOCKETDATA=1 -DHAVE_CURLOPT_COPYPOSTFIELDS=1 -DHAVE_CURLOPT_PROXY_TRANSFER_MODE=1 -DHAVE_CURLOPT_SEEKFUNCTION=1 -DHAVE_CURLOPT_SEEKDATA=1 -DHAVE_CURLOPT_CRLFILE=1 -DHAVE_CURLOPT_ISSUERCERT=1 -DHAVE_CURLOPT_ADDRESS_SCOPE=1 -DHAVE_CURLOPT_CERTINFO=1 -DHAVE_CURLOPT_USERNAME=1 -DHAVE_CURLOPT_PASSWORD=1 -DHAVE_CURLOPT_PROXYUSERNAME=1 -DHAVE_CURLOPT_PROXYPASSWORD=1 -DHAVE_CURLOPT_SSH_HOST_PUBLIC_KEY_MD5=1 -DHAVE_CURLOPT_NOPROXY=1 -DHAVE_CURLOPT_TFTP_BLKSIZE=1 -DHAVE_CURLOPT_SOCKS5_GSSAPI_SERVICE=1 -DHAVE_CURLOPT_SOCKS5_GSSAPI_NEC=1 -DHAVE_CURLOPT_PROTOCOLS=1 -DHAVE_CURLOPT_REDIR_PROTOCOLS=1 -DHAVE_CURLOPT_SSH_AUTH_TYPES=1 -DHAVE_CURLOPT_SSH_PUBLIC_KEYFILE=1 -DHAVE_CURLOPT_SSH_PRIVATE_KEYFILE=1 -DHAVE_CURLOPT_FTP_SSL_CCC=1 -DHAVE_CURLOPT_COOKIELIST=1 -DHAVE_CURLOPT_IGNORE_CONTENT_LENGTH=1 -DHAVE_CURLOPT_FTP_SKIP_PASV_IP=1 -DHAVE_CURLOPT_FTP_FILEMETHOD=1 -DHAVE_CURLOPT_LOCALPORT=1 -DHAVE_CURLOPT_LOCALPORTRANGE=1 -DHAVE_CURLOPT_CONNECT_ONLY=1 -DHAVE_CURLOPT_CONV_FROM_NETWORK_FUNCTION=1 -DHAVE_CURLOPT_CONV_TO_NETWORK_FUNCTION=1 -DHAVE_CURLOPT_CONV_FROM_UTF8_FUNCTION=1 -DHAVE_CURLOPT_MAX_SEND_SPEED_LARGE=1 -DHAVE_CURLOPT_MAX_RECV_SPEED_LARGE=1 -DHAVE_CURLOPT_FTP_ALTERNATIVE_TO_USER=1 -DHAVE_CURLOPT_SOCKOPTFUNCTION=1 -DHAVE_CURLOPT_SOCKOPTDATA=1 -DHAVE_CURLOPT_SSL_SESSIONID_CACHE=1 -I/usr/include/libxml2 -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c curlInit.c -o curlInit.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DHAVE_LIBIDN_FIELD=1 -DHAVE_CURLOPT_URL=1 -DHAVE_CURLINFO_EFFECTIVE_URL=1 -DHAVE_CURLINFO_RESPONSE_CODE=1 -DHAVE_CURLINFO_TOTAL_TIME=1 -DHAVE_CURLINFO_NAMELOOKUP_TIME=1 -DHAVE_CURLINFO_CONNECT_TIME=1 -DHAVE_CURLINFO_PRETRANSFER_TIME=1 -DHAVE_CURLINFO_SIZE_UPLOAD=1 -DHAVE_CURLINFO_SIZE_DOWNLOAD=1 -DHAVE_CURLINFO_SPEED_DOWNLOAD=1 -DHAVE_CURLINFO_SPEED_UPLOAD=1 -DHAVE_CURLINFO_HEADER_SIZE=1 -DHAVE_CURLINFO_REQUEST_SIZE=1 -DHAVE_CURLINFO_SSL_VERIFYRESULT=1 -DHAVE_CURLINFO_FILETIME=1 -DHAVE_CURLINFO_CONTENT_LENGTH_DOWNLOAD=1 -DHAVE_CURLINFO_CONTENT_LENGTH_UPLOAD=1 -DHAVE_CURLINFO_STARTTRANSFER_TIME=1 -DHAVE_CURLINFO_CONTENT_TYPE=1 -DHAVE_CURLINFO_REDIRECT_TIME=1 -DHAVE_CURLINFO_REDIRECT_COUNT=1 -DHAVE_CURLINFO_PRIVATE=1 -DHAVE_CURLINFO_HTTP_CONNECTCODE=1 -DHAVE_CURLINFO_HTTPAUTH_AVAIL=1 -DHAVE_CURLINFO_PROXYAUTH_AVAIL=1 -DHAVE_CURLINFO_OS_ERRNO=1 -DHAVE_CURLINFO_NUM_CONNECTS=1 -DHAVE_CURLINFO_SSL_ENGINES=1 -DHAVE_CURLINFO_COOKIELIST=1 -DHAVE_CURLINFO_LASTSOCKET=1 -DHAVE_CURLINFO_FTP_ENTRY_PATH=1 -DHAVE_CURLINFO_REDIRECT_URL=1 -DHAVE_CURLINFO_PRIMARY_IP=1 -DHAVE_CURLINFO_APPCONNECT_TIME=1 -DHAVE_CURLINFO_CERTINFO=1 -DHAVE_CURLINFO_CONDITION_UNMET=1 -DHAVE_CURLOPT_WRITEDATA=1 -DHAVE_CURLOPT_KEYPASSWD=1 -DHAVE_CURLOPT_DIRLISTONLY=1 -DHAVE_CURLOPT_APPEND=1 -DHAVE_CURLOPT_KRBLEVEL=1 -DHAVE_CURLOPT_USE_SSL=1 -DHAVE_CURLOPT_TIMEOUT_MS=1 -DHAVE_CURLOPT_CONNECTTIMEOUT_MS=1 -DHAVE_CURLOPT_HTTP_TRANSFER_DECODING=1 -DHAVE_CURLOPT_HTTP_CONTENT_DECODING=1 -DHAVE_CURLOPT_NEW_FILE_PERMS=1 -DHAVE_CURLOPT_NEW_DIRECTORY_PERMS=1 -DHAVE_CURLOPT_POSTREDIR=1 -DHAVE_CURLOPT_OPENSOCKETFUNCTION=1 -DHAVE_CURLOPT_OPENSOCKETDATA=1 -DHAVE_CURLOPT_COPYPOSTFIELDS=1 -DHAVE_CURLOPT_PROXY_TRANSFER_MODE=1 -DHAVE_CURLOPT_SEEKFUNCTION=1 -DHAVE_CURLOPT_SEEKDATA=1 -DHAVE_CURLOPT_CRLFILE=1 -DHAVE_CURLOPT_ISSUERCERT=1 -DHAVE_CURLOPT_ADDRESS_SCOPE=1 -DHAVE_CURLOPT_CERTINFO=1 -DHAVE_CURLOPT_USERNAME=1 -DHAVE_CURLOPT_PASSWORD=1 -DHAVE_CURLOPT_PROXYUSERNAME=1 -DHAVE_CURLOPT_PROXYPASSWORD=1 -DHAVE_CURLOPT_SSH_HOST_PUBLIC_KEY_MD5=1 -DHAVE_CURLOPT_NOPROXY=1 -DHAVE_CURLOPT_TFTP_BLKSIZE=1 -DHAVE_CURLOPT_SOCKS5_GSSAPI_SERVICE=1 -DHAVE_CURLOPT_SOCKS5_GSSAPI_NEC=1 -DHAVE_CURLOPT_PROTOCOLS=1 -DHAVE_CURLOPT_REDIR_PROTOCOLS=1 -DHAVE_CURLOPT_SSH_AUTH_TYPES=1 -DHAVE_CURLOPT_SSH_PUBLIC_KEYFILE=1 -DHAVE_CURLOPT_SSH_PRIVATE_KEYFILE=1 -DHAVE_CURLOPT_FTP_SSL_CCC=1 -DHAVE_CURLOPT_COOKIELIST=1 -DHAVE_CURLOPT_IGNORE_CONTENT_LENGTH=1 -DHAVE_CURLOPT_FTP_SKIP_PASV_IP=1 -DHAVE_CURLOPT_FTP_FILEMETHOD=1 -DHAVE_CURLOPT_LOCALPORT=1 -DHAVE_CURLOPT_LOCALPORTRANGE=1 -DHAVE_CURLOPT_CONNECT_ONLY=1 -DHAVE_CURLOPT_CONV_FROM_NETWORK_FUNCTION=1 -DHAVE_CURLOPT_CONV_TO_NETWORK_FUNCTION=1 -DHAVE_CURLOPT_CONV_FROM_UTF8_FUNCTION=1 -DHAVE_CURLOPT_MAX_SEND_SPEED_LARGE=1 -DHAVE_CURLOPT_MAX_RECV_SPEED_LARGE=1 -DHAVE_CURLOPT_FTP_ALTERNATIVE_TO_USER=1 -DHAVE_CURLOPT_SOCKOPTFUNCTION=1 -DHAVE_CURLOPT_SOCKOPTDATA=1 -DHAVE_CURLOPT_SSL_SESSIONID_CACHE=1 -I/usr/include/libxml2 -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c curl_base64.c -o curl_base64.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DHAVE_LIBIDN_FIELD=1 -DHAVE_CURLOPT_URL=1 -DHAVE_CURLINFO_EFFECTIVE_URL=1 -DHAVE_CURLINFO_RESPONSE_CODE=1 -DHAVE_CURLINFO_TOTAL_TIME=1 -DHAVE_CURLINFO_NAMELOOKUP_TIME=1 -DHAVE_CURLINFO_CONNECT_TIME=1 -DHAVE_CURLINFO_PRETRANSFER_TIME=1 -DHAVE_CURLINFO_SIZE_UPLOAD=1 -DHAVE_CURLINFO_SIZE_DOWNLOAD=1 -DHAVE_CURLINFO_SPEED_DOWNLOAD=1 -DHAVE_CURLINFO_SPEED_UPLOAD=1 -DHAVE_CURLINFO_HEADER_SIZE=1 -DHAVE_CURLINFO_REQUEST_SIZE=1 -DHAVE_CURLINFO_SSL_VERIFYRESULT=1 -DHAVE_CURLINFO_FILETIME=1 -DHAVE_CURLINFO_CONTENT_LENGTH_DOWNLOAD=1 -DHAVE_CURLINFO_CONTENT_LENGTH_UPLOAD=1 -DHAVE_CURLINFO_STARTTRANSFER_TIME=1 -DHAVE_CURLINFO_CONTENT_TYPE=1 -DHAVE_CURLINFO_REDIRECT_TIME=1 -DHAVE_CURLINFO_REDIRECT_COUNT=1 -DHAVE_CURLINFO_PRIVATE=1 -DHAVE_CURLINFO_HTTP_CONNECTCODE=1 -DHAVE_CURLINFO_HTTPAUTH_AVAIL=1 -DHAVE_CURLINFO_PROXYAUTH_AVAIL=1 -DHAVE_CURLINFO_OS_ERRNO=1 -DHAVE_CURLINFO_NUM_CONNECTS=1 -DHAVE_CURLINFO_SSL_ENGINES=1 -DHAVE_CURLINFO_COOKIELIST=1 -DHAVE_CURLINFO_LASTSOCKET=1 -DHAVE_CURLINFO_FTP_ENTRY_PATH=1 -DHAVE_CURLINFO_REDIRECT_URL=1 -DHAVE_CURLINFO_PRIMARY_IP=1 -DHAVE_CURLINFO_APPCONNECT_TIME=1 -DHAVE_CURLINFO_CERTINFO=1 -DHAVE_CURLINFO_CONDITION_UNMET=1 -DHAVE_CURLOPT_WRITEDATA=1 -DHAVE_CURLOPT_KEYPASSWD=1 -DHAVE_CURLOPT_DIRLISTONLY=1 -DHAVE_CURLOPT_APPEND=1 -DHAVE_CURLOPT_KRBLEVEL=1 -DHAVE_CURLOPT_USE_SSL=1 -DHAVE_CURLOPT_TIMEOUT_MS=1 -DHAVE_CURLOPT_CONNECTTIMEOUT_MS=1 -DHAVE_CURLOPT_HTTP_TRANSFER_DECODING=1 -DHAVE_CURLOPT_HTTP_CONTENT_DECODING=1 -DHAVE_CURLOPT_NEW_FILE_PERMS=1 -DHAVE_CURLOPT_NEW_DIRECTORY_PERMS=1 -DHAVE_CURLOPT_POSTREDIR=1 -DHAVE_CURLOPT_OPENSOCKETFUNCTION=1 -DHAVE_CURLOPT_OPENSOCKETDATA=1 -DHAVE_CURLOPT_COPYPOSTFIELDS=1 -DHAVE_CURLOPT_PROXY_TRANSFER_MODE=1 -DHAVE_CURLOPT_SEEKFUNCTION=1 -DHAVE_CURLOPT_SEEKDATA=1 -DHAVE_CURLOPT_CRLFILE=1 -DHAVE_CURLOPT_ISSUERCERT=1 -DHAVE_CURLOPT_ADDRESS_SCOPE=1 -DHAVE_CURLOPT_CERTINFO=1 -DHAVE_CURLOPT_USERNAME=1 -DHAVE_CURLOPT_PASSWORD=1 -DHAVE_CURLOPT_PROXYUSERNAME=1 -DHAVE_CURLOPT_PROXYPASSWORD=1 -DHAVE_CURLOPT_SSH_HOST_PUBLIC_KEY_MD5=1 -DHAVE_CURLOPT_NOPROXY=1 -DHAVE_CURLOPT_TFTP_BLKSIZE=1 -DHAVE_CURLOPT_SOCKS5_GSSAPI_SERVICE=1 -DHAVE_CURLOPT_SOCKS5_GSSAPI_NEC=1 -DHAVE_CURLOPT_PROTOCOLS=1 -DHAVE_CURLOPT_REDIR_PROTOCOLS=1 -DHAVE_CURLOPT_SSH_AUTH_TYPES=1 -DHAVE_CURLOPT_SSH_PUBLIC_KEYFILE=1 -DHAVE_CURLOPT_SSH_PRIVATE_KEYFILE=1 -DHAVE_CURLOPT_FTP_SSL_CCC=1 -DHAVE_CURLOPT_COOKIELIST=1 -DHAVE_CURLOPT_IGNORE_CONTENT_LENGTH=1 -DHAVE_CURLOPT_FTP_SKIP_PASV_IP=1 -DHAVE_CURLOPT_FTP_FILEMETHOD=1 -DHAVE_CURLOPT_LOCALPORT=1 -DHAVE_CURLOPT_LOCALPORTRANGE=1 -DHAVE_CURLOPT_CONNECT_ONLY=1 -DHAVE_CURLOPT_CONV_FROM_NETWORK_FUNCTION=1 -DHAVE_CURLOPT_CONV_TO_NETWORK_FUNCTION=1 -DHAVE_CURLOPT_CONV_FROM_UTF8_FUNCTION=1 -DHAVE_CURLOPT_MAX_SEND_SPEED_LARGE=1 -DHAVE_CURLOPT_MAX_RECV_SPEED_LARGE=1 -DHAVE_CURLOPT_FTP_ALTERNATIVE_TO_USER=1 -DHAVE_CURLOPT_SOCKOPTFUNCTION=1 -DHAVE_CURLOPT_SOCKOPTDATA=1 -DHAVE_CURLOPT_SSL_SESSIONID_CACHE=1 -I/usr/include/libxml2 -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c enums.c -o enums.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DHAVE_LIBIDN_FIELD=1 -DHAVE_CURLOPT_URL=1 -DHAVE_CURLINFO_EFFECTIVE_URL=1 -DHAVE_CURLINFO_RESPONSE_CODE=1 -DHAVE_CURLINFO_TOTAL_TIME=1 -DHAVE_CURLINFO_NAMELOOKUP_TIME=1 -DHAVE_CURLINFO_CONNECT_TIME=1 -DHAVE_CURLINFO_PRETRANSFER_TIME=1 -DHAVE_CURLINFO_SIZE_UPLOAD=1 -DHAVE_CURLINFO_SIZE_DOWNLOAD=1 -DHAVE_CURLINFO_SPEED_DOWNLOAD=1 -DHAVE_CURLINFO_SPEED_UPLOAD=1 -DHAVE_CURLINFO_HEADER_SIZE=1 -DHAVE_CURLINFO_REQUEST_SIZE=1 -DHAVE_CURLINFO_SSL_VERIFYRESULT=1 -DHAVE_CURLINFO_FILETIME=1 -DHAVE_CURLINFO_CONTENT_LENGTH_DOWNLOAD=1 -DHAVE_CURLINFO_CONTENT_LENGTH_UPLOAD=1 -DHAVE_CURLINFO_STARTTRANSFER_TIME=1 -DHAVE_CURLINFO_CONTENT_TYPE=1 -DHAVE_CURLINFO_REDIRECT_TIME=1 -DHAVE_CURLINFO_REDIRECT_COUNT=1 -DHAVE_CURLINFO_PRIVATE=1 -DHAVE_CURLINFO_HTTP_CONNECTCODE=1 -DHAVE_CURLINFO_HTTPAUTH_AVAIL=1 -DHAVE_CURLINFO_PROXYAUTH_AVAIL=1 -DHAVE_CURLINFO_OS_ERRNO=1 -DHAVE_CURLINFO_NUM_CONNECTS=1 -DHAVE_CURLINFO_SSL_ENGINES=1 -DHAVE_CURLINFO_COOKIELIST=1 -DHAVE_CURLINFO_LASTSOCKET=1 -DHAVE_CURLINFO_FTP_ENTRY_PATH=1 -DHAVE_CURLINFO_REDIRECT_URL=1 -DHAVE_CURLINFO_PRIMARY_IP=1 -DHAVE_CURLINFO_APPCONNECT_TIME=1 -DHAVE_CURLINFO_CERTINFO=1 -DHAVE_CURLINFO_CONDITION_UNMET=1 -DHAVE_CURLOPT_WRITEDATA=1 -DHAVE_CURLOPT_KEYPASSWD=1 -DHAVE_CURLOPT_DIRLISTONLY=1 -DHAVE_CURLOPT_APPEND=1 -DHAVE_CURLOPT_KRBLEVEL=1 -DHAVE_CURLOPT_USE_SSL=1 -DHAVE_CURLOPT_TIMEOUT_MS=1 -DHAVE_CURLOPT_CONNECTTIMEOUT_MS=1 -DHAVE_CURLOPT_HTTP_TRANSFER_DECODING=1 -DHAVE_CURLOPT_HTTP_CONTENT_DECODING=1 -DHAVE_CURLOPT_NEW_FILE_PERMS=1 -DHAVE_CURLOPT_NEW_DIRECTORY_PERMS=1 -DHAVE_CURLOPT_POSTREDIR=1 -DHAVE_CURLOPT_OPENSOCKETFUNCTION=1 -DHAVE_CURLOPT_OPENSOCKETDATA=1 -DHAVE_CURLOPT_COPYPOSTFIELDS=1 -DHAVE_CURLOPT_PROXY_TRANSFER_MODE=1 -DHAVE_CURLOPT_SEEKFUNCTION=1 -DHAVE_CURLOPT_SEEKDATA=1 -DHAVE_CURLOPT_CRLFILE=1 -DHAVE_CURLOPT_ISSUERCERT=1 -DHAVE_CURLOPT_ADDRESS_SCOPE=1 -DHAVE_CURLOPT_CERTINFO=1 -DHAVE_CURLOPT_USERNAME=1 -DHAVE_CURLOPT_PASSWORD=1 -DHAVE_CURLOPT_PROXYUSERNAME=1 -DHAVE_CURLOPT_PROXYPASSWORD=1 -DHAVE_CURLOPT_SSH_HOST_PUBLIC_KEY_MD5=1 -DHAVE_CURLOPT_NOPROXY=1 -DHAVE_CURLOPT_TFTP_BLKSIZE=1 -DHAVE_CURLOPT_SOCKS5_GSSAPI_SERVICE=1 -DHAVE_CURLOPT_SOCKS5_GSSAPI_NEC=1 -DHAVE_CURLOPT_PROTOCOLS=1 -DHAVE_CURLOPT_REDIR_PROTOCOLS=1 -DHAVE_CURLOPT_SSH_AUTH_TYPES=1 -DHAVE_CURLOPT_SSH_PUBLIC_KEYFILE=1 -DHAVE_CURLOPT_SSH_PRIVATE_KEYFILE=1 -DHAVE_CURLOPT_FTP_SSL_CCC=1 -DHAVE_CURLOPT_COOKIELIST=1 -DHAVE_CURLOPT_IGNORE_CONTENT_LENGTH=1 -DHAVE_CURLOPT_FTP_SKIP_PASV_IP=1 -DHAVE_CURLOPT_FTP_FILEMETHOD=1 -DHAVE_CURLOPT_LOCALPORT=1 -DHAVE_CURLOPT_LOCALPORTRANGE=1 -DHAVE_CURLOPT_CONNECT_ONLY=1 -DHAVE_CURLOPT_CONV_FROM_NETWORK_FUNCTION=1 -DHAVE_CURLOPT_CONV_TO_NETWORK_FUNCTION=1 -DHAVE_CURLOPT_CONV_FROM_UTF8_FUNCTION=1 -DHAVE_CURLOPT_MAX_SEND_SPEED_LARGE=1 -DHAVE_CURLOPT_MAX_RECV_SPEED_LARGE=1 -DHAVE_CURLOPT_FTP_ALTERNATIVE_TO_USER=1 -DHAVE_CURLOPT_SOCKOPTFUNCTION=1 -DHAVE_CURLOPT_SOCKOPTDATA=1 -DHAVE_CURLOPT_SSL_SESSIONID_CACHE=1 -I/usr/include/libxml2 -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c json.c -o json.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DHAVE_LIBIDN_FIELD=1 -DHAVE_CURLOPT_URL=1 -DHAVE_CURLINFO_EFFECTIVE_URL=1 -DHAVE_CURLINFO_RESPONSE_CODE=1 -DHAVE_CURLINFO_TOTAL_TIME=1 -DHAVE_CURLINFO_NAMELOOKUP_TIME=1 -DHAVE_CURLINFO_CONNECT_TIME=1 -DHAVE_CURLINFO_PRETRANSFER_TIME=1 -DHAVE_CURLINFO_SIZE_UPLOAD=1 -DHAVE_CURLINFO_SIZE_DOWNLOAD=1 -DHAVE_CURLINFO_SPEED_DOWNLOAD=1 -DHAVE_CURLINFO_SPEED_UPLOAD=1 -DHAVE_CURLINFO_HEADER_SIZE=1 -DHAVE_CURLINFO_REQUEST_SIZE=1 -DHAVE_CURLINFO_SSL_VERIFYRESULT=1 -DHAVE_CURLINFO_FILETIME=1 -DHAVE_CURLINFO_CONTENT_LENGTH_DOWNLOAD=1 -DHAVE_CURLINFO_CONTENT_LENGTH_UPLOAD=1 -DHAVE_CURLINFO_STARTTRANSFER_TIME=1 -DHAVE_CURLINFO_CONTENT_TYPE=1 -DHAVE_CURLINFO_REDIRECT_TIME=1 -DHAVE_CURLINFO_REDIRECT_COUNT=1 -DHAVE_CURLINFO_PRIVATE=1 -DHAVE_CURLINFO_HTTP_CONNECTCODE=1 -DHAVE_CURLINFO_HTTPAUTH_AVAIL=1 -DHAVE_CURLINFO_PROXYAUTH_AVAIL=1 -DHAVE_CURLINFO_OS_ERRNO=1 -DHAVE_CURLINFO_NUM_CONNECTS=1 -DHAVE_CURLINFO_SSL_ENGINES=1 -DHAVE_CURLINFO_COOKIELIST=1 -DHAVE_CURLINFO_LASTSOCKET=1 -DHAVE_CURLINFO_FTP_ENTRY_PATH=1 -DHAVE_CURLINFO_REDIRECT_URL=1 -DHAVE_CURLINFO_PRIMARY_IP=1 -DHAVE_CURLINFO_APPCONNECT_TIME=1 -DHAVE_CURLINFO_CERTINFO=1 -DHAVE_CURLINFO_CONDITION_UNMET=1 -DHAVE_CURLOPT_WRITEDATA=1 -DHAVE_CURLOPT_KEYPASSWD=1 -DHAVE_CURLOPT_DIRLISTONLY=1 -DHAVE_CURLOPT_APPEND=1 -DHAVE_CURLOPT_KRBLEVEL=1 -DHAVE_CURLOPT_USE_SSL=1 -DHAVE_CURLOPT_TIMEOUT_MS=1 -DHAVE_CURLOPT_CONNECTTIMEOUT_MS=1 -DHAVE_CURLOPT_HTTP_TRANSFER_DECODING=1 -DHAVE_CURLOPT_HTTP_CONTENT_DECODING=1 -DHAVE_CURLOPT_NEW_FILE_PERMS=1 -DHAVE_CURLOPT_NEW_DIRECTORY_PERMS=1 -DHAVE_CURLOPT_POSTREDIR=1 -DHAVE_CURLOPT_OPENSOCKETFUNCTION=1 -DHAVE_CURLOPT_OPENSOCKETDATA=1 -DHAVE_CURLOPT_COPYPOSTFIELDS=1 -DHAVE_CURLOPT_PROXY_TRANSFER_MODE=1 -DHAVE_CURLOPT_SEEKFUNCTION=1 -DHAVE_CURLOPT_SEEKDATA=1 -DHAVE_CURLOPT_CRLFILE=1 -DHAVE_CURLOPT_ISSUERCERT=1 -DHAVE_CURLOPT_ADDRESS_SCOPE=1 -DHAVE_CURLOPT_CERTINFO=1 -DHAVE_CURLOPT_USERNAME=1 -DHAVE_CURLOPT_PASSWORD=1 -DHAVE_CURLOPT_PROXYUSERNAME=1 -DHAVE_CURLOPT_PROXYPASSWORD=1 -DHAVE_CURLOPT_SSH_HOST_PUBLIC_KEY_MD5=1 -DHAVE_CURLOPT_NOPROXY=1 -DHAVE_CURLOPT_TFTP_BLKSIZE=1 -DHAVE_CURLOPT_SOCKS5_GSSAPI_SERVICE=1 -DHAVE_CURLOPT_SOCKS5_GSSAPI_NEC=1 -DHAVE_CURLOPT_PROTOCOLS=1 -DHAVE_CURLOPT_REDIR_PROTOCOLS=1 -DHAVE_CURLOPT_SSH_AUTH_TYPES=1 -DHAVE_CURLOPT_SSH_PUBLIC_KEYFILE=1 -DHAVE_CURLOPT_SSH_PRIVATE_KEYFILE=1 -DHAVE_CURLOPT_FTP_SSL_CCC=1 -DHAVE_CURLOPT_COOKIELIST=1 -DHAVE_CURLOPT_IGNORE_CONTENT_LENGTH=1 -DHAVE_CURLOPT_FTP_SKIP_PASV_IP=1 -DHAVE_CURLOPT_FTP_FILEMETHOD=1 -DHAVE_CURLOPT_LOCALPORT=1 -DHAVE_CURLOPT_LOCALPORTRANGE=1 -DHAVE_CURLOPT_CONNECT_ONLY=1 -DHAVE_CURLOPT_CONV_FROM_NETWORK_FUNCTION=1 -DHAVE_CURLOPT_CONV_TO_NETWORK_FUNCTION=1 -DHAVE_CURLOPT_CONV_FROM_UTF8_FUNCTION=1 -DHAVE_CURLOPT_MAX_SEND_SPEED_LARGE=1 -DHAVE_CURLOPT_MAX_RECV_SPEED_LARGE=1 -DHAVE_CURLOPT_FTP_ALTERNATIVE_TO_USER=1 -DHAVE_CURLOPT_SOCKOPTFUNCTION=1 -DHAVE_CURLOPT_SOCKOPTDATA=1 -DHAVE_CURLOPT_SSL_SESSIONID_CACHE=1 -I/usr/include/libxml2 -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c memoryManagement.c -o memoryManagement.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DHAVE_LIBIDN_FIELD=1 -DHAVE_CURLOPT_URL=1 -DHAVE_CURLINFO_EFFECTIVE_URL=1 -DHAVE_CURLINFO_RESPONSE_CODE=1 -DHAVE_CURLINFO_TOTAL_TIME=1 -DHAVE_CURLINFO_NAMELOOKUP_TIME=1 -DHAVE_CURLINFO_CONNECT_TIME=1 -DHAVE_CURLINFO_PRETRANSFER_TIME=1 -DHAVE_CURLINFO_SIZE_UPLOAD=1 -DHAVE_CURLINFO_SIZE_DOWNLOAD=1 -DHAVE_CURLINFO_SPEED_DOWNLOAD=1 -DHAVE_CURLINFO_SPEED_UPLOAD=1 -DHAVE_CURLINFO_HEADER_SIZE=1 -DHAVE_CURLINFO_REQUEST_SIZE=1 -DHAVE_CURLINFO_SSL_VERIFYRESULT=1 -DHAVE_CURLINFO_FILETIME=1 -DHAVE_CURLINFO_CONTENT_LENGTH_DOWNLOAD=1 -DHAVE_CURLINFO_CONTENT_LENGTH_UPLOAD=1 -DHAVE_CURLINFO_STARTTRANSFER_TIME=1 -DHAVE_CURLINFO_CONTENT_TYPE=1 -DHAVE_CURLINFO_REDIRECT_TIME=1 -DHAVE_CURLINFO_REDIRECT_COUNT=1 -DHAVE_CURLINFO_PRIVATE=1 -DHAVE_CURLINFO_HTTP_CONNECTCODE=1 -DHAVE_CURLINFO_HTTPAUTH_AVAIL=1 -DHAVE_CURLINFO_PROXYAUTH_AVAIL=1 -DHAVE_CURLINFO_OS_ERRNO=1 -DHAVE_CURLINFO_NUM_CONNECTS=1 -DHAVE_CURLINFO_SSL_ENGINES=1 -DHAVE_CURLINFO_COOKIELIST=1 -DHAVE_CURLINFO_LASTSOCKET=1 -DHAVE_CURLINFO_FTP_ENTRY_PATH=1 -DHAVE_CURLINFO_REDIRECT_URL=1 -DHAVE_CURLINFO_PRIMARY_IP=1 -DHAVE_CURLINFO_APPCONNECT_TIME=1 -DHAVE_CURLINFO_CERTINFO=1 -DHAVE_CURLINFO_CONDITION_UNMET=1 -DHAVE_CURLOPT_WRITEDATA=1 -DHAVE_CURLOPT_KEYPASSWD=1 -DHAVE_CURLOPT_DIRLISTONLY=1 -DHAVE_CURLOPT_APPEND=1 -DHAVE_CURLOPT_KRBLEVEL=1 -DHAVE_CURLOPT_USE_SSL=1 -DHAVE_CURLOPT_TIMEOUT_MS=1 -DHAVE_CURLOPT_CONNECTTIMEOUT_MS=1 -DHAVE_CURLOPT_HTTP_TRANSFER_DECODING=1 -DHAVE_CURLOPT_HTTP_CONTENT_DECODING=1 -DHAVE_CURLOPT_NEW_FILE_PERMS=1 -DHAVE_CURLOPT_NEW_DIRECTORY_PERMS=1 -DHAVE_CURLOPT_POSTREDIR=1 -DHAVE_CURLOPT_OPENSOCKETFUNCTION=1 -DHAVE_CURLOPT_OPENSOCKETDATA=1 -DHAVE_CURLOPT_COPYPOSTFIELDS=1 -DHAVE_CURLOPT_PROXY_TRANSFER_MODE=1 -DHAVE_CURLOPT_SEEKFUNCTION=1 -DHAVE_CURLOPT_SEEKDATA=1 -DHAVE_CURLOPT_CRLFILE=1 -DHAVE_CURLOPT_ISSUERCERT=1 -DHAVE_CURLOPT_ADDRESS_SCOPE=1 -DHAVE_CURLOPT_CERTINFO=1 -DHAVE_CURLOPT_USERNAME=1 -DHAVE_CURLOPT_PASSWORD=1 -DHAVE_CURLOPT_PROXYUSERNAME=1 -DHAVE_CURLOPT_PROXYPASSWORD=1 -DHAVE_CURLOPT_SSH_HOST_PUBLIC_KEY_MD5=1 -DHAVE_CURLOPT_NOPROXY=1 -DHAVE_CURLOPT_TFTP_BLKSIZE=1 -DHAVE_CURLOPT_SOCKS5_GSSAPI_SERVICE=1 -DHAVE_CURLOPT_SOCKS5_GSSAPI_NEC=1 -DHAVE_CURLOPT_PROTOCOLS=1 -DHAVE_CURLOPT_REDIR_PROTOCOLS=1 -DHAVE_CURLOPT_SSH_AUTH_TYPES=1 -DHAVE_CURLOPT_SSH_PUBLIC_KEYFILE=1 -DHAVE_CURLOPT_SSH_PRIVATE_KEYFILE=1 -DHAVE_CURLOPT_FTP_SSL_CCC=1 -DHAVE_CURLOPT_COOKIELIST=1 -DHAVE_CURLOPT_IGNORE_CONTENT_LENGTH=1 -DHAVE_CURLOPT_FTP_SKIP_PASV_IP=1 -DHAVE_CURLOPT_FTP_FILEMETHOD=1 -DHAVE_CURLOPT_LOCALPORT=1 -DHAVE_CURLOPT_LOCALPORTRANGE=1 -DHAVE_CURLOPT_CONNECT_ONLY=1 -DHAVE_CURLOPT_CONV_FROM_NETWORK_FUNCTION=1 -DHAVE_CURLOPT_CONV_TO_NETWORK_FUNCTION=1 -DHAVE_CURLOPT_CONV_FROM_UTF8_FUNCTION=1 -DHAVE_CURLOPT_MAX_SEND_SPEED_LARGE=1 -DHAVE_CURLOPT_MAX_RECV_SPEED_LARGE=1 -DHAVE_CURLOPT_FTP_ALTERNATIVE_TO_USER=1 -DHAVE_CURLOPT_SOCKOPTFUNCTION=1 -DHAVE_CURLOPT_SOCKOPTDATA=1 -DHAVE_CURLOPT_SSL_SESSIONID_CACHE=1 -I/usr/include/libxml2 -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c myUTF8.c -o myUTF8.o gcc -std=gnu99 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o RCurl.so base64.o curl.o curlInit.o curl_base64.o enums.o json.o memoryManagement.o myUTF8.o -L/usr/lib/x86_64-linux-gnu -lcurl -lxml2 -L/usr/lib/R/lib -lR installing to /usr/local/lib/R/site-library/RCurl/libs ** R ** data ** inst ** preparing package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded * DONE (RCurl) * installing *source* package 'Rcpp' ... ** package 'Rcpp' successfully unpacked and MD5 sums checked ** libs g++ -I/usr/share/R/include -DNDEBUG -I../inst/include/ -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c Date.cpp -o Date.o g++ -I/usr/share/R/include -DNDEBUG -I../inst/include/ -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c Module.cpp -o Module.o g++ -I/usr/share/R/include -DNDEBUG -I../inst/include/ -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c Rcpp_init.cpp -o Rcpp_init.o g++ -I/usr/share/R/include -DNDEBUG -I../inst/include/ -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c api.cpp -o api.o g++ -I/usr/share/R/include -DNDEBUG -I../inst/include/ -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c attributes.cpp -o attributes.o g++ -I/usr/share/R/include -DNDEBUG -I../inst/include/ -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c barrier.cpp -o barrier.o g++ -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o Rcpp.so Date.o Module.o Rcpp_init.o api.o attributes.o barrier.o -L/usr/lib/R/lib -lR installing to /usr/local/lib/R/site-library/Rcpp/libs ** R ** inst ** preparing package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded * DONE (Rcpp) * installing *source* package 'backports' ... ** package 'backports' successfully unpacked and MD5 sums checked ** libs gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c dotsElt.c -o dotsElt.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c dotsLength.c -o dotsLength.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c init.c -o init.o gcc -std=gnu99 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o backports.so dotsElt.o dotsLength.o init.o -L/usr/lib/R/lib -lR installing to /usr/local/lib/R/site-library/backports/libs ** R ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded * DONE (backports) * installing *source* package 'curl' ... ** package 'curl' successfully unpacked and MD5 sums checked Found pkg-config cflags and libs! Using PKG_CFLAGS= Using PKG_LIBS=-lcurl ** libs rm -f curl.so callbacks.o curl.o download.o escape.o fetch.o form.o getdate.o handle.o ieproxy.o init.o interrupt.o multi.o nslookup.o reflist.o split.o ssl.o utils.o version.o winidn.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c callbacks.c -o callbacks.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c curl.c -o curl.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c download.c -o download.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c escape.c -o escape.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c fetch.c -o fetch.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c form.c -o form.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c getdate.c -o getdate.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c handle.c -o handle.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c ieproxy.c -o ieproxy.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c init.c -o init.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c interrupt.c -o interrupt.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c multi.c -o multi.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c nslookup.c -o nslookup.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c reflist.c -o reflist.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c split.c -o split.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c ssl.c -o ssl.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c utils.c -o utils.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c version.c -o version.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c winidn.c -o winidn.o gcc -std=gnu99 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o curl.so callbacks.o curl.o download.o escape.o fetch.o form.o getdate.o handle.o ieproxy.o init.o interrupt.o multi.o nslookup.o reflist.o split.o ssl.o utils.o version.o winidn.o -lcurl -L/usr/lib/R/lib -lR installing to /usr/local/lib/R/site-library/curl/libs ** R ** data *** moving datasets to lazyload DB ** inst ** preparing package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded * DONE (curl) * installing *source* package 'digest' ... ** package 'digest' successfully unpacked and MD5 sums checked ** libs gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c aes.c -o aes.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c crc32.c -o crc32.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c digest.c -o digest.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c init.c -o init.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c md5.c -o md5.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c pmurhash.c -o pmurhash.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c raes.c -o raes.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c sha1.c -o sha1.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c sha2.c -o sha2.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c sha256.c -o sha256.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c xxhash.c -o xxhash.o gcc -std=gnu99 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o digest.so aes.o crc32.o digest.o init.o md5.o pmurhash.o raes.o sha1.o sha2.o sha256.o xxhash.o -L/usr/lib/R/lib -lR installing to /usr/local/lib/R/site-library/digest/libs ** R ** inst ** preparing package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded * DONE (digest) * installing *source* package 'git2r' ... ** package 'git2r' successfully unpacked and MD5 sums checked checking build system type... x86_64-unknown-linux-gnu checking host system type... x86_64-unknown-linux-gnu checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking for pkg-config... /usr/bin/pkg-config checking pkg-config is at least version 0.9.0... yes checking how to run the C preprocessor... gcc -std=gnu99 -E checking for grep that handles long lines and -e... /bin/grep checking for egrep... /bin/grep -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking size of void*... 8 checking for library containing inflate... -lz checking for library containing EVP_EncryptInit... -lcrypto checking for library containing SSL_library_init... -lssl checking for library containing OPENSSL_init_ssl... no checking for library containing libssh2_version... -lssh2 checking for gawk... no checking for mawk... mawk checking for curl-config... /usr/bin/curl-config checking for the version of libcurl... 7.47.0 checking whether libcurl is usable... yes checking for curl_free... yes checking for struct stat.st_mtim... yes checking for struct stat.st_mtimespec... no checking for struct stat.st_mtime_nsec... no checking for struct stat.st_mtim.tv_nsec... yes checking for futimens... yes checking for qsort_r... yes checking for qsort_s... no ----- Results of the git2r package configure ----- OpenSSL to talk over HTTPS...........: yes LibSSH2 to enable the SSH transport..: yes -------------------------------------------------- configure: creating ./config.status config.status: creating src/Makevars ** libs gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c git2r.c -o git2r.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c git2r_arg.c -o git2r_arg.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c git2r_blame.c -o git2r_blame.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c git2r_blob.c -o git2r_blob.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c git2r_branch.c -o git2r_branch.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c git2r_checkout.c -o git2r_checkout.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c git2r_clone.c -o git2r_clone.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c git2r_commit.c -o git2r_commit.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c git2r_config.c -o git2r_config.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c git2r_cred.c -o git2r_cred.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c git2r_diff.c -o git2r_diff.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c git2r_error.c -o git2r_error.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c git2r_graph.c -o git2r_graph.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c git2r_index.c -o git2r_index.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c git2r_libgit2.c -o git2r_libgit2.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c git2r_merge.c -o git2r_merge.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c git2r_note.c -o git2r_note.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c git2r_object.c -o git2r_object.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c git2r_odb.c -o git2r_odb.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c git2r_oid.c -o git2r_oid.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c git2r_push.c -o git2r_push.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c git2r_reference.c -o git2r_reference.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c git2r_reflog.c -o git2r_reflog.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c git2r_remote.c -o git2r_remote.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c git2r_repository.c -o git2r_repository.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c git2r_reset.c -o git2r_reset.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c git2r_revparse.c -o git2r_revparse.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c git2r_revwalk.c -o git2r_revwalk.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c git2r_signature.c -o git2r_signature.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c git2r_stash.c -o git2r_stash.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c git2r_status.c -o git2r_status.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c git2r_tag.c -o git2r_tag.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c git2r_transfer.c -o git2r_transfer.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c git2r_tree.c -o git2r_tree.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c libgit2/src/annotated_commit.c -o libgit2/src/annotated_commit.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c libgit2/src/apply.c -o libgit2/src/apply.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c libgit2/src/attr_file.c -o libgit2/src/attr_file.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c libgit2/src/attr.c -o libgit2/src/attr.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c libgit2/src/attrcache.c -o libgit2/src/attrcache.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c libgit2/src/blame_git.c -o libgit2/src/blame_git.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c libgit2/src/blame.c -o libgit2/src/blame.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c libgit2/src/blob.c -o libgit2/src/blob.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c libgit2/src/branch.c -o libgit2/src/branch.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c libgit2/src/buf_text.c -o libgit2/src/buf_text.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c libgit2/src/buffer.c -o libgit2/src/buffer.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c libgit2/src/cache.c -o libgit2/src/cache.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c libgit2/src/checkout.c -o libgit2/src/checkout.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c libgit2/src/cherrypick.c -o libgit2/src/cherrypick.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c libgit2/src/clone.c -o libgit2/src/clone.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c libgit2/src/commit_list.c -o libgit2/src/commit_list.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c libgit2/src/commit.c -o libgit2/src/commit.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c libgit2/src/config_cache.c -o libgit2/src/config_cache.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c libgit2/src/config_file.c -o libgit2/src/config_file.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c libgit2/src/config_parse.c -o libgit2/src/config_parse.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c libgit2/src/config.c -o libgit2/src/config.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c libgit2/src/crlf.c -o libgit2/src/crlf.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c libgit2/src/date.c -o libgit2/src/date.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c libgit2/src/delta.c -o libgit2/src/delta.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c libgit2/src/describe.c -o libgit2/src/describe.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c libgit2/src/diff_driver.c -o libgit2/src/diff_driver.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c libgit2/src/diff_file.c -o libgit2/src/diff_file.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c libgit2/src/diff_generate.c -o libgit2/src/diff_generate.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c libgit2/src/diff_parse.c -o libgit2/src/diff_parse.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c libgit2/src/diff_print.c -o libgit2/src/diff_print.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c libgit2/src/diff_stats.c -o libgit2/src/diff_stats.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c libgit2/src/diff_tform.c -o libgit2/src/diff_tform.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c libgit2/src/diff_xdiff.c -o libgit2/src/diff_xdiff.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c libgit2/src/diff.c -o libgit2/src/diff.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c libgit2/src/errors.c -o libgit2/src/errors.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c libgit2/src/fetch.c -o libgit2/src/fetch.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c libgit2/src/fetchhead.c -o libgit2/src/fetchhead.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c libgit2/src/filebuf.c -o libgit2/src/filebuf.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c libgit2/src/fileops.c -o libgit2/src/fileops.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c libgit2/src/filter.c -o libgit2/src/filter.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c libgit2/src/fnmatch.c -o libgit2/src/fnmatch.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c libgit2/src/global.c -o libgit2/src/global.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c libgit2/src/graph.c -o libgit2/src/graph.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c libgit2/src/hash.c -o libgit2/src/hash.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c libgit2/src/hashsig.c -o libgit2/src/hashsig.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c libgit2/src/ident.c -o libgit2/src/ident.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c libgit2/src/idxmap.c -o libgit2/src/idxmap.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c libgit2/src/ignore.c -o libgit2/src/ignore.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c libgit2/src/index.c -o libgit2/src/index.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c libgit2/src/indexer.c -o libgit2/src/indexer.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c libgit2/src/iterator.c -o libgit2/src/iterator.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c libgit2/src/merge_driver.c -o libgit2/src/merge_driver.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c libgit2/src/merge_file.c -o libgit2/src/merge_file.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c libgit2/src/merge.c -o libgit2/src/merge.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c libgit2/src/message.c -o libgit2/src/message.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c libgit2/src/mwindow.c -o libgit2/src/mwindow.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c libgit2/src/netops.c -o libgit2/src/netops.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c libgit2/src/notes.c -o libgit2/src/notes.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c libgit2/src/object_api.c -o libgit2/src/object_api.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c libgit2/src/object.c -o libgit2/src/object.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c libgit2/src/odb_loose.c -o libgit2/src/odb_loose.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c libgit2/src/odb_mempack.c -o libgit2/src/odb_mempack.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c libgit2/src/odb_pack.c -o libgit2/src/odb_pack.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c libgit2/src/odb.c -o libgit2/src/odb.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c libgit2/src/offmap.c -o libgit2/src/offmap.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c libgit2/src/oid.c -o libgit2/src/oid.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c libgit2/src/oidarray.c -o libgit2/src/oidarray.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c libgit2/src/oidmap.c -o libgit2/src/oidmap.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c libgit2/src/pack-objects.c -o libgit2/src/pack-objects.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c libgit2/src/pack.c -o libgit2/src/pack.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c libgit2/src/parse.c -o libgit2/src/parse.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c libgit2/src/patch_generate.c -o libgit2/src/patch_generate.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c libgit2/src/patch_parse.c -o libgit2/src/patch_parse.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c libgit2/src/patch.c -o libgit2/src/patch.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c libgit2/src/path.c -o libgit2/src/path.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c libgit2/src/pathspec.c -o libgit2/src/pathspec.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c libgit2/src/pool.c -o libgit2/src/pool.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c libgit2/src/posix.c -o libgit2/src/posix.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c libgit2/src/pqueue.c -o libgit2/src/pqueue.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c libgit2/src/proxy.c -o libgit2/src/proxy.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c libgit2/src/push.c -o libgit2/src/push.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c libgit2/src/rebase.c -o libgit2/src/rebase.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c libgit2/src/refdb_fs.c -o libgit2/src/refdb_fs.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c libgit2/src/refdb.c -o libgit2/src/refdb.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c libgit2/src/reflog.c -o libgit2/src/reflog.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c libgit2/src/refs.c -o libgit2/src/refs.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c libgit2/src/refspec.c -o libgit2/src/refspec.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c libgit2/src/remote.c -o libgit2/src/remote.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c libgit2/src/repository.c -o libgit2/src/repository.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c libgit2/src/reset.c -o libgit2/src/reset.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c libgit2/src/revert.c -o libgit2/src/revert.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c libgit2/src/revparse.c -o libgit2/src/revparse.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c libgit2/src/revwalk.c -o libgit2/src/revwalk.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c libgit2/src/settings.c -o libgit2/src/settings.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c libgit2/src/sha1_lookup.c -o libgit2/src/sha1_lookup.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c libgit2/src/signature.c -o libgit2/src/signature.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c libgit2/src/sortedcache.c -o libgit2/src/sortedcache.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c libgit2/src/stash.c -o libgit2/src/stash.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c libgit2/src/status.c -o libgit2/src/status.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c libgit2/src/strmap.c -o libgit2/src/strmap.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c libgit2/src/submodule.c -o libgit2/src/submodule.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c libgit2/src/sysdir.c -o libgit2/src/sysdir.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c libgit2/src/tag.c -o libgit2/src/tag.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c libgit2/src/thread-utils.c -o libgit2/src/thread-utils.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c libgit2/src/trace.c -o libgit2/src/trace.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c libgit2/src/transaction.c -o libgit2/src/transaction.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c libgit2/src/transport.c -o libgit2/src/transport.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c libgit2/src/tree-cache.c -o libgit2/src/tree-cache.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c libgit2/src/tree.c -o libgit2/src/tree.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c libgit2/src/tsort.c -o libgit2/src/tsort.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c libgit2/src/util.c -o libgit2/src/util.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c libgit2/src/varint.c -o libgit2/src/varint.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c libgit2/src/vector.c -o libgit2/src/vector.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c libgit2/src/worktree.c -o libgit2/src/worktree.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c libgit2/src/zstream.c -o libgit2/src/zstream.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c libgit2/src/streams/curl.c -o libgit2/src/streams/curl.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c libgit2/src/streams/openssl.c -o libgit2/src/streams/openssl.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c libgit2/src/streams/socket.c -o libgit2/src/streams/socket.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c libgit2/src/streams/stransport.c -o libgit2/src/streams/stransport.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c libgit2/src/streams/tls.c -o libgit2/src/streams/tls.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c libgit2/src/transports/auth.c -o libgit2/src/transports/auth.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c libgit2/src/transports/cred_helpers.c -o libgit2/src/transports/cred_helpers.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c libgit2/src/transports/cred.c -o libgit2/src/transports/cred.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c libgit2/src/transports/git.c -o libgit2/src/transports/git.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c libgit2/src/transports/http.c -o libgit2/src/transports/http.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c libgit2/src/transports/local.c -o libgit2/src/transports/local.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c libgit2/src/transports/smart_pkt.c -o libgit2/src/transports/smart_pkt.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c libgit2/src/transports/smart_protocol.c -o libgit2/src/transports/smart_protocol.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c libgit2/src/transports/smart.c -o libgit2/src/transports/smart.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c libgit2/src/transports/ssh.c -o libgit2/src/transports/ssh.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c libgit2/src/unix/map.c -o libgit2/src/unix/map.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c libgit2/src/unix/realpath.c -o libgit2/src/unix/realpath.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c libgit2/src/xdiff/xdiffi.c -o libgit2/src/xdiff/xdiffi.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c libgit2/src/xdiff/xemit.c -o libgit2/src/xdiff/xemit.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c libgit2/src/xdiff/xhistogram.c -o libgit2/src/xdiff/xhistogram.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c libgit2/src/xdiff/xmerge.c -o libgit2/src/xdiff/xmerge.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c libgit2/src/xdiff/xpatience.c -o libgit2/src/xdiff/xpatience.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c libgit2/src/xdiff/xprepare.c -o libgit2/src/xdiff/xprepare.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c libgit2/src/xdiff/xutils.c -o libgit2/src/xdiff/xutils.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c libgit2/deps/http-parser/http_parser.c -o libgit2/deps/http-parser/http_parser.o ar rcs libmygit.a libgit2/src/annotated_commit.o libgit2/src/apply.o libgit2/src/attr_file.o libgit2/src/attr.o libgit2/src/attrcache.o libgit2/src/blame_git.o libgit2/src/blame.o libgit2/src/blob.o libgit2/src/branch.o libgit2/src/buf_text.o libgit2/src/buffer.o libgit2/src/cache.o libgit2/src/checkout.o libgit2/src/cherrypick.o libgit2/src/clone.o libgit2/src/commit_list.o libgit2/src/commit.o libgit2/src/config_cache.o libgit2/src/config_file.o libgit2/src/config_parse.o libgit2/src/config.o libgit2/src/crlf.o libgit2/src/date.o libgit2/src/delta.o libgit2/src/describe.o libgit2/src/diff_driver.o libgit2/src/diff_file.o libgit2/src/diff_generate.o libgit2/src/diff_parse.o libgit2/src/diff_print.o libgit2/src/diff_stats.o libgit2/src/diff_tform.o libgit2/src/diff_xdiff.o libgit2/src/diff.o libgit2/src/errors.o libgit2/src/fetch.o libgit2/src/fetchhead.o libgit2/src/filebuf.o libgit2/src/fileops.o libgit2/src/filter.o libgit2/src/fnmatch.o libgit2/src/global.o libgit2/src/graph.o libgit2/src/hash.o libgit2/src/hashsig.o libgit2/src/ident.o libgit2/src/idxmap.o libgit2/src/ignore.o libgit2/src/index.o libgit2/src/indexer.o libgit2/src/iterator.o libgit2/src/merge_driver.o libgit2/src/merge_file.o libgit2/src/merge.o libgit2/src/message.o libgit2/src/mwindow.o libgit2/src/netops.o libgit2/src/notes.o libgit2/src/object_api.o libgit2/src/object.o libgit2/src/odb_loose.o libgit2/src/odb_mempack.o libgit2/src/odb_pack.o libgit2/src/odb.o libgit2/src/offmap.o libgit2/src/oid.o libgit2/src/oidarray.o libgit2/src/oidmap.o libgit2/src/pack-objects.o libgit2/src/pack.o libgit2/src/parse.o libgit2/src/patch_generate.o libgit2/src/patch_parse.o libgit2/src/patch.o libgit2/src/path.o libgit2/src/pathspec.o libgit2/src/pool.o libgit2/src/posix.o libgit2/src/pqueue.o libgit2/src/proxy.o libgit2/src/push.o libgit2/src/rebase.o libgit2/src/refdb_fs.o libgit2/src/refdb.o libgit2/src/reflog.o libgit2/src/refs.o libgit2/src/refspec.o libgit2/src/remote.o libgit2/src/repository.o libgit2/src/reset.o libgit2/src/revert.o libgit2/src/revparse.o libgit2/src/revwalk.o libgit2/src/settings.o libgit2/src/sha1_lookup.o libgit2/src/signature.o libgit2/src/sortedcache.o libgit2/src/stash.o libgit2/src/status.o libgit2/src/strmap.o libgit2/src/submodule.o libgit2/src/sysdir.o libgit2/src/tag.o libgit2/src/thread-utils.o libgit2/src/trace.o libgit2/src/transaction.o libgit2/src/transport.o libgit2/src/tree-cache.o libgit2/src/tree.o libgit2/src/tsort.o libgit2/src/util.o libgit2/src/varint.o libgit2/src/vector.o libgit2/src/worktree.o libgit2/src/zstream.o libgit2/src/streams/curl.o libgit2/src/streams/openssl.o libgit2/src/streams/socket.o libgit2/src/streams/stransport.o libgit2/src/streams/tls.o libgit2/src/transports/auth.o libgit2/src/transports/cred_helpers.o libgit2/src/transports/cred.o libgit2/src/transports/git.o libgit2/src/transports/http.o libgit2/src/transports/local.o libgit2/src/transports/smart_pkt.o libgit2/src/transports/smart_protocol.o libgit2/src/transports/smart.o libgit2/src/transports/ssh.o libgit2/src/unix/map.o libgit2/src/unix/realpath.o libgit2/src/xdiff/xdiffi.o libgit2/src/xdiff/xemit.o libgit2/src/xdiff/xhistogram.o libgit2/src/xdiff/xmerge.o libgit2/src/xdiff/xpatience.o libgit2/src/xdiff/xprepare.o libgit2/src/xdiff/xutils.o libgit2/deps/http-parser/http_parser.o gcc -std=gnu99 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o git2r.so git2r.o git2r_arg.o git2r_blame.o git2r_blob.o git2r_branch.o git2r_checkout.o git2r_clone.o git2r_commit.o git2r_config.o git2r_cred.o git2r_diff.o git2r_error.o git2r_graph.o git2r_index.o git2r_libgit2.o git2r_merge.o git2r_note.o git2r_object.o git2r_odb.o git2r_oid.o git2r_push.o git2r_reference.o git2r_reflog.o git2r_remote.o git2r_repository.o git2r_reset.o git2r_revparse.o git2r_revwalk.o git2r_signature.o git2r_stash.o git2r_status.o git2r_tag.o git2r_transfer.o git2r_tree.o -L. -lmygit -lssh2 -lssl -lcrypto -lz -L/usr/lib/x86_64-linux-gnu -lcurl -L/usr/lib/R/lib -lR installing to /usr/local/lib/R/site-library/git2r/libs ** R ** inst ** preparing package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded * DONE (git2r) * installing *source* package 'iterators' ... ** package 'iterators' successfully unpacked and MD5 sums checked ** R ** inst ** preparing package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded * DONE (iterators) * installing *source* package 'limma' ... ** libs gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c init.c -o init.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c normexp.c -o normexp.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c weighted_lowess.c -o weighted_lowess.o gcc -std=gnu99 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o limma.so init.o normexp.o weighted_lowess.o -L/usr/lib/R/lib -lR installing to /usr/local/lib/R/site-library/limma/libs ** R ** inst ** preparing package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded * DONE (limma) * installing *source* package 'openssl' ... ** package 'openssl' successfully unpacked and MD5 sums checked Found pkg-config cflags and libs! Using PKG_CFLAGS= Using PKG_LIBS=-l:libssl.so.1.0.0 -l:libcrypto.so.1.0.0 ** libs rm -f aes.o base64.o bignum.o cert.o compatibility.o diffie.o envelope.o error.o hash.o info.o keygen.o keys.o onload.o openssh.o password.o pem.o pkcs12.o pkcs7.o rand.o rsa.o signing.o ssl.o stream.o write.o openssl.so gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c aes.c -o aes.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c base64.c -o base64.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c bignum.c -o bignum.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c cert.c -o cert.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c compatibility.c -o compatibility.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c diffie.c -o diffie.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c envelope.c -o envelope.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c error.c -o error.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c hash.c -o hash.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c info.c -o info.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c keygen.c -o keygen.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c keys.c -o keys.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c onload.c -o onload.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c openssh.c -o openssh.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c password.c -o password.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c pem.c -o pem.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c pkcs12.c -o pkcs12.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c pkcs7.c -o pkcs7.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c rand.c -o rand.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c rsa.c -o rsa.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c signing.c -o signing.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c ssl.c -o ssl.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c stream.c -o stream.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c write.c -o write.o gcc -std=gnu99 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o openssl.so aes.o base64.o bignum.o cert.o compatibility.o diffie.o envelope.o error.o hash.o info.o keygen.o keys.o onload.o openssh.o password.o pem.o pkcs12.o pkcs7.o rand.o rsa.o signing.o ssl.o stream.o write.o -l:libssl.so.1.0.0 -l:libcrypto.so.1.0.0 -L/usr/lib/R/lib -lR installing to /usr/local/lib/R/site-library/openssl/libs ** R ** inst ** preparing package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded * DONE (openssl) * installing *source* package 'proxy' ... ** package 'proxy' successfully unpacked and MD5 sums checked ** libs gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c apply.c -o apply.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c arrayIndex.c -o arrayIndex.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c distance.c -o distance.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c dll.c -o dll.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c util.c -o util.o gcc -std=gnu99 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o proxy.so apply.o arrayIndex.o distance.o dll.o util.o -L/usr/lib/R/lib -lR installing to /usr/local/lib/R/site-library/proxy/libs ** R ** inst ** preparing package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded * DONE (proxy) * installing *source* package 'registry' ... ** package 'registry' successfully unpacked and MD5 sums checked ** R ** demo ** inst ** preparing package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded * DONE (registry) * installing *source* package 'rlang' ... ** package 'rlang' successfully unpacked and MD5 sums checked ** libs gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c attrs.c -o attrs.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c capture.c -o capture.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c env.c -o env.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c eval.c -o eval.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c export.c -o export.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c formula.c -o formula.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c init.c -o init.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c lang.c -o lang.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c pairlist.c -o pairlist.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c replace-na.c -o replace-na.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c sexp.c -o sexp.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c splice.c -o splice.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c symbol.c -o symbol.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c unquote.c -o unquote.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c utils.c -o utils.o gcc -std=gnu99 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o rlang.so attrs.o capture.o env.o eval.o export.o formula.o init.o lang.o pairlist.o replace-na.o sexp.o splice.o symbol.o unquote.o utils.o -L/usr/lib/R/lib -lR installing to /usr/local/lib/R/site-library/rlang/libs ** R ** inst ** preparing package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded * DONE (rlang) * installing *source* package 'stringi' ... ** package 'stringi' successfully unpacked and MD5 sums checked checking for local ICUDT_DIR... icu55/data checking for R_HOME... /usr/lib/R checking for R... /usr/lib/R/bin/R checking for R >= 3.1.0 for C++11 use... yes checking for R < 3.4.0 for CXX1X flag use... no checking for cat... /bin/cat checking for gcc... gcc -std=gnu99 checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc -std=gnu99 accepts -g... yes checking for gcc -std=gnu99 option to accept ISO C89... none needed checking how to run the C preprocessor... g++ -E checking for grep that handles long lines and -e... /bin/grep checking for egrep... /bin/grep -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking elf.h usability... yes checking elf.h presence... yes checking for elf.h... yes checking whether we are using the GNU C++ compiler... yes checking whether g++ -std=gnu++11 accepts -g... yes checking whether the C++ compiler supports the long long type... yes checking whether the compiler implements namespaces... yes checking whether the compiler supports Standard Template Library... yes checking whether std::map is available... yes checking for pkg-config... /usr/bin/pkg-config checking with pkg-config for the system ICU4C... 55.1 checking for ICU4C >= 52... yes checking for additional required CPPFLAGS, LDFLAGS, and LIBS... done checking whether we may build an ICU4C-based project... yes checking programmatically for sufficient U_ICU_VERSION_MAJOR_NUM... yes checking for available ICU data library (ucnv, uloc, utrans)... yes checking for available ICU data library (ucol)... yes configure: creating ./config.status config.status: creating src/Makevars config.status: creating src/uconfig_local.h config.status: creating src/install.libs.R *** stringi configure summary: ICU_FOUND=1 STRINGI_CXXSTD=CXX_STD=CXX11 STRINGI_CFLAGS= -fpic STRINGI_CPPFLAGS=-I. -I/usr/include/x86_64-linux-gnu -UDEBUG -DNDEBUG -DU_HAVE_ELF_H STRINGI_CXXFLAGS= -fpic STRINGI_LDFLAGS=-L/usr/lib/x86_64-linux-gnu STRINGI_LIBS=-licui18n -licuuc -licudata *** compiler settings used: CC=gcc -std=gnu99 CPP=g++ -E LD=g++ CFLAGS=-g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fpic CPPFLAGS= -UDEBUG -DNDEBUG CXX=g++ -std=gnu++11 CXXFLAGS=-g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fpic LDFLAGS= LIBS= ** libs g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG -I. -I/usr/include/x86_64-linux-gnu -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fpic -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c stri_brkiter.cpp -o stri_brkiter.o g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG -I. -I/usr/include/x86_64-linux-gnu -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fpic -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c stri_collator.cpp -o stri_collator.o g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG -I. -I/usr/include/x86_64-linux-gnu -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fpic -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c stri_common.cpp -o stri_common.o g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG -I. -I/usr/include/x86_64-linux-gnu -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fpic -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c stri_compare.cpp -o stri_compare.o g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG -I. -I/usr/include/x86_64-linux-gnu -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fpic -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c stri_container_base.cpp -o stri_container_base.o g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG -I. -I/usr/include/x86_64-linux-gnu -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fpic -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c stri_container_bytesearch.cpp -o stri_container_bytesearch.o g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG -I. -I/usr/include/x86_64-linux-gnu -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fpic -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c stri_container_listint.cpp -o stri_container_listint.o g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG -I. -I/usr/include/x86_64-linux-gnu -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fpic -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c stri_container_listraw.cpp -o stri_container_listraw.o g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG -I. -I/usr/include/x86_64-linux-gnu -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fpic -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c stri_container_listutf8.cpp -o stri_container_listutf8.o g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG -I. -I/usr/include/x86_64-linux-gnu -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fpic -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c stri_container_regex.cpp -o stri_container_regex.o g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG -I. -I/usr/include/x86_64-linux-gnu -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fpic -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c stri_container_usearch.cpp -o stri_container_usearch.o g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG -I. -I/usr/include/x86_64-linux-gnu -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fpic -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c stri_container_utf16.cpp -o stri_container_utf16.o g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG -I. -I/usr/include/x86_64-linux-gnu -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fpic -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c stri_container_utf8.cpp -o stri_container_utf8.o g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG -I. -I/usr/include/x86_64-linux-gnu -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fpic -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c stri_container_utf8_indexable.cpp -o stri_container_utf8_indexable.o g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG -I. -I/usr/include/x86_64-linux-gnu -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fpic -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c stri_encoding_conversion.cpp -o stri_encoding_conversion.o g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG -I. -I/usr/include/x86_64-linux-gnu -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fpic -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c stri_encoding_detection.cpp -o stri_encoding_detection.o g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG -I. -I/usr/include/x86_64-linux-gnu -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fpic -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c stri_encoding_management.cpp -o stri_encoding_management.o g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG -I. -I/usr/include/x86_64-linux-gnu -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fpic -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c stri_escape.cpp -o stri_escape.o g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG -I. -I/usr/include/x86_64-linux-gnu -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fpic -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c stri_exception.cpp -o stri_exception.o g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG -I. -I/usr/include/x86_64-linux-gnu -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fpic -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c stri_ICU_settings.cpp -o stri_ICU_settings.o g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG -I. -I/usr/include/x86_64-linux-gnu -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fpic -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c stri_join.cpp -o stri_join.o g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG -I. -I/usr/include/x86_64-linux-gnu -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fpic -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c stri_length.cpp -o stri_length.o g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG -I. -I/usr/include/x86_64-linux-gnu -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fpic -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c stri_pad.cpp -o stri_pad.o g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG -I. -I/usr/include/x86_64-linux-gnu -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fpic -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c stri_prepare_arg.cpp -o stri_prepare_arg.o g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG -I. -I/usr/include/x86_64-linux-gnu -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fpic -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c stri_random.cpp -o stri_random.o g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG -I. -I/usr/include/x86_64-linux-gnu -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fpic -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c stri_reverse.cpp -o stri_reverse.o g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG -I. -I/usr/include/x86_64-linux-gnu -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fpic -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c stri_search_class_count.cpp -o stri_search_class_count.o g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG -I. -I/usr/include/x86_64-linux-gnu -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fpic -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c stri_search_class_detect.cpp -o stri_search_class_detect.o g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG -I. -I/usr/include/x86_64-linux-gnu -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fpic -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c stri_search_class_extract.cpp -o stri_search_class_extract.o g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG -I. -I/usr/include/x86_64-linux-gnu -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fpic -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c stri_search_class_locate.cpp -o stri_search_class_locate.o g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG -I. -I/usr/include/x86_64-linux-gnu -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fpic -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c stri_search_class_replace.cpp -o stri_search_class_replace.o g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG -I. -I/usr/include/x86_64-linux-gnu -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fpic -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c stri_search_class_split.cpp -o stri_search_class_split.o g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG -I. -I/usr/include/x86_64-linux-gnu -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fpic -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c stri_search_class_startsendswith.cpp -o stri_search_class_startsendswith.o g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG -I. -I/usr/include/x86_64-linux-gnu -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fpic -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c stri_search_class_subset.cpp -o stri_search_class_subset.o g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG -I. -I/usr/include/x86_64-linux-gnu -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fpic -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c stri_search_class_trim.cpp -o stri_search_class_trim.o g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG -I. -I/usr/include/x86_64-linux-gnu -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fpic -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c stri_search_common.cpp -o stri_search_common.o g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG -I. -I/usr/include/x86_64-linux-gnu -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fpic -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c stri_search_coll_count.cpp -o stri_search_coll_count.o g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG -I. -I/usr/include/x86_64-linux-gnu -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fpic -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c stri_search_coll_detect.cpp -o stri_search_coll_detect.o g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG -I. -I/usr/include/x86_64-linux-gnu -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fpic -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c stri_search_coll_extract.cpp -o stri_search_coll_extract.o g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG -I. -I/usr/include/x86_64-linux-gnu -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fpic -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c stri_search_coll_locate.cpp -o stri_search_coll_locate.o g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG -I. -I/usr/include/x86_64-linux-gnu -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fpic -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c stri_search_coll_replace.cpp -o stri_search_coll_replace.o g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG -I. -I/usr/include/x86_64-linux-gnu -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fpic -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c stri_search_coll_split.cpp -o stri_search_coll_split.o g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG -I. -I/usr/include/x86_64-linux-gnu -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fpic -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c stri_search_coll_startsendswith.cpp -o stri_search_coll_startsendswith.o g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG -I. -I/usr/include/x86_64-linux-gnu -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fpic -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c stri_search_coll_subset.cpp -o stri_search_coll_subset.o g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG -I. -I/usr/include/x86_64-linux-gnu -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fpic -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c stri_search_boundaries_count.cpp -o stri_search_boundaries_count.o g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG -I. -I/usr/include/x86_64-linux-gnu -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fpic -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c stri_search_boundaries_extract.cpp -o stri_search_boundaries_extract.o g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG -I. -I/usr/include/x86_64-linux-gnu -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fpic -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c stri_search_boundaries_locate.cpp -o stri_search_boundaries_locate.o g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG -I. -I/usr/include/x86_64-linux-gnu -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fpic -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c stri_search_boundaries_split.cpp -o stri_search_boundaries_split.o g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG -I. -I/usr/include/x86_64-linux-gnu -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fpic -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c stri_search_fixed_count.cpp -o stri_search_fixed_count.o g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG -I. -I/usr/include/x86_64-linux-gnu -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fpic -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c stri_search_fixed_detect.cpp -o stri_search_fixed_detect.o g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG -I. -I/usr/include/x86_64-linux-gnu -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fpic -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c stri_search_fixed_extract.cpp -o stri_search_fixed_extract.o g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG -I. -I/usr/include/x86_64-linux-gnu -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fpic -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c stri_search_fixed_locate.cpp -o stri_search_fixed_locate.o g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG -I. -I/usr/include/x86_64-linux-gnu -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fpic -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c stri_search_fixed_replace.cpp -o stri_search_fixed_replace.o g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG -I. -I/usr/include/x86_64-linux-gnu -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fpic -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c stri_search_fixed_split.cpp -o stri_search_fixed_split.o g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG -I. -I/usr/include/x86_64-linux-gnu -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fpic -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c stri_search_fixed_subset.cpp -o stri_search_fixed_subset.o g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG -I. -I/usr/include/x86_64-linux-gnu -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fpic -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c stri_search_fixed_startsendswith.cpp -o stri_search_fixed_startsendswith.o g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG -I. -I/usr/include/x86_64-linux-gnu -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fpic -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c stri_search_in.cpp -o stri_search_in.o g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG -I. -I/usr/include/x86_64-linux-gnu -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fpic -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c stri_search_other_replace.cpp -o stri_search_other_replace.o g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG -I. -I/usr/include/x86_64-linux-gnu -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fpic -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c stri_search_other_split.cpp -o stri_search_other_split.o g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG -I. -I/usr/include/x86_64-linux-gnu -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fpic -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c stri_search_regex_count.cpp -o stri_search_regex_count.o g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG -I. -I/usr/include/x86_64-linux-gnu -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fpic -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c stri_search_regex_detect.cpp -o stri_search_regex_detect.o g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG -I. -I/usr/include/x86_64-linux-gnu -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fpic -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c stri_search_regex_extract.cpp -o stri_search_regex_extract.o g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG -I. -I/usr/include/x86_64-linux-gnu -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fpic -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c stri_search_regex_locate.cpp -o stri_search_regex_locate.o g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG -I. -I/usr/include/x86_64-linux-gnu -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fpic -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c stri_search_regex_match.cpp -o stri_search_regex_match.o g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG -I. -I/usr/include/x86_64-linux-gnu -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fpic -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c stri_search_regex_replace.cpp -o stri_search_regex_replace.o g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG -I. -I/usr/include/x86_64-linux-gnu -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fpic -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c stri_search_regex_split.cpp -o stri_search_regex_split.o g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG -I. -I/usr/include/x86_64-linux-gnu -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fpic -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c stri_search_regex_subset.cpp -o stri_search_regex_subset.o g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG -I. -I/usr/include/x86_64-linux-gnu -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fpic -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c stri_sort.cpp -o stri_sort.o g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG -I. -I/usr/include/x86_64-linux-gnu -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fpic -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c stri_stats.cpp -o stri_stats.o g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG -I. -I/usr/include/x86_64-linux-gnu -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fpic -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c stri_stringi.cpp -o stri_stringi.o g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG -I. -I/usr/include/x86_64-linux-gnu -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fpic -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c stri_sub.cpp -o stri_sub.o g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG -I. -I/usr/include/x86_64-linux-gnu -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fpic -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c stri_test.cpp -o stri_test.o g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG -I. -I/usr/include/x86_64-linux-gnu -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fpic -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c stri_time_zone.cpp -o stri_time_zone.o g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG -I. -I/usr/include/x86_64-linux-gnu -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fpic -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c stri_time_calendar.cpp -o stri_time_calendar.o g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG -I. -I/usr/include/x86_64-linux-gnu -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fpic -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c stri_time_symbols.cpp -o stri_time_symbols.o g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG -I. -I/usr/include/x86_64-linux-gnu -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fpic -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c stri_time_format.cpp -o stri_time_format.o g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG -I. -I/usr/include/x86_64-linux-gnu -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fpic -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c stri_trans_casemap.cpp -o stri_trans_casemap.o g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG -I. -I/usr/include/x86_64-linux-gnu -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fpic -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c stri_trans_other.cpp -o stri_trans_other.o g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG -I. -I/usr/include/x86_64-linux-gnu -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fpic -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c stri_trans_normalization.cpp -o stri_trans_normalization.o g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG -I. -I/usr/include/x86_64-linux-gnu -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fpic -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c stri_trans_transliterate.cpp -o stri_trans_transliterate.o g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG -I. -I/usr/include/x86_64-linux-gnu -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fpic -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c stri_ucnv.cpp -o stri_ucnv.o g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG -I. -I/usr/include/x86_64-linux-gnu -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fpic -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c stri_uloc.cpp -o stri_uloc.o g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG -I. -I/usr/include/x86_64-linux-gnu -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fpic -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c stri_utils.cpp -o stri_utils.o g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG -I. -I/usr/include/x86_64-linux-gnu -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fpic -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c stri_wrap.cpp -o stri_wrap.o g++ -std=gnu++11 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o stringi.so stri_brkiter.o stri_collator.o stri_common.o stri_compare.o stri_container_base.o stri_container_bytesearch.o stri_container_listint.o stri_container_listraw.o stri_container_listutf8.o stri_container_regex.o stri_container_usearch.o stri_container_utf16.o stri_container_utf8.o stri_container_utf8_indexable.o stri_encoding_conversion.o stri_encoding_detection.o stri_encoding_management.o stri_escape.o stri_exception.o stri_ICU_settings.o stri_join.o stri_length.o stri_pad.o stri_prepare_arg.o stri_random.o stri_reverse.o stri_search_class_count.o stri_search_class_detect.o stri_search_class_extract.o stri_search_class_locate.o stri_search_class_replace.o stri_search_class_split.o stri_search_class_startsendswith.o stri_search_class_subset.o stri_search_class_trim.o stri_search_common.o stri_search_coll_count.o stri_search_coll_detect.o stri_search_coll_extract.o stri_search_coll_locate.o stri_search_coll_replace.o stri_search_coll_split.o stri_search_coll_startsendswith.o stri_search_coll_subset.o stri_search_boundaries_count.o stri_search_boundaries_extract.o stri_search_boundaries_locate.o stri_search_boundaries_split.o stri_search_fixed_count.o stri_search_fixed_detect.o stri_search_fixed_extract.o stri_search_fixed_locate.o stri_search_fixed_replace.o stri_search_fixed_split.o stri_search_fixed_subset.o stri_search_fixed_startsendswith.o stri_search_in.o stri_search_other_replace.o stri_search_other_split.o stri_search_regex_count.o stri_search_regex_detect.o stri_search_regex_extract.o stri_search_regex_locate.o stri_search_regex_match.o stri_search_regex_replace.o stri_search_regex_split.o stri_search_regex_subset.o stri_sort.o stri_stats.o stri_stringi.o stri_sub.o stri_test.o stri_time_zone.o stri_time_calendar.o stri_time_symbols.o stri_time_format.o stri_trans_casemap.o stri_trans_other.o stri_trans_normalization.o stri_trans_transliterate.o stri_ucnv.o stri_uloc.o stri_utils.o stri_wrap.o -L/usr/lib/x86_64-linux-gnu -licui18n -licuuc -licudata -L/usr/lib/R/lib -lR installing via 'install.libs.R' to /usr/local/lib/R/site-library/stringi ** R ** inst ** preparing package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded * DONE (stringi) * installing *source* package 'withr' ... ** package 'withr' successfully unpacked and MD5 sums checked ** R ** inst ** preparing package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded * DONE (withr) * installing *source* package 'yaml' ... ** package 'yaml' successfully unpacked and MD5 sums checked ** libs gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c api.c -o api.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c dumper.c -o dumper.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c emitter.c -o emitter.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c implicit.c -o implicit.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c loader.c -o loader.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c parser.c -o parser.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c r_emit.c -o r_emit.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c r_ext.c -o r_ext.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c r_parse.c -o r_parse.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c reader.c -o reader.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c scanner.c -o scanner.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c writer.c -o writer.o gcc -std=gnu99 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o yaml.so api.o dumper.o emitter.o implicit.o loader.o parser.o r_emit.o r_ext.o r_parse.o reader.o scanner.o writer.o -L/usr/lib/R/lib -lR installing to /usr/local/lib/R/site-library/yaml/libs ** R ** inst ** preparing package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded * DONE (yaml) * installing *source* package 'pillar' ... ** package 'pillar' successfully unpacked and MD5 sums checked ** R ** preparing package for lazy loading ** help *** installing help indices *** copying figures ** building package indices ** testing if installed package can be loaded * DONE (pillar) * installing *source* package 'GEOquery' ... ** R ** inst ** preparing package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded * DONE (GEOquery) * installing *source* package 'foreach' ... ** package 'foreach' successfully unpacked and MD5 sums checked ** R ** demo ** inst ** preparing package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded * DONE (foreach) * installing *source* package 'hms' ... ** package 'hms' successfully unpacked and MD5 sums checked ** R ** preparing package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded * DONE (hms) * installing *source* package 'knitr' ... ** package 'knitr' successfully unpacked and MD5 sums checked ** R ** demo ** inst ** preparing package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded * DONE (knitr) * installing *source* package 'reshape2' ... ** package 'reshape2' successfully unpacked and MD5 sums checked ** libs g++ -I/usr/share/R/include -DNDEBUG -I"/usr/local/lib/R/site-library/Rcpp/include" -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c RcppExports.cpp -o RcppExports.o g++ -I/usr/share/R/include -DNDEBUG -I"/usr/local/lib/R/site-library/Rcpp/include" -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c melt.cpp -o melt.o g++ -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o reshape2.so RcppExports.o melt.o -L/usr/lib/R/lib -lR installing to /usr/local/lib/R/site-library/reshape2/libs ** R ** data *** moving datasets to lazyload DB ** inst ** preparing package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded * DONE (reshape2) * installing *source* package 'rprojroot' ... ** package 'rprojroot' successfully unpacked and MD5 sums checked ** R ** inst ** preparing package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded * DONE (rprojroot) * installing *source* package 'tidyselect' ... ** package 'tidyselect' successfully unpacked and MD5 sums checked ** libs g++ -I/usr/share/R/include -DNDEBUG -I"/usr/local/lib/R/site-library/Rcpp/include" -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c RcppExports.cpp -o RcppExports.o g++ -I/usr/share/R/include -DNDEBUG -I"/usr/local/lib/R/site-library/Rcpp/include" -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c combine_variables.cpp -o combine_variables.o g++ -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o tidyselect.so RcppExports.o combine_variables.o -L/usr/lib/R/lib -lR installing to /usr/local/lib/R/site-library/tidyselect/libs ** R ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded * DONE (tidyselect) * installing *source* package 'tibble' ... ** package 'tibble' successfully unpacked and MD5 sums checked ** libs gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c coerce.c -o coerce.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c init.c -o init.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c matrixToDataFrame.c -o matrixToDataFrame.o gcc -std=gnu99 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o tibble.so coerce.o init.o matrixToDataFrame.o -L/usr/lib/R/lib -lR installing to /usr/local/lib/R/site-library/tibble/libs ** R ** inst ** preparing package for lazy loading ** help *** installing help indices *** copying figures ** building package indices ** installing vignettes ** testing if installed package can be loaded * DONE (tibble) * installing *source* package 'dbplyr' ... ** package 'dbplyr' successfully unpacked and MD5 sums checked ** R ** inst ** preparing package for lazy loading ** help *** installing help indices *** copying figures ** building package indices ** installing vignettes ** testing if installed package can be loaded * DONE (dbplyr)  The downloaded source packages are in '/tmp/RtmpxNJ6sA/downloaded_packages' trying URL 'https://cran.rstudio.com/src/contrib/XML_3.98-1.9.tar.gz' Content type 'application/x-gzip' length 1599437 bytes (1.5 MB) ================================================== downloaded 1.5 MB trying URL 'https://cran.rstudio.com/src/contrib/bitops_1.0-6.tar.gz' Content type 'application/x-gzip' length 8734 bytes ================================================== downloaded 8734 bytes trying URL 'https://cran.rstudio.com/src/contrib/littler_0.3.3.tar.gz' Content type 'application/x-gzip' length 422170 bytes (412 KB) ================================================== downloaded 412 KB * installing *source* package 'XML' ... ** package 'XML' successfully unpacked and MD5 sums checked checking for gcc... gcc checking for C compiler default output file name... a.out checking whether the C compiler works... yes checking whether we are cross compiling... no checking for suffix of executables... checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking how to run the C preprocessor... gcc -E checking for sed... /bin/sed checking for pkg-config... /usr/bin/pkg-config checking for xml2-config... /usr/bin/xml2-config USE_XML2 = yes SED_EXTENDED_ARG: -E Minor 9, Patch 3 for 2.9.3 Located parser file -I/usr/include/libxml2/parser.h Checking for 1.8: -I/usr/include/libxml2 Using libxml2.* checking for gzopen in -lz... yes checking for xmlParseFile in -lxml2... yes checking for xmlHashSize in -lxml2... yes Using built-in xmlHashSize Checking DTD parsing (presence of externalSubset)... checking for xmlHashSize in -lxml2... yes Found xmlHashSize checking for xmlOutputBufferCreateBuffer in -lxml2... yes have xmlOutputBufferCreateBuffer() checking for xmlDocDumpFormatMemoryEnc in -lxml2... yes checking libxml/xmlversion.h usability... yes checking libxml/xmlversion.h presence... yes checking for libxml/xmlversion.h... yes Expat: FALSE Checking for return type of xmlHashScan element routine. No return value for xmlHashScan xmlNs has a context field Checking for cetype_t enumeration No cetype_t enumeration defined in R headers. checking for xmlsec1-config... no nodegc default xml-debug default Version has XML_WITH_ZLIB Version has xmlHasFeature() **************************************** Configuration information: Libxml settings libxml include directory: -I/usr/include/libxml2 libxml library directory: -lxml2 -lz -lxml2 libxml 2: -DLIBXML2=1 Compilation flags: -DLIBXML -I/usr/include/libxml2 -DUSE_EXTERNAL_SUBSET=1 -DROOT_HAS_DTD_NODE=1 -DDUMP_WITH_ENCODING=1 -DUSE_XML_VERSION_H=1 -DXML_ELEMENT_ETYPE=1 -DXML_ATTRIBUTE_ATYPE=1 -DNO_XML_HASH_SCANNER_RETURN=1 -DLIBXML_NAMESPACE_HAS_CONTEXT=1 -DHAVE_XML_WITH_ZLIB=1 -DHAVE_XML_HAS_FEATURE=1 -DUSE_R=1 -D_R_=1 -DHAVE_VALIDITY=1 -DXML_REF_COUNT_NODES=1 Link flags: -lxml2 -lz -lxml2 **************************************** configure: creating ./config.status config.status: creating src/Makevars config.status: creating R/supports.R config.status: creating inst/scripts/RSXML.csh config.status: creating inst/scripts/RSXML.bsh ** libs gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DLIBXML -I/usr/include/libxml2 -DUSE_EXTERNAL_SUBSET=1 -DROOT_HAS_DTD_NODE=1 -DDUMP_WITH_ENCODING=1 -DUSE_XML_VERSION_H=1 -DXML_ELEMENT_ETYPE=1 -DXML_ATTRIBUTE_ATYPE=1 -DNO_XML_HASH_SCANNER_RETURN=1 -DLIBXML_NAMESPACE_HAS_CONTEXT=1 -DHAVE_XML_WITH_ZLIB=1 -DHAVE_XML_HAS_FEATURE=1 -DUSE_R=1 -D_R_=1 -DHAVE_VALIDITY=1 -DXML_REF_COUNT_NODES=1 -I. -DLIBXML2=1 -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c DocParse.c -o DocParse.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DLIBXML -I/usr/include/libxml2 -DUSE_EXTERNAL_SUBSET=1 -DROOT_HAS_DTD_NODE=1 -DDUMP_WITH_ENCODING=1 -DUSE_XML_VERSION_H=1 -DXML_ELEMENT_ETYPE=1 -DXML_ATTRIBUTE_ATYPE=1 -DNO_XML_HASH_SCANNER_RETURN=1 -DLIBXML_NAMESPACE_HAS_CONTEXT=1 -DHAVE_XML_WITH_ZLIB=1 -DHAVE_XML_HAS_FEATURE=1 -DUSE_R=1 -D_R_=1 -DHAVE_VALIDITY=1 -DXML_REF_COUNT_NODES=1 -I. -DLIBXML2=1 -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c EventParse.c -o EventParse.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DLIBXML -I/usr/include/libxml2 -DUSE_EXTERNAL_SUBSET=1 -DROOT_HAS_DTD_NODE=1 -DDUMP_WITH_ENCODING=1 -DUSE_XML_VERSION_H=1 -DXML_ELEMENT_ETYPE=1 -DXML_ATTRIBUTE_ATYPE=1 -DNO_XML_HASH_SCANNER_RETURN=1 -DLIBXML_NAMESPACE_HAS_CONTEXT=1 -DHAVE_XML_WITH_ZLIB=1 -DHAVE_XML_HAS_FEATURE=1 -DUSE_R=1 -D_R_=1 -DHAVE_VALIDITY=1 -DXML_REF_COUNT_NODES=1 -I. -DLIBXML2=1 -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c ExpatParse.c -o ExpatParse.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DLIBXML -I/usr/include/libxml2 -DUSE_EXTERNAL_SUBSET=1 -DROOT_HAS_DTD_NODE=1 -DDUMP_WITH_ENCODING=1 -DUSE_XML_VERSION_H=1 -DXML_ELEMENT_ETYPE=1 -DXML_ATTRIBUTE_ATYPE=1 -DNO_XML_HASH_SCANNER_RETURN=1 -DLIBXML_NAMESPACE_HAS_CONTEXT=1 -DHAVE_XML_WITH_ZLIB=1 -DHAVE_XML_HAS_FEATURE=1 -DUSE_R=1 -D_R_=1 -DHAVE_VALIDITY=1 -DXML_REF_COUNT_NODES=1 -I. -DLIBXML2=1 -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c HTMLParse.c -o HTMLParse.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DLIBXML -I/usr/include/libxml2 -DUSE_EXTERNAL_SUBSET=1 -DROOT_HAS_DTD_NODE=1 -DDUMP_WITH_ENCODING=1 -DUSE_XML_VERSION_H=1 -DXML_ELEMENT_ETYPE=1 -DXML_ATTRIBUTE_ATYPE=1 -DNO_XML_HASH_SCANNER_RETURN=1 -DLIBXML_NAMESPACE_HAS_CONTEXT=1 -DHAVE_XML_WITH_ZLIB=1 -DHAVE_XML_HAS_FEATURE=1 -DUSE_R=1 -D_R_=1 -DHAVE_VALIDITY=1 -DXML_REF_COUNT_NODES=1 -I. -DLIBXML2=1 -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c NodeGC.c -o NodeGC.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DLIBXML -I/usr/include/libxml2 -DUSE_EXTERNAL_SUBSET=1 -DROOT_HAS_DTD_NODE=1 -DDUMP_WITH_ENCODING=1 -DUSE_XML_VERSION_H=1 -DXML_ELEMENT_ETYPE=1 -DXML_ATTRIBUTE_ATYPE=1 -DNO_XML_HASH_SCANNER_RETURN=1 -DLIBXML_NAMESPACE_HAS_CONTEXT=1 -DHAVE_XML_WITH_ZLIB=1 -DHAVE_XML_HAS_FEATURE=1 -DUSE_R=1 -D_R_=1 -DHAVE_VALIDITY=1 -DXML_REF_COUNT_NODES=1 -I. -DLIBXML2=1 -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c RSDTD.c -o RSDTD.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DLIBXML -I/usr/include/libxml2 -DUSE_EXTERNAL_SUBSET=1 -DROOT_HAS_DTD_NODE=1 -DDUMP_WITH_ENCODING=1 -DUSE_XML_VERSION_H=1 -DXML_ELEMENT_ETYPE=1 -DXML_ATTRIBUTE_ATYPE=1 -DNO_XML_HASH_SCANNER_RETURN=1 -DLIBXML_NAMESPACE_HAS_CONTEXT=1 -DHAVE_XML_WITH_ZLIB=1 -DHAVE_XML_HAS_FEATURE=1 -DUSE_R=1 -D_R_=1 -DHAVE_VALIDITY=1 -DXML_REF_COUNT_NODES=1 -I. -DLIBXML2=1 -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c RUtils.c -o RUtils.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DLIBXML -I/usr/include/libxml2 -DUSE_EXTERNAL_SUBSET=1 -DROOT_HAS_DTD_NODE=1 -DDUMP_WITH_ENCODING=1 -DUSE_XML_VERSION_H=1 -DXML_ELEMENT_ETYPE=1 -DXML_ATTRIBUTE_ATYPE=1 -DNO_XML_HASH_SCANNER_RETURN=1 -DLIBXML_NAMESPACE_HAS_CONTEXT=1 -DHAVE_XML_WITH_ZLIB=1 -DHAVE_XML_HAS_FEATURE=1 -DUSE_R=1 -D_R_=1 -DHAVE_VALIDITY=1 -DXML_REF_COUNT_NODES=1 -I. -DLIBXML2=1 -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c Rcatalog.c -o Rcatalog.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DLIBXML -I/usr/include/libxml2 -DUSE_EXTERNAL_SUBSET=1 -DROOT_HAS_DTD_NODE=1 -DDUMP_WITH_ENCODING=1 -DUSE_XML_VERSION_H=1 -DXML_ELEMENT_ETYPE=1 -DXML_ATTRIBUTE_ATYPE=1 -DNO_XML_HASH_SCANNER_RETURN=1 -DLIBXML_NAMESPACE_HAS_CONTEXT=1 -DHAVE_XML_WITH_ZLIB=1 -DHAVE_XML_HAS_FEATURE=1 -DUSE_R=1 -D_R_=1 -DHAVE_VALIDITY=1 -DXML_REF_COUNT_NODES=1 -I. -DLIBXML2=1 -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c Utils.c -o Utils.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DLIBXML -I/usr/include/libxml2 -DUSE_EXTERNAL_SUBSET=1 -DROOT_HAS_DTD_NODE=1 -DDUMP_WITH_ENCODING=1 -DUSE_XML_VERSION_H=1 -DXML_ELEMENT_ETYPE=1 -DXML_ATTRIBUTE_ATYPE=1 -DNO_XML_HASH_SCANNER_RETURN=1 -DLIBXML_NAMESPACE_HAS_CONTEXT=1 -DHAVE_XML_WITH_ZLIB=1 -DHAVE_XML_HAS_FEATURE=1 -DUSE_R=1 -D_R_=1 -DHAVE_VALIDITY=1 -DXML_REF_COUNT_NODES=1 -I. -DLIBXML2=1 -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c XMLEventParse.c -o XMLEventParse.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DLIBXML -I/usr/include/libxml2 -DUSE_EXTERNAL_SUBSET=1 -DROOT_HAS_DTD_NODE=1 -DDUMP_WITH_ENCODING=1 -DUSE_XML_VERSION_H=1 -DXML_ELEMENT_ETYPE=1 -DXML_ATTRIBUTE_ATYPE=1 -DNO_XML_HASH_SCANNER_RETURN=1 -DLIBXML_NAMESPACE_HAS_CONTEXT=1 -DHAVE_XML_WITH_ZLIB=1 -DHAVE_XML_HAS_FEATURE=1 -DUSE_R=1 -D_R_=1 -DHAVE_VALIDITY=1 -DXML_REF_COUNT_NODES=1 -I. -DLIBXML2=1 -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c XMLHashTree.c -o XMLHashTree.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DLIBXML -I/usr/include/libxml2 -DUSE_EXTERNAL_SUBSET=1 -DROOT_HAS_DTD_NODE=1 -DDUMP_WITH_ENCODING=1 -DUSE_XML_VERSION_H=1 -DXML_ELEMENT_ETYPE=1 -DXML_ATTRIBUTE_ATYPE=1 -DNO_XML_HASH_SCANNER_RETURN=1 -DLIBXML_NAMESPACE_HAS_CONTEXT=1 -DHAVE_XML_WITH_ZLIB=1 -DHAVE_XML_HAS_FEATURE=1 -DUSE_R=1 -D_R_=1 -DHAVE_VALIDITY=1 -DXML_REF_COUNT_NODES=1 -I. -DLIBXML2=1 -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c XMLTree.c -o XMLTree.o XMLTree.c: In function 'R_xmlSearchNs': XMLTree.c:1695:39: warning: comparison of distinct pointer types lacks a cast xmlDocPtr doc = (xmlDocPtr) r_doc == NULL_USER_OBJECT ? NULL : R_ExternalPtrAddr(r_doc); ^ gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DLIBXML -I/usr/include/libxml2 -DUSE_EXTERNAL_SUBSET=1 -DROOT_HAS_DTD_NODE=1 -DDUMP_WITH_ENCODING=1 -DUSE_XML_VERSION_H=1 -DXML_ELEMENT_ETYPE=1 -DXML_ATTRIBUTE_ATYPE=1 -DNO_XML_HASH_SCANNER_RETURN=1 -DLIBXML_NAMESPACE_HAS_CONTEXT=1 -DHAVE_XML_WITH_ZLIB=1 -DHAVE_XML_HAS_FEATURE=1 -DUSE_R=1 -D_R_=1 -DHAVE_VALIDITY=1 -DXML_REF_COUNT_NODES=1 -I. -DLIBXML2=1 -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c fixNS.c -o fixNS.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DLIBXML -I/usr/include/libxml2 -DUSE_EXTERNAL_SUBSET=1 -DROOT_HAS_DTD_NODE=1 -DDUMP_WITH_ENCODING=1 -DUSE_XML_VERSION_H=1 -DXML_ELEMENT_ETYPE=1 -DXML_ATTRIBUTE_ATYPE=1 -DNO_XML_HASH_SCANNER_RETURN=1 -DLIBXML_NAMESPACE_HAS_CONTEXT=1 -DHAVE_XML_WITH_ZLIB=1 -DHAVE_XML_HAS_FEATURE=1 -DUSE_R=1 -D_R_=1 -DHAVE_VALIDITY=1 -DXML_REF_COUNT_NODES=1 -I. -DLIBXML2=1 -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c libxmlFeatures.c -o libxmlFeatures.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DLIBXML -I/usr/include/libxml2 -DUSE_EXTERNAL_SUBSET=1 -DROOT_HAS_DTD_NODE=1 -DDUMP_WITH_ENCODING=1 -DUSE_XML_VERSION_H=1 -DXML_ELEMENT_ETYPE=1 -DXML_ATTRIBUTE_ATYPE=1 -DNO_XML_HASH_SCANNER_RETURN=1 -DLIBXML_NAMESPACE_HAS_CONTEXT=1 -DHAVE_XML_WITH_ZLIB=1 -DHAVE_XML_HAS_FEATURE=1 -DUSE_R=1 -D_R_=1 -DHAVE_VALIDITY=1 -DXML_REF_COUNT_NODES=1 -I. -DLIBXML2=1 -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c schema.c -o schema.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DLIBXML -I/usr/include/libxml2 -DUSE_EXTERNAL_SUBSET=1 -DROOT_HAS_DTD_NODE=1 -DDUMP_WITH_ENCODING=1 -DUSE_XML_VERSION_H=1 -DXML_ELEMENT_ETYPE=1 -DXML_ATTRIBUTE_ATYPE=1 -DNO_XML_HASH_SCANNER_RETURN=1 -DLIBXML_NAMESPACE_HAS_CONTEXT=1 -DHAVE_XML_WITH_ZLIB=1 -DHAVE_XML_HAS_FEATURE=1 -DUSE_R=1 -D_R_=1 -DHAVE_VALIDITY=1 -DXML_REF_COUNT_NODES=1 -I. -DLIBXML2=1 -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c xmlsecurity.c -o xmlsecurity.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DLIBXML -I/usr/include/libxml2 -DUSE_EXTERNAL_SUBSET=1 -DROOT_HAS_DTD_NODE=1 -DDUMP_WITH_ENCODING=1 -DUSE_XML_VERSION_H=1 -DXML_ELEMENT_ETYPE=1 -DXML_ATTRIBUTE_ATYPE=1 -DNO_XML_HASH_SCANNER_RETURN=1 -DLIBXML_NAMESPACE_HAS_CONTEXT=1 -DHAVE_XML_WITH_ZLIB=1 -DHAVE_XML_HAS_FEATURE=1 -DUSE_R=1 -D_R_=1 -DHAVE_VALIDITY=1 -DXML_REF_COUNT_NODES=1 -I. -DLIBXML2=1 -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c xpath.c -o xpath.o gcc -std=gnu99 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o XML.so DocParse.o EventParse.o ExpatParse.o HTMLParse.o NodeGC.o RSDTD.o RUtils.o Rcatalog.o Utils.o XMLEventParse.o XMLHashTree.o XMLTree.o fixNS.o libxmlFeatures.o schema.o xmlsecurity.o xpath.o -lxml2 -lz -lxml2 -L/usr/lib/R/lib -lR installing to /usr/lib/R/site-library/XML/libs ** R ** inst ** preparing package for lazy loading Creating a generic function for 'source' from package 'base' in package 'XML' in method for 'xmlAttrsToDataFrame' with signature '"AsIs"': no definition for class "AsIs" in method for 'readKeyValueDB' with signature '"AsIs"': no definition for class "AsIs" in method for 'readSolrDoc' with signature '"AsIs"': no definition for class "AsIs" ** help *** installing help indices ** building package indices ** testing if installed package can be loaded * DONE (XML) * installing *source* package 'bitops' ... ** package 'bitops' successfully unpacked and MD5 sums checked ** libs gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c bit-ops.c -o bit-ops.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c cksum.c -o cksum.o gcc -std=gnu99 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o bitops.so bit-ops.o cksum.o -L/usr/lib/R/lib -lR installing to /usr/lib/R/site-library/bitops/libs ** R ** preparing package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded * DONE (bitops) * installing *source* package 'littler' ... ** package 'littler' successfully unpacked and MD5 sums checked checking for gcc... gcc -std=gnu99 checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc -std=gnu99 accepts -g... yes checking for gcc -std=gnu99 option to accept ISO C89... none needed checking how to run the C preprocessor... gcc -std=gnu99 -E checking for grep that handles long lines and -e... /bin/grep checking for egrep... /bin/grep -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking getopt.h usability... yes checking getopt.h presence... yes checking for getopt.h... yes checking whether sys/types.h defines makedev... yes checking for setenv... yes checking for gettimeofday... yes checking for time... yes checking if R was built as a shared library... yes checking for install_name_tool... no configure: creating ./config.status config.status: creating src/Makevars config.status: creating src/gitversion.h config.status: creating src/config.h ** libs gcc -std=gnu99 -o r -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -I/usr/share/R/include littler.c -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,--export-dynamic -fopenmp -Wl,-Bsymbolic-functions -Wl,-z,relro -L/usr/lib/R/lib -lR -lpcre -llzma -lbz2 -lz -lrt -ldl -lm -lblas -llapack -Wl,-rpath,/usr/lib/R/lib -Wl,-rpath,/usr/lib/x86_64-linux-gnu -Wl,-rpath,/usr/lib/jvm/default-java/jre/lib/amd64/server -Wl,-rpath,/usr/lib/R/lib -Wl,-rpath,/usr/lib/x86_64-linux-gnu -Wl,-rpath,/usr/lib/jvm/default-java/jre/lib/amd64/server -Wl,-rpath,/usr/lib/R/lib -Wl,-rpath,/usr/lib/x86_64-linux-gnu -Wl,-rpath,/usr/lib/jvm/default-java/jre/lib/amd64/server -Wl,-rpath,/usr/lib/R/lib -Wl,-rpath,/usr/lib/x86_64-linux-gnu -Wl,-rpath,/usr/lib/jvm/default-java/jre/lib/amd64/server * * new binary r installed in bin/ subdirectory * consider adding a symbolic link from, e.g., /usr/local/bin * on OS X, you may have to name this 'lr' instead * ** R ** inst ** preparing package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded * DONE (littler)  The downloaded source packages are in '/tmp/RtmpxNJ6sA/downloaded_packages' trying URL 'https://cran.rstudio.com/src/contrib/MASS_7.3-48.tar.gz' Content type 'application/x-gzip' length 487744 bytes (476 KB) ================================================== downloaded 476 KB trying URL 'https://cran.rstudio.com/src/contrib/Matrix_1.2-12.tar.gz' Content type 'application/x-gzip' length 1821419 bytes (1.7 MB) ================================================== downloaded 1.7 MB trying URL 'https://cran.rstudio.com/src/contrib/codetools_0.2-15.tar.gz' Content type 'application/x-gzip' length 12930 bytes (12 KB) ================================================== downloaded 12 KB trying URL 'https://cran.rstudio.com/src/contrib/lattice_0.20-35.tar.gz' Content type 'application/x-gzip' length 359813 bytes (351 KB) ================================================== downloaded 351 KB trying URL 'https://cran.rstudio.com/src/contrib/spatial_7.3-11.tar.gz' Content type 'application/x-gzip' length 44666 bytes (43 KB) ================================================== downloaded 43 KB * installing *source* package 'MASS' ... ** package 'MASS' successfully unpacked and MD5 sums checked ** libs gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c MASS.c -o MASS.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c lqs.c -o lqs.o gcc -std=gnu99 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o MASS.so MASS.o lqs.o -L/usr/lib/R/lib -lR installing to /usr/lib/R/library/MASS/libs ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded * DONE (MASS) * installing *source* package 'codetools' ... ** package 'codetools' successfully unpacked and MD5 sums checked ** R ** preparing package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded * DONE (codetools) * installing *source* package 'lattice' ... ** package 'lattice' successfully unpacked and MD5 sums checked ** libs gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c init.c -o init.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c threeDplot.c -o threeDplot.o gcc -std=gnu99 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o lattice.so init.o threeDplot.o -L/usr/lib/R/lib -lR installing to /usr/lib/R/library/lattice/libs ** R ** data *** moving datasets to lazyload DB ** demo ** inst ** preparing package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded * DONE (lattice) * installing *source* package 'spatial' ... ** package 'spatial' successfully unpacked and MD5 sums checked ** libs gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c init.c -o init.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c krc.c -o krc.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c pps.c -o pps.o gcc -std=gnu99 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o spatial.so init.o krc.o pps.o -L/usr/lib/R/lib -lR installing to /usr/lib/R/library/spatial/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded * DONE (spatial) * installing *source* package 'Matrix' ... ** package 'Matrix' successfully unpacked and MD5 sums checked ** libs gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DNTIMER -I./SuiteSparse_config -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c CHMfactor.c -o CHMfactor.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DNTIMER -I./SuiteSparse_config -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c Csparse.c -o Csparse.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DNTIMER -I./SuiteSparse_config -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c TMatrix_as.c -o TMatrix_as.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DNTIMER -I./SuiteSparse_config -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c Tsparse.c -o Tsparse.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DNTIMER -I./SuiteSparse_config -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c init.c -o init.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DNTIMER -I./SuiteSparse_config -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c Mutils.c -o Mutils.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DNTIMER -I./SuiteSparse_config -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c chm_common.c -o chm_common.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DNTIMER -I./SuiteSparse_config -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c cs.c -o cs.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DNTIMER -I./SuiteSparse_config -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c cs_utils.c -o cs_utils.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DNTIMER -I./SuiteSparse_config -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c dense.c -o dense.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DNTIMER -I./SuiteSparse_config -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c dgCMatrix.c -o dgCMatrix.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DNTIMER -I./SuiteSparse_config -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c dgTMatrix.c -o dgTMatrix.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DNTIMER -I./SuiteSparse_config -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c dgeMatrix.c -o dgeMatrix.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DNTIMER -I./SuiteSparse_config -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c dpoMatrix.c -o dpoMatrix.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DNTIMER -I./SuiteSparse_config -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c dppMatrix.c -o dppMatrix.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DNTIMER -I./SuiteSparse_config -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c dsCMatrix.c -o dsCMatrix.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DNTIMER -I./SuiteSparse_config -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c dsyMatrix.c -o dsyMatrix.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DNTIMER -I./SuiteSparse_config -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c dspMatrix.c -o dspMatrix.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DNTIMER -I./SuiteSparse_config -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c dtCMatrix.c -o dtCMatrix.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DNTIMER -I./SuiteSparse_config -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c dtTMatrix.c -o dtTMatrix.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DNTIMER -I./SuiteSparse_config -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c dtrMatrix.c -o dtrMatrix.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DNTIMER -I./SuiteSparse_config -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c dtpMatrix.c -o dtpMatrix.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DNTIMER -I./SuiteSparse_config -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c factorizations.c -o factorizations.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DNTIMER -I./SuiteSparse_config -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c ldense.c -o ldense.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DNTIMER -I./SuiteSparse_config -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c lgCMatrix.c -o lgCMatrix.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DNTIMER -I./SuiteSparse_config -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c sparseQR.c -o sparseQR.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DNTIMER -I./SuiteSparse_config -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c abIndex.c -o abIndex.o make[1]: Entering directory '/tmp/RtmpjCenu2/R.INSTALL1c1a759a784d/Matrix/src/CHOLMOD' ( cd Lib ; make clean ) make[2]: Entering directory '/tmp/RtmpjCenu2/R.INSTALL1c1a759a784d/Matrix/src/CHOLMOD/Lib' make[2]: Leaving directory '/tmp/RtmpjCenu2/R.INSTALL1c1a759a784d/Matrix/src/CHOLMOD/Lib' make[1]: Leaving directory '/tmp/RtmpjCenu2/R.INSTALL1c1a759a784d/Matrix/src/CHOLMOD' make[1]: Entering directory '/tmp/RtmpjCenu2/R.INSTALL1c1a759a784d/Matrix/src/COLAMD' ( cd Source ; make clean ) make[2]: Entering directory '/tmp/RtmpjCenu2/R.INSTALL1c1a759a784d/Matrix/src/COLAMD/Source' make[2]: Leaving directory '/tmp/RtmpjCenu2/R.INSTALL1c1a759a784d/Matrix/src/COLAMD/Source' make[1]: Leaving directory '/tmp/RtmpjCenu2/R.INSTALL1c1a759a784d/Matrix/src/COLAMD' make[1]: Entering directory '/tmp/RtmpjCenu2/R.INSTALL1c1a759a784d/Matrix/src/AMD' ( cd Source ; make clean ) make[2]: Entering directory '/tmp/RtmpjCenu2/R.INSTALL1c1a759a784d/Matrix/src/AMD/Source' make[2]: Leaving directory '/tmp/RtmpjCenu2/R.INSTALL1c1a759a784d/Matrix/src/AMD/Source' make[1]: Leaving directory '/tmp/RtmpjCenu2/R.INSTALL1c1a759a784d/Matrix/src/AMD' make[1]: Entering directory '/tmp/RtmpjCenu2/R.INSTALL1c1a759a784d/Matrix/src/SuiteSparse_config' make[1]: Leaving directory '/tmp/RtmpjCenu2/R.INSTALL1c1a759a784d/Matrix/src/SuiteSparse_config' make[1]: Entering directory '/tmp/RtmpjCenu2/R.INSTALL1c1a759a784d/Matrix/src/CHOLMOD' ( cd Lib ; make -f "/usr/lib/R/etc/Makeconf" -f Makefile ) make[2]: Entering directory '/tmp/RtmpjCenu2/R.INSTALL1c1a759a784d/Matrix/src/CHOLMOD/Lib' gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c ../Core/cholmod_aat.c -o cholmod_aat.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c ../Core/cholmod_add.c -o cholmod_add.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c ../Core/cholmod_band.c -o cholmod_band.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c ../Core/cholmod_change_factor.c -o cholmod_change_factor.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c ../Core/cholmod_common.c -o cholmod_common.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c ../Core/cholmod_complex.c -o cholmod_complex.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c ../Core/cholmod_copy.c -o cholmod_copy.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c ../Core/cholmod_dense.c -o cholmod_dense.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c ../Core/cholmod_error.c -o cholmod_error.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c ../Core/cholmod_factor.c -o cholmod_factor.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c ../Core/cholmod_memory.c -o cholmod_memory.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c ../Core/cholmod_sparse.c -o cholmod_sparse.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c ../Core/cholmod_transpose.c -o cholmod_transpose.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c ../Core/cholmod_triplet.c -o cholmod_triplet.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c ../Core/cholmod_version.c -o cholmod_version.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c ../Check/cholmod_check.c -o cholmod_check.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c ../Check/cholmod_read.c -o cholmod_read.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c ../Check/cholmod_write.c -o cholmod_write.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c ../Cholesky/cholmod_amd.c -o cholmod_amd.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c ../Cholesky/cholmod_analyze.c -o cholmod_analyze.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c ../Cholesky/cholmod_colamd.c -o cholmod_colamd.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c ../Cholesky/cholmod_etree.c -o cholmod_etree.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c ../Cholesky/cholmod_factorize.c -o cholmod_factorize.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c ../Cholesky/cholmod_postorder.c -o cholmod_postorder.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c ../Cholesky/cholmod_rcond.c -o cholmod_rcond.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c ../Cholesky/cholmod_resymbol.c -o cholmod_resymbol.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c ../Cholesky/cholmod_rowcolcounts.c -o cholmod_rowcolcounts.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c ../Cholesky/cholmod_rowfac.c -o cholmod_rowfac.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c ../Cholesky/cholmod_solve.c -o cholmod_solve.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c ../Cholesky/cholmod_spsolve.c -o cholmod_spsolve.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c ../MatrixOps/cholmod_drop.c -o cholmod_drop.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c ../MatrixOps/cholmod_horzcat.c -o cholmod_horzcat.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c ../MatrixOps/cholmod_norm.c -o cholmod_norm.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c ../MatrixOps/cholmod_scale.c -o cholmod_scale.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c ../MatrixOps/cholmod_sdmult.c -o cholmod_sdmult.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c ../MatrixOps/cholmod_ssmult.c -o cholmod_ssmult.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c ../MatrixOps/cholmod_submatrix.c -o cholmod_submatrix.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c ../MatrixOps/cholmod_vertcat.c -o cholmod_vertcat.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c ../MatrixOps/cholmod_symmetry.c -o cholmod_symmetry.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c ../Modify/cholmod_rowadd.c -o cholmod_rowadd.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c ../Modify/cholmod_rowdel.c -o cholmod_rowdel.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c ../Modify/cholmod_updown.c -o cholmod_updown.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c ../Supernodal/cholmod_super_numeric.c -o cholmod_super_numeric.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c ../Supernodal/cholmod_super_solve.c -o cholmod_super_solve.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c ../Supernodal/cholmod_super_symbolic.c -o cholmod_super_symbolic.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -DDLONG -c ../Core/cholmod_aat.c -o cholmod_l_aat.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -DDLONG -c ../Core/cholmod_add.c -o cholmod_l_add.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -DDLONG -c ../Core/cholmod_band.c -o cholmod_l_band.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -DDLONG -c ../Core/cholmod_change_factor.c -o cholmod_l_change_factor.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -DDLONG -c ../Core/cholmod_common.c -o cholmod_l_common.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -DDLONG -c ../Core/cholmod_complex.c -o cholmod_l_complex.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -DDLONG -c ../Core/cholmod_copy.c -o cholmod_l_copy.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -DDLONG -c ../Core/cholmod_dense.c -o cholmod_l_dense.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -DDLONG -c ../Core/cholmod_error.c -o cholmod_l_error.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -DDLONG -c ../Core/cholmod_factor.c -o cholmod_l_factor.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -DDLONG -c ../Core/cholmod_memory.c -o cholmod_l_memory.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -DDLONG -c ../Core/cholmod_sparse.c -o cholmod_l_sparse.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -DDLONG -c ../Core/cholmod_transpose.c -o cholmod_l_transpose.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -DDLONG -c ../Core/cholmod_triplet.c -o cholmod_l_triplet.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -DDLONG -c ../Core/cholmod_version.c -o cholmod_l_version.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -DDLONG -c ../Check/cholmod_check.c -o cholmod_l_check.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -DDLONG -c ../Check/cholmod_read.c -o cholmod_l_read.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -DDLONG -c ../Check/cholmod_write.c -o cholmod_l_write.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -DDLONG -c ../Cholesky/cholmod_amd.c -o cholmod_l_amd.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -DDLONG -c ../Cholesky/cholmod_analyze.c -o cholmod_l_analyze.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -DDLONG -c ../Cholesky/cholmod_colamd.c -o cholmod_l_colamd.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -DDLONG -c ../Cholesky/cholmod_etree.c -o cholmod_l_etree.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -DDLONG -c ../Cholesky/cholmod_factorize.c -o cholmod_l_factorize.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -DDLONG -c ../Cholesky/cholmod_postorder.c -o cholmod_l_postorder.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -DDLONG -c ../Cholesky/cholmod_rcond.c -o cholmod_l_rcond.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -DDLONG -c ../Cholesky/cholmod_resymbol.c -o cholmod_l_resymbol.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -DDLONG -c ../Cholesky/cholmod_rowcolcounts.c -o cholmod_l_rowcolcounts.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -DDLONG -c ../Cholesky/cholmod_rowfac.c -o cholmod_l_rowfac.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -DDLONG -c ../Cholesky/cholmod_solve.c -o cholmod_l_solve.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -DDLONG -c ../Cholesky/cholmod_spsolve.c -o cholmod_l_spsolve.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -DDLONG -c ../MatrixOps/cholmod_drop.c -o cholmod_l_drop.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -DDLONG -c ../MatrixOps/cholmod_horzcat.c -o cholmod_l_horzcat.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -DDLONG -c ../MatrixOps/cholmod_norm.c -o cholmod_l_norm.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -DDLONG -c ../MatrixOps/cholmod_scale.c -o cholmod_l_scale.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -DDLONG -c ../MatrixOps/cholmod_sdmult.c -o cholmod_l_sdmult.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -DDLONG -c ../MatrixOps/cholmod_ssmult.c -o cholmod_l_ssmult.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -DDLONG -c ../MatrixOps/cholmod_submatrix.c -o cholmod_l_submatrix.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -DDLONG -c ../MatrixOps/cholmod_vertcat.c -o cholmod_l_vertcat.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -DDLONG -c ../MatrixOps/cholmod_symmetry.c -o cholmod_l_symmetry.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -DDLONG -c ../Modify/cholmod_rowadd.c -o cholmod_l_rowadd.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -DDLONG -c ../Modify/cholmod_rowdel.c -o cholmod_l_rowdel.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -DDLONG -c ../Modify/cholmod_updown.c -o cholmod_l_updown.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -DDLONG -c ../Supernodal/cholmod_super_numeric.c -o cholmod_l_super_numeric.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -DDLONG -c ../Supernodal/cholmod_super_solve.c -o cholmod_l_super_solve.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -DDLONG -c ../Supernodal/cholmod_super_symbolic.c -o cholmod_l_super_symbolic.o ar -rucs ../../CHOLMOD.a cholmod_aat.o cholmod_add.o cholmod_band.o cholmod_change_factor.o cholmod_common.o cholmod_complex.o cholmod_copy.o cholmod_dense.o cholmod_error.o cholmod_factor.o cholmod_memory.o cholmod_sparse.o cholmod_transpose.o cholmod_triplet.o cholmod_version.o cholmod_check.o cholmod_read.o cholmod_write.o cholmod_amd.o cholmod_analyze.o cholmod_colamd.o cholmod_etree.o cholmod_factorize.o cholmod_postorder.o cholmod_rcond.o cholmod_resymbol.o cholmod_rowcolcounts.o cholmod_rowfac.o cholmod_solve.o cholmod_spsolve.o cholmod_drop.o cholmod_horzcat.o cholmod_norm.o cholmod_scale.o cholmod_sdmult.o cholmod_ssmult.o cholmod_submatrix.o cholmod_vertcat.o cholmod_symmetry.o cholmod_rowadd.o cholmod_rowdel.o cholmod_updown.o cholmod_super_numeric.o cholmod_super_solve.o cholmod_super_symbolic.o cholmod_l_aat.o cholmod_l_add.o cholmod_l_band.o cholmod_l_change_factor.o cholmod_l_common.o cholmod_l_complex.o cholmod_l_copy.o cholmod_l_dense.o cholmod_l_error.o cholmod_l_factor.o cholmod_l_memory.o cholmod_l_sparse.o cholmod_l_transpose.o cholmod_l_triplet.o cholmod_l_version.o cholmod_l_check.o cholmod_l_read.o cholmod_l_write.o cholmod_l_amd.o cholmod_l_analyze.o cholmod_l_colamd.o cholmod_l_etree.o cholmod_l_factorize.o cholmod_l_postorder.o cholmod_l_rcond.o cholmod_l_resymbol.o cholmod_l_rowcolcounts.o cholmod_l_rowfac.o cholmod_l_solve.o cholmod_l_spsolve.o cholmod_l_drop.o cholmod_l_horzcat.o cholmod_l_norm.o cholmod_l_scale.o cholmod_l_sdmult.o cholmod_l_ssmult.o cholmod_l_submatrix.o cholmod_l_vertcat.o cholmod_l_symmetry.o cholmod_l_rowadd.o cholmod_l_rowdel.o cholmod_l_updown.o cholmod_l_super_numeric.o cholmod_l_super_solve.o cholmod_l_super_symbolic.o ar: `u' modifier ignored since `D' is the default (see `U') make[2]: Leaving directory '/tmp/RtmpjCenu2/R.INSTALL1c1a759a784d/Matrix/src/CHOLMOD/Lib' make[1]: Leaving directory '/tmp/RtmpjCenu2/R.INSTALL1c1a759a784d/Matrix/src/CHOLMOD' make[1]: Entering directory '/tmp/RtmpjCenu2/R.INSTALL1c1a759a784d/Matrix/src/COLAMD' ( cd Source ; make -f "/usr/lib/R/etc/Makeconf" -f Makefile lib ) make[2]: Entering directory '/tmp/RtmpjCenu2/R.INSTALL1c1a759a784d/Matrix/src/COLAMD/Source' gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../Include -I../../SuiteSparse_config -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c colamd_global.c -o colamd_global.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../Include -I../../SuiteSparse_config -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c colamd.c -o colamd.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../Include -I../../SuiteSparse_config -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -I../Include -DDLONG -c colamd.c -o colamd_l.o ar -rucs ../../COLAMD.a colamd_global.o colamd.o colamd_l.o ar: `u' modifier ignored since `D' is the default (see `U') make[2]: Leaving directory '/tmp/RtmpjCenu2/R.INSTALL1c1a759a784d/Matrix/src/COLAMD/Source' make[1]: Leaving directory '/tmp/RtmpjCenu2/R.INSTALL1c1a759a784d/Matrix/src/COLAMD' make[1]: Entering directory '/tmp/RtmpjCenu2/R.INSTALL1c1a759a784d/Matrix/src/AMD' ( cd Source ; make -f "/usr/lib/R/etc/Makeconf" -f Makefile lib ) make[2]: Entering directory '/tmp/RtmpjCenu2/R.INSTALL1c1a759a784d/Matrix/src/AMD/Source' gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../Include -I../../SuiteSparse_config -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -I../Include -DDINT -c amd_aat.c -o amd_i_aat.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../Include -I../../SuiteSparse_config -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -I../Include -DDLONG -c amd_aat.c -o amd_l_aat.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../Include -I../../SuiteSparse_config -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -I../Include -DDINT -c amd_1.c -o amd_i_1.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../Include -I../../SuiteSparse_config -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -I../Include -DDLONG -c amd_1.c -o amd_l_1.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../Include -I../../SuiteSparse_config -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -I../Include -DDINT -c amd_2.c -o amd_i_2.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../Include -I../../SuiteSparse_config -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -I../Include -DDLONG -c amd_2.c -o amd_l_2.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../Include -I../../SuiteSparse_config -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -I../Include -DDINT -c amd_postorder.c -o amd_i_postorder.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../Include -I../../SuiteSparse_config -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -I../Include -DDLONG -c amd_postorder.c -o amd_l_postorder.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../Include -I../../SuiteSparse_config -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -I../Include -DDINT -c amd_post_tree.c -o amd_i_post_tree.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../Include -I../../SuiteSparse_config -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -I../Include -DDLONG -c amd_post_tree.c -o amd_l_post_tree.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../Include -I../../SuiteSparse_config -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -I../Include -DDINT -c amd_defaults.c -o amd_i_defaults.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../Include -I../../SuiteSparse_config -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -I../Include -DDLONG -c amd_defaults.c -o amd_l_defaults.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../Include -I../../SuiteSparse_config -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -I../Include -DDINT -c amd_order.c -o amd_i_order.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../Include -I../../SuiteSparse_config -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -I../Include -DDLONG -c amd_order.c -o amd_l_order.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../Include -I../../SuiteSparse_config -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -I../Include -DDINT -c amd_control.c -o amd_i_control.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../Include -I../../SuiteSparse_config -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -I../Include -DDLONG -c amd_control.c -o amd_l_control.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../Include -I../../SuiteSparse_config -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -I../Include -DDINT -c amd_info.c -o amd_i_info.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../Include -I../../SuiteSparse_config -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -I../Include -DDLONG -c amd_info.c -o amd_l_info.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../Include -I../../SuiteSparse_config -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -I../Include -DDINT -c amd_valid.c -o amd_i_valid.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../Include -I../../SuiteSparse_config -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -I../Include -DDLONG -c amd_valid.c -o amd_l_valid.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../Include -I../../SuiteSparse_config -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -I../Include -DDINT -c amd_preprocess.c -o amd_i_preprocess.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../Include -I../../SuiteSparse_config -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -I../Include -DDLONG -c amd_preprocess.c -o amd_l_preprocess.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../Include -I../../SuiteSparse_config -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -I../Include -DDINT -c amd_dump.c -o amd_i_dump.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../Include -I../../SuiteSparse_config -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -I../Include -DDLONG -c amd_dump.c -o amd_l_dump.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../Include -I../../SuiteSparse_config -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -I../Include -DDINT -c amd_global.c -o amd_i_global.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../Include -I../../SuiteSparse_config -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -I../Include -DDLONG -c amd_global.c -o amd_l_global.o ar -rucs ../../AMD.a amd_i_aat.o amd_l_aat.o amd_i_1.o amd_l_1.o amd_i_2.o amd_l_2.o amd_i_postorder.o amd_l_postorder.o amd_i_post_tree.o amd_l_post_tree.o amd_i_defaults.o amd_l_defaults.o amd_i_order.o amd_l_order.o amd_i_control.o amd_l_control.o amd_i_info.o amd_l_info.o amd_i_valid.o amd_l_valid.o amd_i_preprocess.o amd_l_preprocess.o amd_i_dump.o amd_l_dump.o amd_i_global.o amd_l_global.o ar: `u' modifier ignored since `D' is the default (see `U') make[2]: Leaving directory '/tmp/RtmpjCenu2/R.INSTALL1c1a759a784d/Matrix/src/AMD/Source' make[1]: Leaving directory '/tmp/RtmpjCenu2/R.INSTALL1c1a759a784d/Matrix/src/AMD' make[1]: Entering directory '/tmp/RtmpjCenu2/R.INSTALL1c1a759a784d/Matrix/src/SuiteSparse_config' gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DNTIMER -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c SuiteSparse_config.c -o SuiteSparse_config.o ar -rucs ../SuiteSparse_config.a SuiteSparse_config.o ar: `u' modifier ignored since `D' is the default (see `U') make[1]: Leaving directory '/tmp/RtmpjCenu2/R.INSTALL1c1a759a784d/Matrix/src/SuiteSparse_config' gcc -std=gnu99 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o Matrix.so CHMfactor.o Csparse.o TMatrix_as.o Tsparse.o init.o Mutils.o chm_common.o cs.o cs_utils.o dense.o dgCMatrix.o dgTMatrix.o dgeMatrix.o dpoMatrix.o dppMatrix.o dsCMatrix.o dsyMatrix.o dspMatrix.o dtCMatrix.o dtTMatrix.o dtrMatrix.o dtpMatrix.o factorizations.o ldense.o lgCMatrix.o sparseQR.o abIndex.o CHOLMOD.a COLAMD.a AMD.a SuiteSparse_config.a -llapack -lblas -lgfortran -lm -lquadmath -L/usr/lib/R/lib -lR installing to /usr/lib/R/library/Matrix/libs ** R ** data ** inst ** preparing package for lazy loading Creating a generic function for 'chol2inv' from 'base' in package 'Matrix' (from the saved implicit definition) Creating a generic function for 'chol2inv' from package 'base' in package 'Matrix' Creating a generic function for 'diag' from package 'base' in package 'Matrix' Creating a generic function for 'drop' from package 'base' in package 'Matrix' Creating a generic function for 'cov2cor' from package 'stats' in package 'Matrix' Creating a generic function for 'unname' from package 'base' in package 'Matrix' Creating a generic function for 'norm' from package 'base' in package 'Matrix' Creating a generic function for 'rcond' from 'base' in package 'Matrix' (from the saved implicit definition) Creating a generic function for 'rcond' from package 'base' in package 'Matrix' in method for 'coerce' with signature '"matrix.csr","dgRMatrix"': no definition for class "matrix.csr" in method for 'coerce' with signature '"dgRMatrix","matrix.csr"': no definition for class "matrix.csr" in method for 'coerce' with signature '"matrix.csc","dgCMatrix"': no definition for class "matrix.csc" in method for 'coerce' with signature '"dgCMatrix","matrix.csc"': no definition for class "matrix.csc" in method for 'coerce' with signature '"matrix.coo","dgTMatrix"': no definition for class "matrix.coo" in method for 'coerce' with signature '"dgTMatrix","matrix.coo"': no definition for class "matrix.coo" in method for 'coerce' with signature '"dsparseMatrix","matrix.csr"': no definition for class "matrix.csr" in method for 'coerce' with signature '"matrix.csr","dgCMatrix"': no definition for class "matrix.csr" in method for 'coerce' with signature '"matrix.coo","dgCMatrix"': no definition for class "matrix.coo" in method for 'coerce' with signature '"matrix.csr","RsparseMatrix"': no definition for class "matrix.csr" in method for 'coerce' with signature '"matrix.csc","CsparseMatrix"': no definition for class "matrix.csc" in method for 'coerce' with signature '"matrix.coo","TsparseMatrix"': no definition for class "matrix.coo" in method for 'coerce' with signature '"matrix.csr","CsparseMatrix"': no definition for class "matrix.csr" in method for 'coerce' with signature '"matrix.coo","CsparseMatrix"': no definition for class "matrix.coo" in method for 'coerce' with signature '"matrix.csc","TsparseMatrix"': no definition for class "matrix.csc" in method for 'coerce' with signature '"matrix.csr","TsparseMatrix"': no definition for class "matrix.csr" in method for 'coerce' with signature '"CsparseMatrix","matrix.csr"': no definition for class "matrix.csr" in method for 'coerce' with signature '"CsparseMatrix","matrix.coo"': no definition for class "matrix.coo" in method for 'coerce' with signature '"CsparseMatrix","matrix.csc"': no definition for class "matrix.csc" in method for 'coerce' with signature '"matrix.csr","Matrix"': no definition for class "matrix.csr" in method for 'coerce' with signature '"matrix.coo","Matrix"': no definition for class "matrix.coo" in method for 'coerce' with signature '"matrix.csc","Matrix"': no definition for class "matrix.csc" Creating a generic function for 'colSums' from package 'base' in package 'Matrix' Creating a generic function for 'colMeans' from package 'base' in package 'Matrix' Creating a generic function for 'rowSums' from package 'base' in package 'Matrix' Creating a generic function for 'rowMeans' from package 'base' in package 'Matrix' in method for 'colSums' with signature 'x="igCMatrix"': no definition for class "igCMatrix" in method for 'rowSums' with signature 'x="igCMatrix"': no definition for class "igCMatrix" in method for 'colMeans' with signature 'x="igCMatrix"': no definition for class "igCMatrix" in method for 'rowMeans' with signature 'x="igCMatrix"': no definition for class "igCMatrix" Creating a generic function for 'zapsmall' from package 'base' in package 'Matrix' Creating a generic function for 'diag<-' from package 'base' in package 'Matrix' Creating a generic function for 'crossprod' from package 'base' in package 'Matrix' Creating a generic function for 'tcrossprod' from package 'base' in package 'Matrix' Creating a generic function for 'which' from package 'base' in package 'Matrix' in method for 'coerce' with signature '"graphAM","sparseMatrix"': no definition for class "graphAM" in method for 'coerce' with signature '"graph","CsparseMatrix"': no definition for class "graph" in method for 'coerce' with signature '"graph","Matrix"': no definition for class "graph" in method for 'coerce' with signature '"graphNEL","CsparseMatrix"': no definition for class "graphNEL" in method for 'coerce' with signature '"graphNEL","TsparseMatrix"': no definition for class "graphNEL" in method for 'coerce' with signature '"sparseMatrix","graph"': no definition for class "graph" in method for 'coerce' with signature '"sparseMatrix","graphNEL"': no definition for class "graphNEL" in method for 'coerce' with signature '"TsparseMatrix","graphNEL"': no definition for class "graphNEL" Creating a generic function for 'qr.R' from package 'base' in package 'Matrix' Creating a generic function for 'qr.Q' from package 'base' in package 'Matrix' Creating a generic function for 'qr.qy' from package 'base' in package 'Matrix' Creating a generic function for 'qr.qty' from package 'base' in package 'Matrix' Creating a generic function for 'qr.coef' from package 'base' in package 'Matrix' Creating a generic function for 'qr.resid' from package 'base' in package 'Matrix' Creating a generic function for 'qr.fitted' from package 'base' in package 'Matrix' Creating a generic function for 'toeplitz' from package 'stats' in package 'Matrix' ** help *** installing help indices ** building package indices Loading required package: Matrix ** installing vignettes ** testing if installed package can be loaded * DONE (Matrix)  The downloaded source packages are in '/tmp/RtmpxNJ6sA/downloaded_packages' Updating HTML index of packages in '.Library' Making 'packages.html' ... done Installing packages into '/usr/local/lib/R/site-library' (as 'lib' is unspecified) also installing the dependencies 'checkmate', 'htmlwidgets', 'DEoptimR', 'mvtnorm', 'pcaPP', 'Formula', 'latticeExtra', 'acepack', 'data.table', 'htmlTable', 'viridis', 'fit.models', 'robustbase', 'rrcov', 'beeswarm', 'vipor', 'dynamicTreeCut', 'fastcluster', 'Hmisc', 'robust' trying URL 'https://cran.rstudio.com/src/contrib/checkmate_1.8.5.tar.gz' Content type 'application/x-gzip' length 182266 bytes (177 KB) ================================================== downloaded 177 KB trying URL 'https://cran.rstudio.com/src/contrib/htmlwidgets_0.9.tar.gz' Content type 'application/x-gzip' length 944851 bytes (922 KB) ================================================== downloaded 922 KB trying URL 'https://cran.rstudio.com/src/contrib/DEoptimR_1.0-8.tar.gz' Content type 'application/x-gzip' length 35401 bytes (34 KB) ================================================== downloaded 34 KB trying URL 'https://cran.rstudio.com/src/contrib/mvtnorm_1.0-6.tar.gz' Content type 'application/x-gzip' length 159232 bytes (155 KB) ================================================== downloaded 155 KB trying URL 'https://cran.rstudio.com/src/contrib/pcaPP_1.9-72.tar.gz' Content type 'application/x-gzip' length 197829 bytes (193 KB) ================================================== downloaded 193 KB trying URL 'https://cran.rstudio.com/src/contrib/Formula_1.2-2.tar.gz' Content type 'application/x-gzip' length 150946 bytes (147 KB) ================================================== downloaded 147 KB trying URL 'https://cran.rstudio.com/src/contrib/latticeExtra_0.6-28.tar.gz' Content type 'application/x-gzip' length 1294369 bytes (1.2 MB) ================================================== downloaded 1.2 MB trying URL 'https://cran.rstudio.com/src/contrib/acepack_1.4.1.tar.gz' Content type 'application/x-gzip' length 34848 bytes (34 KB) ================================================== downloaded 34 KB trying URL 'https://cran.rstudio.com/src/contrib/data.table_1.10.4-3.tar.gz' Content type 'application/x-gzip' length 3071833 bytes (2.9 MB) ================================================== downloaded 2.9 MB trying URL 'https://cran.rstudio.com/src/contrib/htmlTable_1.11.1.tar.gz' Content type 'application/x-gzip' length 170724 bytes (166 KB) ================================================== downloaded 166 KB trying URL 'https://cran.rstudio.com/src/contrib/viridis_0.4.0.tar.gz' Content type 'application/x-gzip' length 1787731 bytes (1.7 MB) ================================================== downloaded 1.7 MB trying URL 'https://cran.rstudio.com/src/contrib/fit.models_0.5-14.tar.gz' Content type 'application/x-gzip' length 24125 bytes (23 KB) ================================================== downloaded 23 KB trying URL 'https://cran.rstudio.com/src/contrib/robustbase_0.92-8.tar.gz' Content type 'application/x-gzip' length 3479092 bytes (3.3 MB) ================================================== downloaded 3.3 MB trying URL 'https://cran.rstudio.com/src/contrib/rrcov_1.4-3.tar.gz' Content type 'application/x-gzip' length 1017409 bytes (993 KB) ================================================== downloaded 993 KB trying URL 'https://cran.rstudio.com/src/contrib/beeswarm_0.2.3.tar.gz' Content type 'application/x-gzip' length 19850 bytes (19 KB) ================================================== downloaded 19 KB trying URL 'https://cran.rstudio.com/src/contrib/vipor_0.4.5.tar.gz' Content type 'application/x-gzip' length 4699815 bytes (4.5 MB) ================================================== downloaded 4.5 MB trying URL 'https://cran.rstudio.com/src/contrib/dynamicTreeCut_1.63-1.tar.gz' Content type 'application/x-gzip' length 24027 bytes (23 KB) ================================================== downloaded 23 KB trying URL 'https://cran.rstudio.com/src/contrib/fastcluster_1.1.24.tar.gz' Content type 'application/x-gzip' length 188690 bytes (184 KB) ================================================== downloaded 184 KB trying URL 'https://cran.rstudio.com/src/contrib/Hmisc_4.1-1.tar.gz' Content type 'application/x-gzip' length 711786 bytes (695 KB) ================================================== downloaded 695 KB trying URL 'https://cran.rstudio.com/src/contrib/robust_0.4-18.tar.gz' Content type 'application/x-gzip' length 233385 bytes (227 KB) ================================================== downloaded 227 KB trying URL 'https://cran.rstudio.com/src/contrib/cba_0.2-19.tar.gz' Content type 'application/x-gzip' length 122611 bytes (119 KB) ================================================== downloaded 119 KB trying URL 'https://cran.rstudio.com/src/contrib/cowplot_0.9.2.tar.gz' Content type 'application/x-gzip' length 2393202 bytes (2.3 MB) ================================================== downloaded 2.3 MB trying URL 'https://cran.rstudio.com/src/contrib/devtools_1.13.4.tar.gz' Content type 'application/x-gzip' length 486348 bytes (474 KB) ================================================== downloaded 474 KB trying URL 'https://cran.rstudio.com/src/contrib/doRNG_1.6.6.tar.gz' Content type 'application/x-gzip' length 388414 bytes (379 KB) ================================================== downloaded 379 KB trying URL 'https://cran.rstudio.com/src/contrib/ggbeeswarm_0.6.0.tar.gz' Content type 'application/x-gzip' length 1494271 bytes (1.4 MB) ================================================== downloaded 1.4 MB trying URL 'https://cran.rstudio.com/src/contrib/ggrepel_0.7.0.tar.gz' Content type 'application/x-gzip' length 613978 bytes (599 KB) ================================================== downloaded 599 KB trying URL 'https://cran.rstudio.com/src/contrib/statmod_1.4.30.tar.gz' Content type 'application/x-gzip' length 57309 bytes (55 KB) ================================================== downloaded 55 KB trying URL 'https://cran.rstudio.com/src/contrib/WGCNA_1.61.tar.gz' Content type 'application/x-gzip' length 1137821 bytes (1.1 MB) ================================================== downloaded 1.1 MB * installing *source* package 'checkmate' ... ** package 'checkmate' successfully unpacked and MD5 sums checked ** libs gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c all_missing.c -o all_missing.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c all_nchar.c -o all_nchar.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c any_infinite.c -o any_infinite.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c any_missing.c -o any_missing.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c any_nan.c -o any_nan.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c checks.c -o checks.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c guess_type.c -o guess_type.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c helper.c -o helper.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c init.c -o init.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c is_integerish.c -o is_integerish.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c qassert.c -o qassert.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c which_first.c -o which_first.o gcc -std=gnu99 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o checkmate.so all_missing.o all_nchar.o any_infinite.o any_missing.o any_nan.o checks.o guess_type.o helper.o init.o is_integerish.o qassert.o which_first.o -L/usr/lib/R/lib -lR installing to /usr/local/lib/R/site-library/checkmate/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded * DONE (checkmate) * installing *source* package 'htmlwidgets' ... ** package 'htmlwidgets' successfully unpacked and MD5 sums checked ** R ** inst ** preparing package for lazy loading Failed with error: 'there is no package called 'shiny'' ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded * DONE (htmlwidgets) * installing *source* package 'DEoptimR' ... ** package 'DEoptimR' successfully unpacked and MD5 sums checked ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded * DONE (DEoptimR) * installing *source* package 'mvtnorm' ... ** package 'mvtnorm' successfully unpacked and MD5 sums checked ** libs gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c C_FORTRAN_interface.c -o C_FORTRAN_interface.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c miwa.c -o miwa.o gfortran -fpic -g -O2 -fstack-protector-strong -c mvt.f -o mvt.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c mvtnorm-init.c -o mvtnorm-init.o gfortran -fpic -g -O2 -fstack-protector-strong -c tvpack.f -o tvpack.o gcc -std=gnu99 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o mvtnorm.so C_FORTRAN_interface.o miwa.o mvt.o mvtnorm-init.o tvpack.o -lgfortran -lm -lquadmath -L/usr/lib/R/lib -lR installing to /usr/local/lib/R/site-library/mvtnorm/libs ** R ** inst ** preparing package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded * DONE (mvtnorm) * installing *source* package 'Formula' ... ** package 'Formula' successfully unpacked and MD5 sums checked ** R ** inst ** preparing package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded * DONE (Formula) * installing *source* package 'latticeExtra' ... ** package 'latticeExtra' successfully unpacked and MD5 sums checked ** R ** data *** moving datasets to lazyload DB ** inst ** preparing package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded * DONE (latticeExtra) * installing *source* package 'acepack' ... ** package 'acepack' successfully unpacked and MD5 sums checked ** libs gfortran -fpic -g -O2 -fstack-protector-strong -c ace.f -o ace.o gfortran -fpic -g -O2 -fstack-protector-strong -c avas.f -o avas.o gfortran -fpic -g -O2 -fstack-protector-strong -c rlsmo.f -o rlsmo.o gcc -std=gnu99 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o acepack.so ace.o avas.o rlsmo.o -lgfortran -lm -lquadmath -L/usr/lib/R/lib -lR installing to /usr/local/lib/R/site-library/acepack/libs ** R ** inst ** preparing package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded * DONE (acepack) * installing *source* package 'data.table' ... ** package 'data.table' successfully unpacked and MD5 sums checked ** libs gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c assign.c -o assign.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c between.c -o between.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c bmerge.c -o bmerge.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c chmatch.c -o chmatch.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c dogroups.c -o dogroups.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c fastmean.c -o fastmean.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c fcast.c -o fcast.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c fmelt.c -o fmelt.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c forder.c -o forder.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c frank.c -o frank.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c fread.c -o fread.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c fsort.c -o fsort.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c fwrite.c -o fwrite.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c gsumm.c -o gsumm.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c ijoin.c -o ijoin.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c init.c -o init.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c inrange.c -o inrange.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c openmp-utils.c -o openmp-utils.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c quickselect.c -o quickselect.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c rbindlist.c -o rbindlist.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c reorder.c -o reorder.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c shift.c -o shift.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c subset.c -o subset.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c transpose.c -o transpose.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c uniqlist.c -o uniqlist.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c vecseq.c -o vecseq.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c wrappers.c -o wrappers.o gcc -std=gnu99 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o data.table.so assign.o between.o bmerge.o chmatch.o dogroups.o fastmean.o fcast.o fmelt.o forder.o frank.o fread.o fsort.o fwrite.o gsumm.o ijoin.o init.o inrange.o openmp-utils.o quickselect.o rbindlist.o reorder.o shift.o subset.o transpose.o uniqlist.o vecseq.o wrappers.o -fopenmp -L/usr/lib/R/lib -lR mv data.table.so datatable.so if [ "" != "Windows_NT" ] && [ `uname -s` = 'Darwin' ]; then install_name_tool -id datatable.so datatable.so; fi installing to /usr/local/lib/R/site-library/data.table/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded * DONE (data.table) * installing *source* package 'viridis' ... ** package 'viridis' successfully unpacked and MD5 sums checked ** R ** inst ** preparing package for lazy loading ** help *** installing help indices *** copying figures ** building package indices ** installing vignettes ** testing if installed package can be loaded * DONE (viridis) * installing *source* package 'fit.models' ... ** package 'fit.models' successfully unpacked and MD5 sums checked ** R ** preparing package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded * DONE (fit.models) * installing *source* package 'beeswarm' ... ** package 'beeswarm' successfully unpacked and MD5 sums checked ** R ** data ** preparing package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded * DONE (beeswarm) * installing *source* package 'vipor' ... ** package 'vipor' successfully unpacked and MD5 sums checked ** R ** data *** moving datasets to lazyload DB ** inst ** preparing package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded * DONE (vipor) * installing *source* package 'dynamicTreeCut' ... ** package 'dynamicTreeCut' successfully unpacked and MD5 sums checked ** R ** preparing package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded * DONE (dynamicTreeCut) * installing *source* package 'fastcluster' ... ** package 'fastcluster' successfully unpacked and MD5 sums checked ** libs g++ -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c fastcluster_R.cpp -o fastcluster_R.o In file included from fastcluster_R.cpp:36:0: fastcluster.cpp:53:118: note: #pragma message: Use fenv header. If there is a warning about unknown #pragma STDC FENV_ACCESS, this can be ignored. #pragma message("Use fenv header. If there is a warning about unknown #pragma STDC FENV_ACCESS, this can be ignored.") ^ g++ -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o fastcluster.so fastcluster_R.o -L/usr/lib/R/lib -lR installing to /usr/local/lib/R/site-library/fastcluster/libs ** R ** inst ** preparing package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded * DONE (fastcluster) * installing *source* package 'cba' ... ** package 'cba' successfully unpacked and MD5 sums checked ** libs gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c arrayIndex.c -o arrayIndex.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c ccfkms.c -o ccfkms.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c cluster.c -o cluster.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c coding.c -o coding.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c dll.c -o dll.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c gknn.c -o gknn.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c greedy.c -o greedy.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c interpolate.c -o interpolate.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c optimal.c -o optimal.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c proximus.c -o proximus.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c rock.c -o rock.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c sdists.c -o sdists.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c stress.c -o stress.o gcc -std=gnu99 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o cba.so arrayIndex.o ccfkms.o cluster.o coding.o dll.o gknn.o greedy.o interpolate.o optimal.o proximus.o rock.o sdists.o stress.o -L/usr/lib/R/lib -lR installing to /usr/local/lib/R/site-library/cba/libs ** R ** data ** preparing package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded * DONE (cba) * installing *source* package 'cowplot' ... ** package 'cowplot' successfully unpacked and MD5 sums checked ** R ** inst ** preparing package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded * DONE (cowplot) * installing *source* package 'devtools' ... ** package 'devtools' successfully unpacked and MD5 sums checked ** R ** inst ** preparing package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded * DONE (devtools) * installing *source* package 'doRNG' ... ** package 'doRNG' successfully unpacked and MD5 sums checked ** R ** demo ** inst ** preparing package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded * DONE (doRNG) * installing *source* package 'ggrepel' ... ** package 'ggrepel' successfully unpacked and MD5 sums checked ** libs g++ -I/usr/share/R/include -DNDEBUG -I"/usr/local/lib/R/site-library/Rcpp/include" -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c RcppExports.cpp -o RcppExports.o g++ -I/usr/share/R/include -DNDEBUG -I"/usr/local/lib/R/site-library/Rcpp/include" -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c repel_boxes.cpp -o repel_boxes.o g++ -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o ggrepel.so RcppExports.o repel_boxes.o -L/usr/lib/R/lib -lR installing to /usr/local/lib/R/site-library/ggrepel/libs ** R ** inst ** preparing package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded * DONE (ggrepel) * installing *source* package 'statmod' ... ** package 'statmod' successfully unpacked and MD5 sums checked ** libs gfortran -fpic -g -O2 -fstack-protector-strong -c gaussq2.f -o gaussq2.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c init.c -o init.o gcc -std=gnu99 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o statmod.so gaussq2.o init.o -lgfortran -lm -lquadmath -L/usr/lib/R/lib -lR installing to /usr/local/lib/R/site-library/statmod/libs ** R ** data ** inst ** preparing package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded * DONE (statmod) * installing *source* package 'pcaPP' ... ** package 'pcaPP' successfully unpacked and MD5 sums checked ** libs g++ -I/usr/share/R/include -DNDEBUG -DR_PACKAGE_FILE -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c L1Median_HoCr.cpp -o L1Median_HoCr.o In file included from smat.h:28:0, from L1Median.h:5, from L1Median_HoCr.cpp:1: smat.base.h:401:29: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (dwIdx < GetSize ()) ; ^ smat.base.h:458:29: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (dwIdx < GetSize ()) ; ^ smat.base.h:498:40: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (HasRawCap (dwOffset + dwSize)) ; ^ smat.base.h:520:53: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (HasRawCap (m_dwOffset + dwOffset + dwSize)) ; ^ smat.base.h:540:44: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (HasRawCap (GetOffset () + dwSize)) ; ^ smat.base.h:553:29: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (HasRawCap (dwSize)) ; ^ smat.base.h:662:65: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] inline const t_size GetDim (t_size p) const { THROW (p < P) ; return m_adwDim [p] ; } ^ smat.base.h:665:68: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] inline const t_size * GetDimPtr (t_size p) const { THROW (p < P) ; return m_adwDim + p ; } ^ smat.base.h:669:60: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] inline t_size & GetDimRef (t_size p) { THROW (p < P) ; return m_adwDim [p] ; } ^ In file included from smat.h:28:0, from L1Median.h:5, from L1Median_HoCr.cpp:1: smat.base.h:735:63: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] const t_this &operator = (const t_this &p ) const { THROW (0) ;} // this MUST never be called, as you can't change a constant matrix! Thus it's protected! ^ smat.base.h:747:39: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (dwSize <= t_base::GetSize ()) ; ^ smat.base.h:759:45: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (m.DimProd () <= t_base::GetSize ()) ; ^ smat.base.h:887:32: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (this->EqualDims (vec)) ; ^ smat.base.h:911:30: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (n < t_this::size ()) ; ^ smat.base.h:1063:67: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] const t_this &operator = (const t_this &p ) const { THROW (FALSE) ;} // this MUST never be called, as you can't change a constant matrix! Thus it's protected! ^ smat.base.h:1067:45: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (m.DimProd () <= t_base::GetSize ()) ; ^ smat.base.h:1079:48: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (dwRows * dwCols <= t_base::GetSize ()) ; ^ smat.base.h:1243:47: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (t_this::nrow () == t_this::m.nrow ()) ; ^ smat.base.h:1244:39: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (dwSource < t_this::m.ncol ()) ; ^ smat.base.h:1245:35: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (dwDest < t_this::ncol ()) ; ^ smat.base.h:1268:32: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (this->EqualDims (mat)) ; ^ smat.base.h:1286:46: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (t_this::ncol () == order.GetSize ()) ; ^ smat.base.h:1287:41: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (t_this::nrow () == mat.nrow ()) ; ^ smat.base.h:1363:66: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (ref.GetSize () <= dwRows * dwCols * dwSize * sizeof (T)) ; ^ smat.base.h:1388:70: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] tc_item &Item (t_size idx) const { THROW (idx < t_this::GetSize ()) ; return *m_apData [idx] ; } ^ In file included from smat.h:29:0, from L1Median.h:5, from L1Median_HoCr.cpp:1: smat.elop.h:181:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.nrow () == c.size ()) ; ^ smat.elop.h:189:26: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.EqualDims (b)) ; ^ smat.elop.h:190:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.nrow () == c.size ()) ; ^ smat.elop.h:222:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.ncol () == c.size ()) ; ^ smat.elop.h:230:26: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.EqualDims (b)) ; ^ smat.elop.h:231:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.ncol () == c.size ()) ; ^ smat.elop.h:262:26: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.EqualDims (c)) ; ^ smat.elop.h:263:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (b.size () == c.nrow ()) ; ^ smat.elop.h:264:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (d.size () == c.ncol ()) ; ^ smat.elop.h:307:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.nrow () == b.size ()) ; ^ smat.elop.h:308:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.ncol () == c.size ()) ; ^ smat.elop.h:342:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.ncol () == b.ncol ()) ; ^ smat.elop.h:343:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (b.nrow () == c.size ()) ; ^ smat.elop.h:344:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (b.nrow () == d.size ()) ; ^ smat.elop.h:354:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.ncol () == b.ncol ()) ; ^ smat.elop.h:355:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (b.nrow () == c.size ()) ; ^ smat.elop.h:356:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (b.nrow () == d.size ()) ; ^ smat.elop.h:357:37: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (CountTrue (d) == a.nrow ()) ; ^ smat.elop.h:399:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.ncol () == b.ncol ()) ; ^ smat.elop.h:400:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (b.ncol () == c.size ()) ; ^ smat.elop.h:401:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (b.nrow () == d.size ()) ; ^ smat.elop.h:411:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.ncol () == b.ncol ()) ; ^ smat.elop.h:412:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (b.ncol () == c.size ()) ; ^ smat.elop.h:413:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (b.nrow () == d.size ()) ; ^ smat.elop.h:414:37: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (CountTrue (d) == a.nrow ()) ; ^ smat.elop.h:453:34: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (c.ncol () == b.nsize ()) ; ^ smat.elop.h:454:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (c.nrow () == e.size ()) ; ^ smat.elop.h:464:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.ncol () == c.ncol ()) ; ^ smat.elop.h:465:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.ncol () == b.size ()) ; ^ smat.elop.h:466:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (c.nrow () == e.size ()) ; ^ smat.elop.h:467:43: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (CountMatches (e, d) == a.nrow ()) ; ^ smat.elop.h:515:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (b.size () == c.ncol ()) ; ^ smat.elop.h:516:36: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (getMaxIdx (d) < c.nrow ()) ; ^ smat.elop.h:530:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.ncol () == c.ncol ()) ; ^ smat.elop.h:531:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.nrow () == d.size ()) ; ^ smat.elop.h:532:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (b.size () == c.ncol ()) ; ^ smat.elop.h:533:36: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (getMaxIdx (d) < c.nrow ()) ; ^ smat.elop.h:571:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.ncol () == b.size ()) ; ^ smat.elop.h:611:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (c.size () == d.size ()) ; ^ smat.elop.h:690:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (b.size () == c.size ()) ; ^ smat.elop.h:735:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (b.size () == c.size ()) ; ^ smat.elop.h:761:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (c.nrow () == e.size ()) ; ^ smat.elop.h:801:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (b.size () == c.ncol ()) ; ^ smat.elop.h:802:36: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (getMaxIdx (d) < c.nrow ()) ; ^ smat.elop.h:838:34: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.size () == b.size ()) ; ^ smat.elop.h:839:34: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.size () == c.size ()) ; ^ smat.elop.h:866:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.size () == b.nrow ()) ; ^ smat.elop.h:896:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.size () == b.nrow ()) ; ^ smat.elop.h:897:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (c.size () == b.ncol ()) ; ^ smat.elop.h:928:34: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.size () == b.ncols ()) ; ^ smat.elop.h:950:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.size () == b.ncol ()) ; ^ smat.elop.h:951:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (c.size () == b.nrow ()) ; ^ smat.elop.h:1010:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.size () == d.size ()) ; ^ smat.elop.h:1034:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (b.size () == d.size ()) ; ^ smat.elop.h:1056:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.size () == c.size ()) ; ^ smat.elop.h:1079:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.size () == b.ncol ()) ; ^ smat.elop.h:1108:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.size () == b.ncol ()) ; ^ smat.elop.h:1109:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (c.size () == b.nrow ()) ; ^ smat.elop.h:1110:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (d.size () == b.nrow ()) ; ^ smat.elop.h:1146:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (b.size () == c.size ()) ; ^ smat.elop.h:1147:37: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (CountTrue (c) == a.size ()) ; ^ smat.elop.h:1177:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.size () == b.size ()) ; ^ smat.elop.h:1203:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.size () == b.size ()) ; ^ smat.elop.h:1228:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.size () == b.size ()) ; ^ In file included from smat.h:31:0, from L1Median.h:5, from L1Median_HoCr.cpp:1: smat.mem.h:25:24: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (c < b.nrow ()) ; ^ smat.mem.h:34:24: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (c < b.nrow ()) ; ^ smat.mem.h:35:31: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.size () == b.ncol()) ; ^ smat.mem.h:59:24: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (c < a.nrow ()) ; ^ smat.mem.h:60:32: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.ncol () == b.size ()) ; ^ smat.mem.h:84:24: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (c < a.nrow ()) ; ^ smat.mem.h:156:32: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.size () == b.size ()) ; ^ smat.mem.h:177:38: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (v.nsize () == m.GetMinDim ()) ; ^ smat.mem.h:193:27: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (dwCol < b.ncol ()) ; ^ smat.mem.h:207:26: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (dwStart <= dwEnd) ; ^ smat.mem.h:208:28: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (dwEnd <= b.ncol ()) ; ^ smat.mem.h:209:32: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.nrow () == b.nrow ()) ; ^ smat.mem.h:210:38: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.ncol () == dwEnd - dwStart) ; ^ In file included from smat.h:32:0, from L1Median.h:5, from L1Median_HoCr.cpp:1: smat.matop.h:82:31: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.ncol() == b.size ()) ; ^ smat.matop.h:83:31: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.nrow() == b.size ()) ; ^ smat.matop.h:128:32: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.ncol () == a.nrow ()) ; ^ smat.matop.h:156:32: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.ncol () == a.nrow ()) ; ^ In file included from smat.h:33:0, from L1Median.h:5, from L1Median_HoCr.cpp:1: smat.misc.h:32:16: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (l <= u) ; ^ In file included from smat.h:36:0, from L1Median.h:5, from L1Median_HoCr.cpp:1: smat.stat.h:172:32: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.size () == b.ncol ()) ; ^ smat.stat.h:212:32: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.size () == b.ncol ()) ; ^ g++ -I/usr/share/R/include -DNDEBUG -DR_PACKAGE_FILE -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c L1Median_VardiZhang.cpp -o L1Median_VardiZhang.o In file included from smat.h:28:0, from L1Median.h:5, from L1Median_VardiZhang.cpp:1: smat.base.h:401:29: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (dwIdx < GetSize ()) ; ^ smat.base.h:458:29: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (dwIdx < GetSize ()) ; ^ smat.base.h:498:40: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (HasRawCap (dwOffset + dwSize)) ; ^ smat.base.h:520:53: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (HasRawCap (m_dwOffset + dwOffset + dwSize)) ; ^ smat.base.h:540:44: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (HasRawCap (GetOffset () + dwSize)) ; ^ smat.base.h:553:29: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (HasRawCap (dwSize)) ; ^ smat.base.h:662:65: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] inline const t_size GetDim (t_size p) const { THROW (p < P) ; return m_adwDim [p] ; } ^ smat.base.h:665:68: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] inline const t_size * GetDimPtr (t_size p) const { THROW (p < P) ; return m_adwDim + p ; } ^ smat.base.h:669:60: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] inline t_size & GetDimRef (t_size p) { THROW (p < P) ; return m_adwDim [p] ; } ^ In file included from smat.h:28:0, from L1Median.h:5, from L1Median_VardiZhang.cpp:1: smat.base.h:735:63: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] const t_this &operator = (const t_this &p ) const { THROW (0) ;} // this MUST never be called, as you can't change a constant matrix! Thus it's protected! ^ smat.base.h:747:39: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (dwSize <= t_base::GetSize ()) ; ^ smat.base.h:759:45: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (m.DimProd () <= t_base::GetSize ()) ; ^ smat.base.h:887:32: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (this->EqualDims (vec)) ; ^ smat.base.h:911:30: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (n < t_this::size ()) ; ^ smat.base.h:1063:67: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] const t_this &operator = (const t_this &p ) const { THROW (FALSE) ;} // this MUST never be called, as you can't change a constant matrix! Thus it's protected! ^ smat.base.h:1067:45: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (m.DimProd () <= t_base::GetSize ()) ; ^ smat.base.h:1079:48: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (dwRows * dwCols <= t_base::GetSize ()) ; ^ smat.base.h:1243:47: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (t_this::nrow () == t_this::m.nrow ()) ; ^ smat.base.h:1244:39: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (dwSource < t_this::m.ncol ()) ; ^ smat.base.h:1245:35: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (dwDest < t_this::ncol ()) ; ^ smat.base.h:1268:32: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (this->EqualDims (mat)) ; ^ smat.base.h:1286:46: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (t_this::ncol () == order.GetSize ()) ; ^ smat.base.h:1287:41: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (t_this::nrow () == mat.nrow ()) ; ^ smat.base.h:1363:66: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (ref.GetSize () <= dwRows * dwCols * dwSize * sizeof (T)) ; ^ smat.base.h:1388:70: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] tc_item &Item (t_size idx) const { THROW (idx < t_this::GetSize ()) ; return *m_apData [idx] ; } ^ In file included from smat.h:29:0, from L1Median.h:5, from L1Median_VardiZhang.cpp:1: smat.elop.h:181:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.nrow () == c.size ()) ; ^ smat.elop.h:189:26: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.EqualDims (b)) ; ^ smat.elop.h:190:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.nrow () == c.size ()) ; ^ smat.elop.h:222:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.ncol () == c.size ()) ; ^ smat.elop.h:230:26: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.EqualDims (b)) ; ^ smat.elop.h:231:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.ncol () == c.size ()) ; ^ smat.elop.h:262:26: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.EqualDims (c)) ; ^ smat.elop.h:263:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (b.size () == c.nrow ()) ; ^ smat.elop.h:264:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (d.size () == c.ncol ()) ; ^ smat.elop.h:307:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.nrow () == b.size ()) ; ^ smat.elop.h:308:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.ncol () == c.size ()) ; ^ smat.elop.h:342:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.ncol () == b.ncol ()) ; ^ smat.elop.h:343:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (b.nrow () == c.size ()) ; ^ smat.elop.h:344:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (b.nrow () == d.size ()) ; ^ smat.elop.h:354:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.ncol () == b.ncol ()) ; ^ smat.elop.h:355:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (b.nrow () == c.size ()) ; ^ smat.elop.h:356:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (b.nrow () == d.size ()) ; ^ smat.elop.h:357:37: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (CountTrue (d) == a.nrow ()) ; ^ smat.elop.h:399:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.ncol () == b.ncol ()) ; ^ smat.elop.h:400:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (b.ncol () == c.size ()) ; ^ smat.elop.h:401:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (b.nrow () == d.size ()) ; ^ smat.elop.h:411:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.ncol () == b.ncol ()) ; ^ smat.elop.h:412:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (b.ncol () == c.size ()) ; ^ smat.elop.h:413:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (b.nrow () == d.size ()) ; ^ smat.elop.h:414:37: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (CountTrue (d) == a.nrow ()) ; ^ smat.elop.h:453:34: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (c.ncol () == b.nsize ()) ; ^ smat.elop.h:454:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (c.nrow () == e.size ()) ; ^ smat.elop.h:464:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.ncol () == c.ncol ()) ; ^ smat.elop.h:465:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.ncol () == b.size ()) ; ^ smat.elop.h:466:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (c.nrow () == e.size ()) ; ^ smat.elop.h:467:43: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (CountMatches (e, d) == a.nrow ()) ; ^ smat.elop.h:515:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (b.size () == c.ncol ()) ; ^ smat.elop.h:516:36: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (getMaxIdx (d) < c.nrow ()) ; ^ smat.elop.h:530:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.ncol () == c.ncol ()) ; ^ smat.elop.h:531:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.nrow () == d.size ()) ; ^ smat.elop.h:532:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (b.size () == c.ncol ()) ; ^ smat.elop.h:533:36: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (getMaxIdx (d) < c.nrow ()) ; ^ smat.elop.h:571:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.ncol () == b.size ()) ; ^ smat.elop.h:611:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (c.size () == d.size ()) ; ^ smat.elop.h:690:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (b.size () == c.size ()) ; ^ smat.elop.h:735:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (b.size () == c.size ()) ; ^ smat.elop.h:761:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (c.nrow () == e.size ()) ; ^ smat.elop.h:801:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (b.size () == c.ncol ()) ; ^ smat.elop.h:802:36: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (getMaxIdx (d) < c.nrow ()) ; ^ smat.elop.h:838:34: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.size () == b.size ()) ; ^ smat.elop.h:839:34: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.size () == c.size ()) ; ^ smat.elop.h:866:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.size () == b.nrow ()) ; ^ smat.elop.h:896:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.size () == b.nrow ()) ; ^ smat.elop.h:897:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (c.size () == b.ncol ()) ; ^ smat.elop.h:928:34: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.size () == b.ncols ()) ; ^ smat.elop.h:950:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.size () == b.ncol ()) ; ^ smat.elop.h:951:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (c.size () == b.nrow ()) ; ^ smat.elop.h:1010:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.size () == d.size ()) ; ^ smat.elop.h:1034:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (b.size () == d.size ()) ; ^ smat.elop.h:1056:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.size () == c.size ()) ; ^ smat.elop.h:1079:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.size () == b.ncol ()) ; ^ smat.elop.h:1108:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.size () == b.ncol ()) ; ^ smat.elop.h:1109:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (c.size () == b.nrow ()) ; ^ smat.elop.h:1110:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (d.size () == b.nrow ()) ; ^ smat.elop.h:1146:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (b.size () == c.size ()) ; ^ smat.elop.h:1147:37: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (CountTrue (c) == a.size ()) ; ^ smat.elop.h:1177:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.size () == b.size ()) ; ^ smat.elop.h:1203:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.size () == b.size ()) ; ^ smat.elop.h:1228:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.size () == b.size ()) ; ^ In file included from smat.h:31:0, from L1Median.h:5, from L1Median_VardiZhang.cpp:1: smat.mem.h:25:24: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (c < b.nrow ()) ; ^ smat.mem.h:34:24: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (c < b.nrow ()) ; ^ smat.mem.h:35:31: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.size () == b.ncol()) ; ^ smat.mem.h:59:24: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (c < a.nrow ()) ; ^ smat.mem.h:60:32: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.ncol () == b.size ()) ; ^ smat.mem.h:84:24: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (c < a.nrow ()) ; ^ smat.mem.h:156:32: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.size () == b.size ()) ; ^ smat.mem.h:177:38: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (v.nsize () == m.GetMinDim ()) ; ^ smat.mem.h:193:27: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (dwCol < b.ncol ()) ; ^ smat.mem.h:207:26: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (dwStart <= dwEnd) ; ^ smat.mem.h:208:28: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (dwEnd <= b.ncol ()) ; ^ smat.mem.h:209:32: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.nrow () == b.nrow ()) ; ^ smat.mem.h:210:38: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.ncol () == dwEnd - dwStart) ; ^ In file included from smat.h:32:0, from L1Median.h:5, from L1Median_VardiZhang.cpp:1: smat.matop.h:82:31: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.ncol() == b.size ()) ; ^ smat.matop.h:83:31: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.nrow() == b.size ()) ; ^ smat.matop.h:128:32: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.ncol () == a.nrow ()) ; ^ smat.matop.h:156:32: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.ncol () == a.nrow ()) ; ^ In file included from smat.h:33:0, from L1Median.h:5, from L1Median_VardiZhang.cpp:1: smat.misc.h:32:16: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (l <= u) ; ^ In file included from smat.h:36:0, from L1Median.h:5, from L1Median_VardiZhang.cpp:1: smat.stat.h:172:32: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.size () == b.ncol ()) ; ^ smat.stat.h:212:32: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.size () == b.ncol ()) ; ^ g++ -I/usr/share/R/include -DNDEBUG -DR_PACKAGE_FILE -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c ML_meal.cpp -o ML_meal.o g++ -I/usr/share/R/include -DNDEBUG -DR_PACKAGE_FILE -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c ML_package.cpp -o ML_package.o g++ -I/usr/share/R/include -DNDEBUG -DR_PACKAGE_FILE -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c ML_passrng.cpp -o ML_passrng.o g++ -I/usr/share/R/include -DNDEBUG -DR_PACKAGE_FILE -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c PCAgrid.cpp -o PCAgrid.o In file included from smat.h:28:0, from pcaPP.h:7, from PCAgrid.h:4, from PCAgrid.cpp:1: smat.base.h:401:29: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (dwIdx < GetSize ()) ; ^ smat.base.h:458:29: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (dwIdx < GetSize ()) ; ^ smat.base.h:498:40: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (HasRawCap (dwOffset + dwSize)) ; ^ smat.base.h:520:53: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (HasRawCap (m_dwOffset + dwOffset + dwSize)) ; ^ smat.base.h:540:44: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (HasRawCap (GetOffset () + dwSize)) ; ^ smat.base.h:553:29: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (HasRawCap (dwSize)) ; ^ smat.base.h:662:65: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] inline const t_size GetDim (t_size p) const { THROW (p < P) ; return m_adwDim [p] ; } ^ smat.base.h:665:68: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] inline const t_size * GetDimPtr (t_size p) const { THROW (p < P) ; return m_adwDim + p ; } ^ smat.base.h:669:60: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] inline t_size & GetDimRef (t_size p) { THROW (p < P) ; return m_adwDim [p] ; } ^ In file included from smat.h:28:0, from pcaPP.h:7, from PCAgrid.h:4, from PCAgrid.cpp:1: smat.base.h:735:63: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] const t_this &operator = (const t_this &p ) const { THROW (0) ;} // this MUST never be called, as you can't change a constant matrix! Thus it's protected! ^ smat.base.h:747:39: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (dwSize <= t_base::GetSize ()) ; ^ smat.base.h:759:45: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (m.DimProd () <= t_base::GetSize ()) ; ^ smat.base.h:887:32: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (this->EqualDims (vec)) ; ^ smat.base.h:911:30: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (n < t_this::size ()) ; ^ smat.base.h:1063:67: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] const t_this &operator = (const t_this &p ) const { THROW (FALSE) ;} // this MUST never be called, as you can't change a constant matrix! Thus it's protected! ^ smat.base.h:1067:45: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (m.DimProd () <= t_base::GetSize ()) ; ^ smat.base.h:1079:48: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (dwRows * dwCols <= t_base::GetSize ()) ; ^ smat.base.h:1243:47: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (t_this::nrow () == t_this::m.nrow ()) ; ^ smat.base.h:1244:39: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (dwSource < t_this::m.ncol ()) ; ^ smat.base.h:1245:35: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (dwDest < t_this::ncol ()) ; ^ smat.base.h:1268:32: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (this->EqualDims (mat)) ; ^ smat.base.h:1286:46: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (t_this::ncol () == order.GetSize ()) ; ^ smat.base.h:1287:41: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (t_this::nrow () == mat.nrow ()) ; ^ smat.base.h:1363:66: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (ref.GetSize () <= dwRows * dwCols * dwSize * sizeof (T)) ; ^ smat.base.h:1388:70: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] tc_item &Item (t_size idx) const { THROW (idx < t_this::GetSize ()) ; return *m_apData [idx] ; } ^ In file included from smat.h:29:0, from pcaPP.h:7, from PCAgrid.h:4, from PCAgrid.cpp:1: smat.elop.h:181:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.nrow () == c.size ()) ; ^ smat.elop.h:189:26: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.EqualDims (b)) ; ^ smat.elop.h:190:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.nrow () == c.size ()) ; ^ smat.elop.h:222:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.ncol () == c.size ()) ; ^ smat.elop.h:230:26: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.EqualDims (b)) ; ^ smat.elop.h:231:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.ncol () == c.size ()) ; ^ smat.elop.h:262:26: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.EqualDims (c)) ; ^ smat.elop.h:263:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (b.size () == c.nrow ()) ; ^ smat.elop.h:264:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (d.size () == c.ncol ()) ; ^ smat.elop.h:307:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.nrow () == b.size ()) ; ^ smat.elop.h:308:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.ncol () == c.size ()) ; ^ smat.elop.h:342:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.ncol () == b.ncol ()) ; ^ smat.elop.h:343:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (b.nrow () == c.size ()) ; ^ smat.elop.h:344:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (b.nrow () == d.size ()) ; ^ smat.elop.h:354:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.ncol () == b.ncol ()) ; ^ smat.elop.h:355:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (b.nrow () == c.size ()) ; ^ smat.elop.h:356:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (b.nrow () == d.size ()) ; ^ smat.elop.h:357:37: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (CountTrue (d) == a.nrow ()) ; ^ smat.elop.h:399:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.ncol () == b.ncol ()) ; ^ smat.elop.h:400:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (b.ncol () == c.size ()) ; ^ smat.elop.h:401:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (b.nrow () == d.size ()) ; ^ smat.elop.h:411:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.ncol () == b.ncol ()) ; ^ smat.elop.h:412:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (b.ncol () == c.size ()) ; ^ smat.elop.h:413:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (b.nrow () == d.size ()) ; ^ smat.elop.h:414:37: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (CountTrue (d) == a.nrow ()) ; ^ smat.elop.h:453:34: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (c.ncol () == b.nsize ()) ; ^ smat.elop.h:454:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (c.nrow () == e.size ()) ; ^ smat.elop.h:464:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.ncol () == c.ncol ()) ; ^ smat.elop.h:465:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.ncol () == b.size ()) ; ^ smat.elop.h:466:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (c.nrow () == e.size ()) ; ^ smat.elop.h:467:43: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (CountMatches (e, d) == a.nrow ()) ; ^ smat.elop.h:515:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (b.size () == c.ncol ()) ; ^ smat.elop.h:516:36: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (getMaxIdx (d) < c.nrow ()) ; ^ smat.elop.h:530:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.ncol () == c.ncol ()) ; ^ smat.elop.h:531:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.nrow () == d.size ()) ; ^ smat.elop.h:532:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (b.size () == c.ncol ()) ; ^ smat.elop.h:533:36: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (getMaxIdx (d) < c.nrow ()) ; ^ smat.elop.h:571:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.ncol () == b.size ()) ; ^ smat.elop.h:611:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (c.size () == d.size ()) ; ^ smat.elop.h:690:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (b.size () == c.size ()) ; ^ smat.elop.h:735:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (b.size () == c.size ()) ; ^ smat.elop.h:761:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (c.nrow () == e.size ()) ; ^ smat.elop.h:801:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (b.size () == c.ncol ()) ; ^ smat.elop.h:802:36: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (getMaxIdx (d) < c.nrow ()) ; ^ smat.elop.h:838:34: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.size () == b.size ()) ; ^ smat.elop.h:839:34: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.size () == c.size ()) ; ^ smat.elop.h:866:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.size () == b.nrow ()) ; ^ smat.elop.h:896:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.size () == b.nrow ()) ; ^ smat.elop.h:897:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (c.size () == b.ncol ()) ; ^ smat.elop.h:928:34: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.size () == b.ncols ()) ; ^ smat.elop.h:950:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.size () == b.ncol ()) ; ^ smat.elop.h:951:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (c.size () == b.nrow ()) ; ^ smat.elop.h:1010:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.size () == d.size ()) ; ^ smat.elop.h:1034:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (b.size () == d.size ()) ; ^ smat.elop.h:1056:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.size () == c.size ()) ; ^ smat.elop.h:1079:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.size () == b.ncol ()) ; ^ smat.elop.h:1108:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.size () == b.ncol ()) ; ^ smat.elop.h:1109:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (c.size () == b.nrow ()) ; ^ smat.elop.h:1110:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (d.size () == b.nrow ()) ; ^ smat.elop.h:1146:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (b.size () == c.size ()) ; ^ smat.elop.h:1147:37: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (CountTrue (c) == a.size ()) ; ^ smat.elop.h:1177:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.size () == b.size ()) ; ^ smat.elop.h:1203:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.size () == b.size ()) ; ^ smat.elop.h:1228:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.size () == b.size ()) ; ^ In file included from smat.h:31:0, from pcaPP.h:7, from PCAgrid.h:4, from PCAgrid.cpp:1: smat.mem.h:25:24: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (c < b.nrow ()) ; ^ smat.mem.h:34:24: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (c < b.nrow ()) ; ^ smat.mem.h:35:31: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.size () == b.ncol()) ; ^ smat.mem.h:59:24: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (c < a.nrow ()) ; ^ smat.mem.h:60:32: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.ncol () == b.size ()) ; ^ smat.mem.h:84:24: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (c < a.nrow ()) ; ^ smat.mem.h:156:32: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.size () == b.size ()) ; ^ smat.mem.h:177:38: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (v.nsize () == m.GetMinDim ()) ; ^ smat.mem.h:193:27: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (dwCol < b.ncol ()) ; ^ smat.mem.h:207:26: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (dwStart <= dwEnd) ; ^ smat.mem.h:208:28: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (dwEnd <= b.ncol ()) ; ^ smat.mem.h:209:32: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.nrow () == b.nrow ()) ; ^ smat.mem.h:210:38: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.ncol () == dwEnd - dwStart) ; ^ In file included from smat.h:32:0, from pcaPP.h:7, from PCAgrid.h:4, from PCAgrid.cpp:1: smat.matop.h:82:31: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.ncol() == b.size ()) ; ^ smat.matop.h:83:31: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.nrow() == b.size ()) ; ^ smat.matop.h:128:32: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.ncol () == a.nrow ()) ; ^ smat.matop.h:156:32: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.ncol () == a.nrow ()) ; ^ In file included from smat.h:33:0, from pcaPP.h:7, from PCAgrid.h:4, from PCAgrid.cpp:1: smat.misc.h:32:16: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (l <= u) ; ^ In file included from smat.h:36:0, from pcaPP.h:7, from PCAgrid.h:4, from PCAgrid.cpp:1: smat.stat.h:172:32: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.size () == b.ncol ()) ; ^ smat.stat.h:212:32: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.size () == b.ncol ()) ; ^ g++ -I/usr/share/R/include -DNDEBUG -DR_PACKAGE_FILE -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c PCAproj.cpp -o PCAproj.o In file included from smat.h:28:0, from pcaPP.h:7, from PCAproj.h:1, from PCAproj.cpp:1: smat.base.h:401:29: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (dwIdx < GetSize ()) ; ^ smat.base.h:458:29: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (dwIdx < GetSize ()) ; ^ smat.base.h:498:40: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (HasRawCap (dwOffset + dwSize)) ; ^ smat.base.h:520:53: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (HasRawCap (m_dwOffset + dwOffset + dwSize)) ; ^ smat.base.h:540:44: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (HasRawCap (GetOffset () + dwSize)) ; ^ smat.base.h:553:29: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (HasRawCap (dwSize)) ; ^ smat.base.h:662:65: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] inline const t_size GetDim (t_size p) const { THROW (p < P) ; return m_adwDim [p] ; } ^ smat.base.h:665:68: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] inline const t_size * GetDimPtr (t_size p) const { THROW (p < P) ; return m_adwDim + p ; } ^ smat.base.h:669:60: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] inline t_size & GetDimRef (t_size p) { THROW (p < P) ; return m_adwDim [p] ; } ^ In file included from smat.h:28:0, from pcaPP.h:7, from PCAproj.h:1, from PCAproj.cpp:1: smat.base.h:735:63: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] const t_this &operator = (const t_this &p ) const { THROW (0) ;} // this MUST never be called, as you can't change a constant matrix! Thus it's protected! ^ smat.base.h:747:39: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (dwSize <= t_base::GetSize ()) ; ^ smat.base.h:759:45: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (m.DimProd () <= t_base::GetSize ()) ; ^ smat.base.h:887:32: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (this->EqualDims (vec)) ; ^ smat.base.h:911:30: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (n < t_this::size ()) ; ^ smat.base.h:1063:67: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] const t_this &operator = (const t_this &p ) const { THROW (FALSE) ;} // this MUST never be called, as you can't change a constant matrix! Thus it's protected! ^ smat.base.h:1067:45: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (m.DimProd () <= t_base::GetSize ()) ; ^ smat.base.h:1079:48: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (dwRows * dwCols <= t_base::GetSize ()) ; ^ smat.base.h:1243:47: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (t_this::nrow () == t_this::m.nrow ()) ; ^ smat.base.h:1244:39: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (dwSource < t_this::m.ncol ()) ; ^ smat.base.h:1245:35: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (dwDest < t_this::ncol ()) ; ^ smat.base.h:1268:32: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (this->EqualDims (mat)) ; ^ smat.base.h:1286:46: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (t_this::ncol () == order.GetSize ()) ; ^ smat.base.h:1287:41: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (t_this::nrow () == mat.nrow ()) ; ^ smat.base.h:1363:66: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (ref.GetSize () <= dwRows * dwCols * dwSize * sizeof (T)) ; ^ smat.base.h:1388:70: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] tc_item &Item (t_size idx) const { THROW (idx < t_this::GetSize ()) ; return *m_apData [idx] ; } ^ In file included from smat.h:29:0, from pcaPP.h:7, from PCAproj.h:1, from PCAproj.cpp:1: smat.elop.h:181:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.nrow () == c.size ()) ; ^ smat.elop.h:189:26: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.EqualDims (b)) ; ^ smat.elop.h:190:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.nrow () == c.size ()) ; ^ smat.elop.h:222:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.ncol () == c.size ()) ; ^ smat.elop.h:230:26: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.EqualDims (b)) ; ^ smat.elop.h:231:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.ncol () == c.size ()) ; ^ smat.elop.h:262:26: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.EqualDims (c)) ; ^ smat.elop.h:263:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (b.size () == c.nrow ()) ; ^ smat.elop.h:264:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (d.size () == c.ncol ()) ; ^ smat.elop.h:307:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.nrow () == b.size ()) ; ^ smat.elop.h:308:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.ncol () == c.size ()) ; ^ smat.elop.h:342:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.ncol () == b.ncol ()) ; ^ smat.elop.h:343:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (b.nrow () == c.size ()) ; ^ smat.elop.h:344:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (b.nrow () == d.size ()) ; ^ smat.elop.h:354:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.ncol () == b.ncol ()) ; ^ smat.elop.h:355:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (b.nrow () == c.size ()) ; ^ smat.elop.h:356:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (b.nrow () == d.size ()) ; ^ smat.elop.h:357:37: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (CountTrue (d) == a.nrow ()) ; ^ smat.elop.h:399:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.ncol () == b.ncol ()) ; ^ smat.elop.h:400:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (b.ncol () == c.size ()) ; ^ smat.elop.h:401:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (b.nrow () == d.size ()) ; ^ smat.elop.h:411:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.ncol () == b.ncol ()) ; ^ smat.elop.h:412:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (b.ncol () == c.size ()) ; ^ smat.elop.h:413:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (b.nrow () == d.size ()) ; ^ smat.elop.h:414:37: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (CountTrue (d) == a.nrow ()) ; ^ smat.elop.h:453:34: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (c.ncol () == b.nsize ()) ; ^ smat.elop.h:454:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (c.nrow () == e.size ()) ; ^ smat.elop.h:464:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.ncol () == c.ncol ()) ; ^ smat.elop.h:465:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.ncol () == b.size ()) ; ^ smat.elop.h:466:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (c.nrow () == e.size ()) ; ^ smat.elop.h:467:43: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (CountMatches (e, d) == a.nrow ()) ; ^ smat.elop.h:515:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (b.size () == c.ncol ()) ; ^ smat.elop.h:516:36: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (getMaxIdx (d) < c.nrow ()) ; ^ smat.elop.h:530:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.ncol () == c.ncol ()) ; ^ smat.elop.h:531:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.nrow () == d.size ()) ; ^ smat.elop.h:532:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (b.size () == c.ncol ()) ; ^ smat.elop.h:533:36: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (getMaxIdx (d) < c.nrow ()) ; ^ smat.elop.h:571:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.ncol () == b.size ()) ; ^ smat.elop.h:611:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (c.size () == d.size ()) ; ^ smat.elop.h:690:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (b.size () == c.size ()) ; ^ smat.elop.h:735:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (b.size () == c.size ()) ; ^ smat.elop.h:761:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (c.nrow () == e.size ()) ; ^ smat.elop.h:801:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (b.size () == c.ncol ()) ; ^ smat.elop.h:802:36: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (getMaxIdx (d) < c.nrow ()) ; ^ smat.elop.h:838:34: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.size () == b.size ()) ; ^ smat.elop.h:839:34: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.size () == c.size ()) ; ^ smat.elop.h:866:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.size () == b.nrow ()) ; ^ smat.elop.h:896:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.size () == b.nrow ()) ; ^ smat.elop.h:897:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (c.size () == b.ncol ()) ; ^ smat.elop.h:928:34: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.size () == b.ncols ()) ; ^ smat.elop.h:950:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.size () == b.ncol ()) ; ^ smat.elop.h:951:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (c.size () == b.nrow ()) ; ^ smat.elop.h:1010:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.size () == d.size ()) ; ^ smat.elop.h:1034:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (b.size () == d.size ()) ; ^ smat.elop.h:1056:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.size () == c.size ()) ; ^ smat.elop.h:1079:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.size () == b.ncol ()) ; ^ smat.elop.h:1108:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.size () == b.ncol ()) ; ^ smat.elop.h:1109:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (c.size () == b.nrow ()) ; ^ smat.elop.h:1110:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (d.size () == b.nrow ()) ; ^ smat.elop.h:1146:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (b.size () == c.size ()) ; ^ smat.elop.h:1147:37: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (CountTrue (c) == a.size ()) ; ^ smat.elop.h:1177:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.size () == b.size ()) ; ^ smat.elop.h:1203:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.size () == b.size ()) ; ^ smat.elop.h:1228:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.size () == b.size ()) ; ^ In file included from smat.h:31:0, from pcaPP.h:7, from PCAproj.h:1, from PCAproj.cpp:1: smat.mem.h:25:24: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (c < b.nrow ()) ; ^ smat.mem.h:34:24: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (c < b.nrow ()) ; ^ smat.mem.h:35:31: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.size () == b.ncol()) ; ^ smat.mem.h:59:24: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (c < a.nrow ()) ; ^ smat.mem.h:60:32: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.ncol () == b.size ()) ; ^ smat.mem.h:84:24: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (c < a.nrow ()) ; ^ smat.mem.h:156:32: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.size () == b.size ()) ; ^ smat.mem.h:177:38: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (v.nsize () == m.GetMinDim ()) ; ^ smat.mem.h:193:27: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (dwCol < b.ncol ()) ; ^ smat.mem.h:207:26: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (dwStart <= dwEnd) ; ^ smat.mem.h:208:28: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (dwEnd <= b.ncol ()) ; ^ smat.mem.h:209:32: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.nrow () == b.nrow ()) ; ^ smat.mem.h:210:38: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.ncol () == dwEnd - dwStart) ; ^ In file included from smat.h:32:0, from pcaPP.h:7, from PCAproj.h:1, from PCAproj.cpp:1: smat.matop.h:82:31: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.ncol() == b.size ()) ; ^ smat.matop.h:83:31: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.nrow() == b.size ()) ; ^ smat.matop.h:128:32: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.ncol () == a.nrow ()) ; ^ smat.matop.h:156:32: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.ncol () == a.nrow ()) ; ^ In file included from smat.h:33:0, from pcaPP.h:7, from PCAproj.h:1, from PCAproj.cpp:1: smat.misc.h:32:16: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (l <= u) ; ^ In file included from smat.h:36:0, from pcaPP.h:7, from PCAproj.h:1, from PCAproj.cpp:1: smat.stat.h:172:32: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.size () == b.ncol ()) ; ^ smat.stat.h:212:32: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.size () == b.ncol ()) ; ^ PCAproj.cpp:13:20: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (n <= nDimN) ; ^ g++ -I/usr/share/R/include -DNDEBUG -DR_PACKAGE_FILE -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c R_meal.cpp -o R_meal.o g++ -I/usr/share/R/include -DNDEBUG -DR_PACKAGE_FILE -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c R_meal_BLAS.cpp -o R_meal_BLAS.o g++ -I/usr/share/R/include -DNDEBUG -DR_PACKAGE_FILE -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c R_package.cpp -o R_package.o In file included from smat.h:28:0, from pcaPP.h:7, from PCAgrid.h:4, from R_package.cpp:6: smat.base.h:401:29: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (dwIdx < GetSize ()) ; ^ smat.base.h:458:29: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (dwIdx < GetSize ()) ; ^ smat.base.h:498:40: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (HasRawCap (dwOffset + dwSize)) ; ^ smat.base.h:520:53: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (HasRawCap (m_dwOffset + dwOffset + dwSize)) ; ^ smat.base.h:540:44: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (HasRawCap (GetOffset () + dwSize)) ; ^ smat.base.h:553:29: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (HasRawCap (dwSize)) ; ^ smat.base.h:662:65: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] inline const t_size GetDim (t_size p) const { THROW (p < P) ; return m_adwDim [p] ; } ^ smat.base.h:665:68: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] inline const t_size * GetDimPtr (t_size p) const { THROW (p < P) ; return m_adwDim + p ; } ^ smat.base.h:669:60: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] inline t_size & GetDimRef (t_size p) { THROW (p < P) ; return m_adwDim [p] ; } ^ In file included from smat.h:28:0, from pcaPP.h:7, from PCAgrid.h:4, from R_package.cpp:6: smat.base.h:735:63: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] const t_this &operator = (const t_this &p ) const { THROW (0) ;} // this MUST never be called, as you can't change a constant matrix! Thus it's protected! ^ smat.base.h:747:39: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (dwSize <= t_base::GetSize ()) ; ^ smat.base.h:759:45: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (m.DimProd () <= t_base::GetSize ()) ; ^ smat.base.h:887:32: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (this->EqualDims (vec)) ; ^ smat.base.h:911:30: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (n < t_this::size ()) ; ^ smat.base.h:1063:67: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] const t_this &operator = (const t_this &p ) const { THROW (FALSE) ;} // this MUST never be called, as you can't change a constant matrix! Thus it's protected! ^ smat.base.h:1067:45: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (m.DimProd () <= t_base::GetSize ()) ; ^ smat.base.h:1079:48: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (dwRows * dwCols <= t_base::GetSize ()) ; ^ smat.base.h:1243:47: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (t_this::nrow () == t_this::m.nrow ()) ; ^ smat.base.h:1244:39: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (dwSource < t_this::m.ncol ()) ; ^ smat.base.h:1245:35: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (dwDest < t_this::ncol ()) ; ^ smat.base.h:1268:32: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (this->EqualDims (mat)) ; ^ smat.base.h:1286:46: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (t_this::ncol () == order.GetSize ()) ; ^ smat.base.h:1287:41: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (t_this::nrow () == mat.nrow ()) ; ^ smat.base.h:1363:66: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (ref.GetSize () <= dwRows * dwCols * dwSize * sizeof (T)) ; ^ smat.base.h:1388:70: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] tc_item &Item (t_size idx) const { THROW (idx < t_this::GetSize ()) ; return *m_apData [idx] ; } ^ In file included from smat.h:29:0, from pcaPP.h:7, from PCAgrid.h:4, from R_package.cpp:6: smat.elop.h:181:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.nrow () == c.size ()) ; ^ smat.elop.h:189:26: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.EqualDims (b)) ; ^ smat.elop.h:190:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.nrow () == c.size ()) ; ^ smat.elop.h:222:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.ncol () == c.size ()) ; ^ smat.elop.h:230:26: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.EqualDims (b)) ; ^ smat.elop.h:231:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.ncol () == c.size ()) ; ^ smat.elop.h:262:26: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.EqualDims (c)) ; ^ smat.elop.h:263:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (b.size () == c.nrow ()) ; ^ smat.elop.h:264:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (d.size () == c.ncol ()) ; ^ smat.elop.h:307:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.nrow () == b.size ()) ; ^ smat.elop.h:308:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.ncol () == c.size ()) ; ^ smat.elop.h:342:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.ncol () == b.ncol ()) ; ^ smat.elop.h:343:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (b.nrow () == c.size ()) ; ^ smat.elop.h:344:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (b.nrow () == d.size ()) ; ^ smat.elop.h:354:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.ncol () == b.ncol ()) ; ^ smat.elop.h:355:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (b.nrow () == c.size ()) ; ^ smat.elop.h:356:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (b.nrow () == d.size ()) ; ^ smat.elop.h:357:37: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (CountTrue (d) == a.nrow ()) ; ^ smat.elop.h:399:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.ncol () == b.ncol ()) ; ^ smat.elop.h:400:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (b.ncol () == c.size ()) ; ^ smat.elop.h:401:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (b.nrow () == d.size ()) ; ^ smat.elop.h:411:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.ncol () == b.ncol ()) ; ^ smat.elop.h:412:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (b.ncol () == c.size ()) ; ^ smat.elop.h:413:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (b.nrow () == d.size ()) ; ^ smat.elop.h:414:37: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (CountTrue (d) == a.nrow ()) ; ^ smat.elop.h:453:34: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (c.ncol () == b.nsize ()) ; ^ smat.elop.h:454:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (c.nrow () == e.size ()) ; ^ smat.elop.h:464:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.ncol () == c.ncol ()) ; ^ smat.elop.h:465:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.ncol () == b.size ()) ; ^ smat.elop.h:466:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (c.nrow () == e.size ()) ; ^ smat.elop.h:467:43: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (CountMatches (e, d) == a.nrow ()) ; ^ smat.elop.h:515:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (b.size () == c.ncol ()) ; ^ smat.elop.h:516:36: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (getMaxIdx (d) < c.nrow ()) ; ^ smat.elop.h:530:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.ncol () == c.ncol ()) ; ^ smat.elop.h:531:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.nrow () == d.size ()) ; ^ smat.elop.h:532:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (b.size () == c.ncol ()) ; ^ smat.elop.h:533:36: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (getMaxIdx (d) < c.nrow ()) ; ^ smat.elop.h:571:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.ncol () == b.size ()) ; ^ smat.elop.h:611:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (c.size () == d.size ()) ; ^ smat.elop.h:690:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (b.size () == c.size ()) ; ^ smat.elop.h:735:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (b.size () == c.size ()) ; ^ smat.elop.h:761:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (c.nrow () == e.size ()) ; ^ smat.elop.h:801:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (b.size () == c.ncol ()) ; ^ smat.elop.h:802:36: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (getMaxIdx (d) < c.nrow ()) ; ^ smat.elop.h:838:34: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.size () == b.size ()) ; ^ smat.elop.h:839:34: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.size () == c.size ()) ; ^ smat.elop.h:866:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.size () == b.nrow ()) ; ^ smat.elop.h:896:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.size () == b.nrow ()) ; ^ smat.elop.h:897:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (c.size () == b.ncol ()) ; ^ smat.elop.h:928:34: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.size () == b.ncols ()) ; ^ smat.elop.h:950:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.size () == b.ncol ()) ; ^ smat.elop.h:951:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (c.size () == b.nrow ()) ; ^ smat.elop.h:1010:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.size () == d.size ()) ; ^ smat.elop.h:1034:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (b.size () == d.size ()) ; ^ smat.elop.h:1056:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.size () == c.size ()) ; ^ smat.elop.h:1079:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.size () == b.ncol ()) ; ^ smat.elop.h:1108:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.size () == b.ncol ()) ; ^ smat.elop.h:1109:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (c.size () == b.nrow ()) ; ^ smat.elop.h:1110:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (d.size () == b.nrow ()) ; ^ smat.elop.h:1146:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (b.size () == c.size ()) ; ^ smat.elop.h:1147:37: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (CountTrue (c) == a.size ()) ; ^ smat.elop.h:1177:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.size () == b.size ()) ; ^ smat.elop.h:1203:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.size () == b.size ()) ; ^ smat.elop.h:1228:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.size () == b.size ()) ; ^ In file included from smat.h:31:0, from pcaPP.h:7, from PCAgrid.h:4, from R_package.cpp:6: smat.mem.h:25:24: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (c < b.nrow ()) ; ^ smat.mem.h:34:24: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (c < b.nrow ()) ; ^ smat.mem.h:35:31: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.size () == b.ncol()) ; ^ smat.mem.h:59:24: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (c < a.nrow ()) ; ^ smat.mem.h:60:32: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.ncol () == b.size ()) ; ^ smat.mem.h:84:24: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (c < a.nrow ()) ; ^ smat.mem.h:156:32: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.size () == b.size ()) ; ^ smat.mem.h:177:38: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (v.nsize () == m.GetMinDim ()) ; ^ smat.mem.h:193:27: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (dwCol < b.ncol ()) ; ^ smat.mem.h:207:26: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (dwStart <= dwEnd) ; ^ smat.mem.h:208:28: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (dwEnd <= b.ncol ()) ; ^ smat.mem.h:209:32: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.nrow () == b.nrow ()) ; ^ smat.mem.h:210:38: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.ncol () == dwEnd - dwStart) ; ^ In file included from smat.h:32:0, from pcaPP.h:7, from PCAgrid.h:4, from R_package.cpp:6: smat.matop.h:82:31: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.ncol() == b.size ()) ; ^ smat.matop.h:83:31: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.nrow() == b.size ()) ; ^ smat.matop.h:128:32: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.ncol () == a.nrow ()) ; ^ smat.matop.h:156:32: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.ncol () == a.nrow ()) ; ^ In file included from smat.h:33:0, from pcaPP.h:7, from PCAgrid.h:4, from R_package.cpp:6: smat.misc.h:32:16: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (l <= u) ; ^ In file included from smat.h:36:0, from pcaPP.h:7, from PCAgrid.h:4, from R_package.cpp:6: smat.stat.h:172:32: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.size () == b.ncol ()) ; ^ smat.stat.h:212:32: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.size () == b.ncol ()) ; ^ g++ -I/usr/share/R/include -DNDEBUG -DR_PACKAGE_FILE -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c cov.kendall.cpp -o cov.kendall.o g++ -I/usr/share/R/include -DNDEBUG -DR_PACKAGE_FILE -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c hess.cpp -o hess.o g++ -I/usr/share/R/include -DNDEBUG -DR_PACKAGE_FILE -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c l1median.cpp -o l1median.o g++ -I/usr/share/R/include -DNDEBUG -DR_PACKAGE_FILE -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c outSDo.cpp -o outSDo.o In file included from smat.h:28:0, from pcaPP.h:7, from outSDo.h:1, from outSDo.cpp:1: smat.base.h:401:29: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (dwIdx < GetSize ()) ; ^ smat.base.h:458:29: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (dwIdx < GetSize ()) ; ^ smat.base.h:498:40: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (HasRawCap (dwOffset + dwSize)) ; ^ smat.base.h:520:53: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (HasRawCap (m_dwOffset + dwOffset + dwSize)) ; ^ smat.base.h:540:44: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (HasRawCap (GetOffset () + dwSize)) ; ^ smat.base.h:553:29: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (HasRawCap (dwSize)) ; ^ smat.base.h:662:65: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] inline const t_size GetDim (t_size p) const { THROW (p < P) ; return m_adwDim [p] ; } ^ smat.base.h:665:68: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] inline const t_size * GetDimPtr (t_size p) const { THROW (p < P) ; return m_adwDim + p ; } ^ smat.base.h:669:60: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] inline t_size & GetDimRef (t_size p) { THROW (p < P) ; return m_adwDim [p] ; } ^ In file included from smat.h:28:0, from pcaPP.h:7, from outSDo.h:1, from outSDo.cpp:1: smat.base.h:735:63: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] const t_this &operator = (const t_this &p ) const { THROW (0) ;} // this MUST never be called, as you can't change a constant matrix! Thus it's protected! ^ smat.base.h:747:39: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (dwSize <= t_base::GetSize ()) ; ^ smat.base.h:759:45: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (m.DimProd () <= t_base::GetSize ()) ; ^ smat.base.h:887:32: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (this->EqualDims (vec)) ; ^ smat.base.h:911:30: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (n < t_this::size ()) ; ^ smat.base.h:1063:67: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] const t_this &operator = (const t_this &p ) const { THROW (FALSE) ;} // this MUST never be called, as you can't change a constant matrix! Thus it's protected! ^ smat.base.h:1067:45: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (m.DimProd () <= t_base::GetSize ()) ; ^ smat.base.h:1079:48: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (dwRows * dwCols <= t_base::GetSize ()) ; ^ smat.base.h:1243:47: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (t_this::nrow () == t_this::m.nrow ()) ; ^ smat.base.h:1244:39: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (dwSource < t_this::m.ncol ()) ; ^ smat.base.h:1245:35: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (dwDest < t_this::ncol ()) ; ^ smat.base.h:1268:32: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (this->EqualDims (mat)) ; ^ smat.base.h:1286:46: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (t_this::ncol () == order.GetSize ()) ; ^ smat.base.h:1287:41: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (t_this::nrow () == mat.nrow ()) ; ^ smat.base.h:1363:66: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (ref.GetSize () <= dwRows * dwCols * dwSize * sizeof (T)) ; ^ smat.base.h:1388:70: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] tc_item &Item (t_size idx) const { THROW (idx < t_this::GetSize ()) ; return *m_apData [idx] ; } ^ In file included from smat.h:29:0, from pcaPP.h:7, from outSDo.h:1, from outSDo.cpp:1: smat.elop.h:181:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.nrow () == c.size ()) ; ^ smat.elop.h:189:26: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.EqualDims (b)) ; ^ smat.elop.h:190:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.nrow () == c.size ()) ; ^ smat.elop.h:222:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.ncol () == c.size ()) ; ^ smat.elop.h:230:26: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.EqualDims (b)) ; ^ smat.elop.h:231:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.ncol () == c.size ()) ; ^ smat.elop.h:262:26: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.EqualDims (c)) ; ^ smat.elop.h:263:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (b.size () == c.nrow ()) ; ^ smat.elop.h:264:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (d.size () == c.ncol ()) ; ^ smat.elop.h:307:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.nrow () == b.size ()) ; ^ smat.elop.h:308:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.ncol () == c.size ()) ; ^ smat.elop.h:342:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.ncol () == b.ncol ()) ; ^ smat.elop.h:343:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (b.nrow () == c.size ()) ; ^ smat.elop.h:344:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (b.nrow () == d.size ()) ; ^ smat.elop.h:354:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.ncol () == b.ncol ()) ; ^ smat.elop.h:355:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (b.nrow () == c.size ()) ; ^ smat.elop.h:356:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (b.nrow () == d.size ()) ; ^ smat.elop.h:357:37: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (CountTrue (d) == a.nrow ()) ; ^ smat.elop.h:399:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.ncol () == b.ncol ()) ; ^ smat.elop.h:400:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (b.ncol () == c.size ()) ; ^ smat.elop.h:401:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (b.nrow () == d.size ()) ; ^ smat.elop.h:411:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.ncol () == b.ncol ()) ; ^ smat.elop.h:412:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (b.ncol () == c.size ()) ; ^ smat.elop.h:413:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (b.nrow () == d.size ()) ; ^ smat.elop.h:414:37: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (CountTrue (d) == a.nrow ()) ; ^ smat.elop.h:453:34: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (c.ncol () == b.nsize ()) ; ^ smat.elop.h:454:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (c.nrow () == e.size ()) ; ^ smat.elop.h:464:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.ncol () == c.ncol ()) ; ^ smat.elop.h:465:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.ncol () == b.size ()) ; ^ smat.elop.h:466:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (c.nrow () == e.size ()) ; ^ smat.elop.h:467:43: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (CountMatches (e, d) == a.nrow ()) ; ^ smat.elop.h:515:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (b.size () == c.ncol ()) ; ^ smat.elop.h:516:36: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (getMaxIdx (d) < c.nrow ()) ; ^ smat.elop.h:530:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.ncol () == c.ncol ()) ; ^ smat.elop.h:531:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.nrow () == d.size ()) ; ^ smat.elop.h:532:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (b.size () == c.ncol ()) ; ^ smat.elop.h:533:36: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (getMaxIdx (d) < c.nrow ()) ; ^ smat.elop.h:571:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.ncol () == b.size ()) ; ^ smat.elop.h:611:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (c.size () == d.size ()) ; ^ smat.elop.h:690:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (b.size () == c.size ()) ; ^ smat.elop.h:735:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (b.size () == c.size ()) ; ^ smat.elop.h:761:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (c.nrow () == e.size ()) ; ^ smat.elop.h:801:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (b.size () == c.ncol ()) ; ^ smat.elop.h:802:36: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (getMaxIdx (d) < c.nrow ()) ; ^ smat.elop.h:838:34: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.size () == b.size ()) ; ^ smat.elop.h:839:34: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.size () == c.size ()) ; ^ smat.elop.h:866:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.size () == b.nrow ()) ; ^ smat.elop.h:896:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.size () == b.nrow ()) ; ^ smat.elop.h:897:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (c.size () == b.ncol ()) ; ^ smat.elop.h:928:34: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.size () == b.ncols ()) ; ^ smat.elop.h:950:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.size () == b.ncol ()) ; ^ smat.elop.h:951:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (c.size () == b.nrow ()) ; ^ smat.elop.h:1010:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.size () == d.size ()) ; ^ smat.elop.h:1034:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (b.size () == d.size ()) ; ^ smat.elop.h:1056:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.size () == c.size ()) ; ^ smat.elop.h:1079:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.size () == b.ncol ()) ; ^ smat.elop.h:1108:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.size () == b.ncol ()) ; ^ smat.elop.h:1109:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (c.size () == b.nrow ()) ; ^ smat.elop.h:1110:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (d.size () == b.nrow ()) ; ^ smat.elop.h:1146:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (b.size () == c.size ()) ; ^ smat.elop.h:1147:37: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (CountTrue (c) == a.size ()) ; ^ smat.elop.h:1177:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.size () == b.size ()) ; ^ smat.elop.h:1203:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.size () == b.size ()) ; ^ smat.elop.h:1228:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.size () == b.size ()) ; ^ In file included from smat.h:31:0, from pcaPP.h:7, from outSDo.h:1, from outSDo.cpp:1: smat.mem.h:25:24: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (c < b.nrow ()) ; ^ smat.mem.h:34:24: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (c < b.nrow ()) ; ^ smat.mem.h:35:31: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.size () == b.ncol()) ; ^ smat.mem.h:59:24: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (c < a.nrow ()) ; ^ smat.mem.h:60:32: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.ncol () == b.size ()) ; ^ smat.mem.h:84:24: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (c < a.nrow ()) ; ^ smat.mem.h:156:32: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.size () == b.size ()) ; ^ smat.mem.h:177:38: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (v.nsize () == m.GetMinDim ()) ; ^ smat.mem.h:193:27: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (dwCol < b.ncol ()) ; ^ smat.mem.h:207:26: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (dwStart <= dwEnd) ; ^ smat.mem.h:208:28: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (dwEnd <= b.ncol ()) ; ^ smat.mem.h:209:32: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.nrow () == b.nrow ()) ; ^ smat.mem.h:210:38: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.ncol () == dwEnd - dwStart) ; ^ In file included from smat.h:32:0, from pcaPP.h:7, from outSDo.h:1, from outSDo.cpp:1: smat.matop.h:82:31: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.ncol() == b.size ()) ; ^ smat.matop.h:83:31: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.nrow() == b.size ()) ; ^ smat.matop.h:128:32: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.ncol () == a.nrow ()) ; ^ smat.matop.h:156:32: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.ncol () == a.nrow ()) ; ^ In file included from smat.h:33:0, from pcaPP.h:7, from outSDo.h:1, from outSDo.cpp:1: smat.misc.h:32:16: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (l <= u) ; ^ In file included from smat.h:36:0, from pcaPP.h:7, from outSDo.h:1, from outSDo.cpp:1: smat.stat.h:172:32: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.size () == b.ncol ()) ; ^ smat.stat.h:212:32: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.size () == b.ncol ()) ; ^ g++ -I/usr/share/R/include -DNDEBUG -DR_PACKAGE_FILE -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c pcaPP.cpp -o pcaPP.o In file included from smat.h:28:0, from pcaPP.h:7, from pcaPP.cpp:1: smat.base.h:401:29: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (dwIdx < GetSize ()) ; ^ smat.base.h:458:29: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (dwIdx < GetSize ()) ; ^ smat.base.h:498:40: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (HasRawCap (dwOffset + dwSize)) ; ^ smat.base.h:520:53: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (HasRawCap (m_dwOffset + dwOffset + dwSize)) ; ^ smat.base.h:540:44: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (HasRawCap (GetOffset () + dwSize)) ; ^ smat.base.h:553:29: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (HasRawCap (dwSize)) ; ^ smat.base.h:662:65: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] inline const t_size GetDim (t_size p) const { THROW (p < P) ; return m_adwDim [p] ; } ^ smat.base.h:665:68: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] inline const t_size * GetDimPtr (t_size p) const { THROW (p < P) ; return m_adwDim + p ; } ^ smat.base.h:669:60: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] inline t_size & GetDimRef (t_size p) { THROW (p < P) ; return m_adwDim [p] ; } ^ In file included from smat.h:28:0, from pcaPP.h:7, from pcaPP.cpp:1: smat.base.h:735:63: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] const t_this &operator = (const t_this &p ) const { THROW (0) ;} // this MUST never be called, as you can't change a constant matrix! Thus it's protected! ^ smat.base.h:747:39: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (dwSize <= t_base::GetSize ()) ; ^ smat.base.h:759:45: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (m.DimProd () <= t_base::GetSize ()) ; ^ smat.base.h:887:32: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (this->EqualDims (vec)) ; ^ smat.base.h:911:30: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (n < t_this::size ()) ; ^ smat.base.h:1063:67: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] const t_this &operator = (const t_this &p ) const { THROW (FALSE) ;} // this MUST never be called, as you can't change a constant matrix! Thus it's protected! ^ smat.base.h:1067:45: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (m.DimProd () <= t_base::GetSize ()) ; ^ smat.base.h:1079:48: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (dwRows * dwCols <= t_base::GetSize ()) ; ^ smat.base.h:1243:47: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (t_this::nrow () == t_this::m.nrow ()) ; ^ smat.base.h:1244:39: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (dwSource < t_this::m.ncol ()) ; ^ smat.base.h:1245:35: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (dwDest < t_this::ncol ()) ; ^ smat.base.h:1268:32: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (this->EqualDims (mat)) ; ^ smat.base.h:1286:46: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (t_this::ncol () == order.GetSize ()) ; ^ smat.base.h:1287:41: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (t_this::nrow () == mat.nrow ()) ; ^ smat.base.h:1363:66: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (ref.GetSize () <= dwRows * dwCols * dwSize * sizeof (T)) ; ^ smat.base.h:1388:70: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] tc_item &Item (t_size idx) const { THROW (idx < t_this::GetSize ()) ; return *m_apData [idx] ; } ^ In file included from smat.h:29:0, from pcaPP.h:7, from pcaPP.cpp:1: smat.elop.h:181:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.nrow () == c.size ()) ; ^ smat.elop.h:189:26: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.EqualDims (b)) ; ^ smat.elop.h:190:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.nrow () == c.size ()) ; ^ smat.elop.h:222:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.ncol () == c.size ()) ; ^ smat.elop.h:230:26: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.EqualDims (b)) ; ^ smat.elop.h:231:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.ncol () == c.size ()) ; ^ smat.elop.h:262:26: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.EqualDims (c)) ; ^ smat.elop.h:263:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (b.size () == c.nrow ()) ; ^ smat.elop.h:264:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (d.size () == c.ncol ()) ; ^ smat.elop.h:307:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.nrow () == b.size ()) ; ^ smat.elop.h:308:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.ncol () == c.size ()) ; ^ smat.elop.h:342:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.ncol () == b.ncol ()) ; ^ smat.elop.h:343:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (b.nrow () == c.size ()) ; ^ smat.elop.h:344:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (b.nrow () == d.size ()) ; ^ smat.elop.h:354:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.ncol () == b.ncol ()) ; ^ smat.elop.h:355:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (b.nrow () == c.size ()) ; ^ smat.elop.h:356:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (b.nrow () == d.size ()) ; ^ smat.elop.h:357:37: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (CountTrue (d) == a.nrow ()) ; ^ smat.elop.h:399:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.ncol () == b.ncol ()) ; ^ smat.elop.h:400:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (b.ncol () == c.size ()) ; ^ smat.elop.h:401:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (b.nrow () == d.size ()) ; ^ smat.elop.h:411:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.ncol () == b.ncol ()) ; ^ smat.elop.h:412:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (b.ncol () == c.size ()) ; ^ smat.elop.h:413:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (b.nrow () == d.size ()) ; ^ smat.elop.h:414:37: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (CountTrue (d) == a.nrow ()) ; ^ smat.elop.h:453:34: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (c.ncol () == b.nsize ()) ; ^ smat.elop.h:454:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (c.nrow () == e.size ()) ; ^ smat.elop.h:464:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.ncol () == c.ncol ()) ; ^ smat.elop.h:465:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.ncol () == b.size ()) ; ^ smat.elop.h:466:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (c.nrow () == e.size ()) ; ^ smat.elop.h:467:43: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (CountMatches (e, d) == a.nrow ()) ; ^ smat.elop.h:515:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (b.size () == c.ncol ()) ; ^ smat.elop.h:516:36: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (getMaxIdx (d) < c.nrow ()) ; ^ smat.elop.h:530:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.ncol () == c.ncol ()) ; ^ smat.elop.h:531:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.nrow () == d.size ()) ; ^ smat.elop.h:532:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (b.size () == c.ncol ()) ; ^ smat.elop.h:533:36: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (getMaxIdx (d) < c.nrow ()) ; ^ smat.elop.h:571:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.ncol () == b.size ()) ; ^ smat.elop.h:611:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (c.size () == d.size ()) ; ^ smat.elop.h:690:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (b.size () == c.size ()) ; ^ smat.elop.h:735:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (b.size () == c.size ()) ; ^ smat.elop.h:761:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (c.nrow () == e.size ()) ; ^ smat.elop.h:801:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (b.size () == c.ncol ()) ; ^ smat.elop.h:802:36: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (getMaxIdx (d) < c.nrow ()) ; ^ smat.elop.h:838:34: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.size () == b.size ()) ; ^ smat.elop.h:839:34: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.size () == c.size ()) ; ^ smat.elop.h:866:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.size () == b.nrow ()) ; ^ smat.elop.h:896:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.size () == b.nrow ()) ; ^ smat.elop.h:897:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (c.size () == b.ncol ()) ; ^ smat.elop.h:928:34: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.size () == b.ncols ()) ; ^ smat.elop.h:950:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.size () == b.ncol ()) ; ^ smat.elop.h:951:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (c.size () == b.nrow ()) ; ^ smat.elop.h:1010:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.size () == d.size ()) ; ^ smat.elop.h:1034:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (b.size () == d.size ()) ; ^ smat.elop.h:1056:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.size () == c.size ()) ; ^ smat.elop.h:1079:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.size () == b.ncol ()) ; ^ smat.elop.h:1108:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.size () == b.ncol ()) ; ^ smat.elop.h:1109:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (c.size () == b.nrow ()) ; ^ smat.elop.h:1110:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (d.size () == b.nrow ()) ; ^ smat.elop.h:1146:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (b.size () == c.size ()) ; ^ smat.elop.h:1147:37: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (CountTrue (c) == a.size ()) ; ^ smat.elop.h:1177:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.size () == b.size ()) ; ^ smat.elop.h:1203:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.size () == b.size ()) ; ^ smat.elop.h:1228:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.size () == b.size ()) ; ^ In file included from smat.h:31:0, from pcaPP.h:7, from pcaPP.cpp:1: smat.mem.h:25:24: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (c < b.nrow ()) ; ^ smat.mem.h:34:24: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (c < b.nrow ()) ; ^ smat.mem.h:35:31: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.size () == b.ncol()) ; ^ smat.mem.h:59:24: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (c < a.nrow ()) ; ^ smat.mem.h:60:32: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.ncol () == b.size ()) ; ^ smat.mem.h:84:24: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (c < a.nrow ()) ; ^ smat.mem.h:156:32: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.size () == b.size ()) ; ^ smat.mem.h:177:38: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (v.nsize () == m.GetMinDim ()) ; ^ smat.mem.h:193:27: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (dwCol < b.ncol ()) ; ^ smat.mem.h:207:26: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (dwStart <= dwEnd) ; ^ smat.mem.h:208:28: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (dwEnd <= b.ncol ()) ; ^ smat.mem.h:209:32: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.nrow () == b.nrow ()) ; ^ smat.mem.h:210:38: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.ncol () == dwEnd - dwStart) ; ^ In file included from smat.h:32:0, from pcaPP.h:7, from pcaPP.cpp:1: smat.matop.h:82:31: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.ncol() == b.size ()) ; ^ smat.matop.h:83:31: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.nrow() == b.size ()) ; ^ smat.matop.h:128:32: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.ncol () == a.nrow ()) ; ^ smat.matop.h:156:32: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.ncol () == a.nrow ()) ; ^ In file included from smat.h:33:0, from pcaPP.h:7, from pcaPP.cpp:1: smat.misc.h:32:16: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (l <= u) ; ^ In file included from smat.h:36:0, from pcaPP.h:7, from pcaPP.cpp:1: smat.stat.h:172:32: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.size () == b.ncol ()) ; ^ smat.stat.h:212:32: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.size () == b.ncol ()) ; ^ gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DR_PACKAGE_FILE -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c pcaPP_init.c -o pcaPP_init.o g++ -I/usr/share/R/include -DNDEBUG -DR_PACKAGE_FILE -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c qnn.cpp -o qnn.o In file included from smat.h:28:0, from qnn.h:5, from qnn.cpp:1: smat.base.h:401:29: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (dwIdx < GetSize ()) ; ^ smat.base.h:458:29: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (dwIdx < GetSize ()) ; ^ smat.base.h:498:40: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (HasRawCap (dwOffset + dwSize)) ; ^ smat.base.h:520:53: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (HasRawCap (m_dwOffset + dwOffset + dwSize)) ; ^ smat.base.h:540:44: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (HasRawCap (GetOffset () + dwSize)) ; ^ smat.base.h:553:29: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (HasRawCap (dwSize)) ; ^ smat.base.h:662:65: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] inline const t_size GetDim (t_size p) const { THROW (p < P) ; return m_adwDim [p] ; } ^ smat.base.h:665:68: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] inline const t_size * GetDimPtr (t_size p) const { THROW (p < P) ; return m_adwDim + p ; } ^ smat.base.h:669:60: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] inline t_size & GetDimRef (t_size p) { THROW (p < P) ; return m_adwDim [p] ; } ^ In file included from smat.h:28:0, from qnn.h:5, from qnn.cpp:1: smat.base.h:735:63: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] const t_this &operator = (const t_this &p ) const { THROW (0) ;} // this MUST never be called, as you can't change a constant matrix! Thus it's protected! ^ smat.base.h:747:39: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (dwSize <= t_base::GetSize ()) ; ^ smat.base.h:759:45: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (m.DimProd () <= t_base::GetSize ()) ; ^ smat.base.h:887:32: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (this->EqualDims (vec)) ; ^ smat.base.h:911:30: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (n < t_this::size ()) ; ^ smat.base.h:1063:67: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] const t_this &operator = (const t_this &p ) const { THROW (FALSE) ;} // this MUST never be called, as you can't change a constant matrix! Thus it's protected! ^ smat.base.h:1067:45: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (m.DimProd () <= t_base::GetSize ()) ; ^ smat.base.h:1079:48: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (dwRows * dwCols <= t_base::GetSize ()) ; ^ smat.base.h:1243:47: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (t_this::nrow () == t_this::m.nrow ()) ; ^ smat.base.h:1244:39: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (dwSource < t_this::m.ncol ()) ; ^ smat.base.h:1245:35: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (dwDest < t_this::ncol ()) ; ^ smat.base.h:1268:32: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (this->EqualDims (mat)) ; ^ smat.base.h:1286:46: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (t_this::ncol () == order.GetSize ()) ; ^ smat.base.h:1287:41: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (t_this::nrow () == mat.nrow ()) ; ^ smat.base.h:1363:66: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (ref.GetSize () <= dwRows * dwCols * dwSize * sizeof (T)) ; ^ smat.base.h:1388:70: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] tc_item &Item (t_size idx) const { THROW (idx < t_this::GetSize ()) ; return *m_apData [idx] ; } ^ In file included from smat.h:29:0, from qnn.h:5, from qnn.cpp:1: smat.elop.h:181:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.nrow () == c.size ()) ; ^ smat.elop.h:189:26: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.EqualDims (b)) ; ^ smat.elop.h:190:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.nrow () == c.size ()) ; ^ smat.elop.h:222:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.ncol () == c.size ()) ; ^ smat.elop.h:230:26: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.EqualDims (b)) ; ^ smat.elop.h:231:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.ncol () == c.size ()) ; ^ smat.elop.h:262:26: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.EqualDims (c)) ; ^ smat.elop.h:263:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (b.size () == c.nrow ()) ; ^ smat.elop.h:264:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (d.size () == c.ncol ()) ; ^ smat.elop.h:307:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.nrow () == b.size ()) ; ^ smat.elop.h:308:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.ncol () == c.size ()) ; ^ smat.elop.h:342:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.ncol () == b.ncol ()) ; ^ smat.elop.h:343:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (b.nrow () == c.size ()) ; ^ smat.elop.h:344:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (b.nrow () == d.size ()) ; ^ smat.elop.h:354:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.ncol () == b.ncol ()) ; ^ smat.elop.h:355:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (b.nrow () == c.size ()) ; ^ smat.elop.h:356:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (b.nrow () == d.size ()) ; ^ smat.elop.h:357:37: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (CountTrue (d) == a.nrow ()) ; ^ smat.elop.h:399:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.ncol () == b.ncol ()) ; ^ smat.elop.h:400:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (b.ncol () == c.size ()) ; ^ smat.elop.h:401:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (b.nrow () == d.size ()) ; ^ smat.elop.h:411:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.ncol () == b.ncol ()) ; ^ smat.elop.h:412:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (b.ncol () == c.size ()) ; ^ smat.elop.h:413:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (b.nrow () == d.size ()) ; ^ smat.elop.h:414:37: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (CountTrue (d) == a.nrow ()) ; ^ smat.elop.h:453:34: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (c.ncol () == b.nsize ()) ; ^ smat.elop.h:454:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (c.nrow () == e.size ()) ; ^ smat.elop.h:464:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.ncol () == c.ncol ()) ; ^ smat.elop.h:465:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.ncol () == b.size ()) ; ^ smat.elop.h:466:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (c.nrow () == e.size ()) ; ^ smat.elop.h:467:43: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (CountMatches (e, d) == a.nrow ()) ; ^ smat.elop.h:515:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (b.size () == c.ncol ()) ; ^ smat.elop.h:516:36: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (getMaxIdx (d) < c.nrow ()) ; ^ smat.elop.h:530:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.ncol () == c.ncol ()) ; ^ smat.elop.h:531:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.nrow () == d.size ()) ; ^ smat.elop.h:532:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (b.size () == c.ncol ()) ; ^ smat.elop.h:533:36: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (getMaxIdx (d) < c.nrow ()) ; ^ smat.elop.h:571:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.ncol () == b.size ()) ; ^ smat.elop.h:611:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (c.size () == d.size ()) ; ^ smat.elop.h:690:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (b.size () == c.size ()) ; ^ smat.elop.h:735:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (b.size () == c.size ()) ; ^ smat.elop.h:761:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (c.nrow () == e.size ()) ; ^ smat.elop.h:801:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (b.size () == c.ncol ()) ; ^ smat.elop.h:802:36: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (getMaxIdx (d) < c.nrow ()) ; ^ smat.elop.h:838:34: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.size () == b.size ()) ; ^ smat.elop.h:839:34: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.size () == c.size ()) ; ^ smat.elop.h:866:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.size () == b.nrow ()) ; ^ smat.elop.h:896:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.size () == b.nrow ()) ; ^ smat.elop.h:897:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (c.size () == b.ncol ()) ; ^ smat.elop.h:928:34: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.size () == b.ncols ()) ; ^ smat.elop.h:950:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.size () == b.ncol ()) ; ^ smat.elop.h:951:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (c.size () == b.nrow ()) ; ^ smat.elop.h:1010:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.size () == d.size ()) ; ^ smat.elop.h:1034:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (b.size () == d.size ()) ; ^ smat.elop.h:1056:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.size () == c.size ()) ; ^ smat.elop.h:1079:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.size () == b.ncol ()) ; ^ smat.elop.h:1108:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.size () == b.ncol ()) ; ^ smat.elop.h:1109:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (c.size () == b.nrow ()) ; ^ smat.elop.h:1110:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (d.size () == b.nrow ()) ; ^ smat.elop.h:1146:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (b.size () == c.size ()) ; ^ smat.elop.h:1147:37: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (CountTrue (c) == a.size ()) ; ^ smat.elop.h:1177:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.size () == b.size ()) ; ^ smat.elop.h:1203:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.size () == b.size ()) ; ^ smat.elop.h:1228:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.size () == b.size ()) ; ^ In file included from smat.h:31:0, from qnn.h:5, from qnn.cpp:1: smat.mem.h:25:24: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (c < b.nrow ()) ; ^ smat.mem.h:34:24: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (c < b.nrow ()) ; ^ smat.mem.h:35:31: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.size () == b.ncol()) ; ^ smat.mem.h:59:24: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (c < a.nrow ()) ; ^ smat.mem.h:60:32: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.ncol () == b.size ()) ; ^ smat.mem.h:84:24: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (c < a.nrow ()) ; ^ smat.mem.h:156:32: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.size () == b.size ()) ; ^ smat.mem.h:177:38: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (v.nsize () == m.GetMinDim ()) ; ^ smat.mem.h:193:27: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (dwCol < b.ncol ()) ; ^ smat.mem.h:207:26: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (dwStart <= dwEnd) ; ^ smat.mem.h:208:28: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (dwEnd <= b.ncol ()) ; ^ smat.mem.h:209:32: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.nrow () == b.nrow ()) ; ^ smat.mem.h:210:38: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.ncol () == dwEnd - dwStart) ; ^ In file included from smat.h:32:0, from qnn.h:5, from qnn.cpp:1: smat.matop.h:82:31: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.ncol() == b.size ()) ; ^ smat.matop.h:83:31: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.nrow() == b.size ()) ; ^ smat.matop.h:128:32: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.ncol () == a.nrow ()) ; ^ smat.matop.h:156:32: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.ncol () == a.nrow ()) ; ^ In file included from smat.h:33:0, from qnn.h:5, from qnn.cpp:1: smat.misc.h:32:16: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (l <= u) ; ^ In file included from smat.h:36:0, from qnn.h:5, from qnn.cpp:1: smat.stat.h:172:32: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.size () == b.ncol ()) ; ^ smat.stat.h:212:32: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.size () == b.ncol ()) ; ^ g++ -I/usr/share/R/include -DNDEBUG -DR_PACKAGE_FILE -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c smat.cpp -o smat.o In file included from smat.h:28:0, from smat.cpp:20: smat.base.h:401:29: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (dwIdx < GetSize ()) ; ^ smat.base.h:458:29: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (dwIdx < GetSize ()) ; ^ smat.base.h:498:40: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (HasRawCap (dwOffset + dwSize)) ; ^ smat.base.h:520:53: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (HasRawCap (m_dwOffset + dwOffset + dwSize)) ; ^ smat.base.h:540:44: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (HasRawCap (GetOffset () + dwSize)) ; ^ smat.base.h:553:29: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (HasRawCap (dwSize)) ; ^ smat.base.h:662:65: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] inline const t_size GetDim (t_size p) const { THROW (p < P) ; return m_adwDim [p] ; } ^ smat.base.h:665:68: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] inline const t_size * GetDimPtr (t_size p) const { THROW (p < P) ; return m_adwDim + p ; } ^ smat.base.h:669:60: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] inline t_size & GetDimRef (t_size p) { THROW (p < P) ; return m_adwDim [p] ; } ^ In file included from smat.h:28:0, from smat.cpp:20: smat.base.h:735:63: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] const t_this &operator = (const t_this &p ) const { THROW (0) ;} // this MUST never be called, as you can't change a constant matrix! Thus it's protected! ^ smat.base.h:747:39: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (dwSize <= t_base::GetSize ()) ; ^ smat.base.h:759:45: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (m.DimProd () <= t_base::GetSize ()) ; ^ smat.base.h:887:32: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (this->EqualDims (vec)) ; ^ smat.base.h:911:30: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (n < t_this::size ()) ; ^ smat.base.h:1063:67: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] const t_this &operator = (const t_this &p ) const { THROW (FALSE) ;} // this MUST never be called, as you can't change a constant matrix! Thus it's protected! ^ smat.base.h:1067:45: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (m.DimProd () <= t_base::GetSize ()) ; ^ smat.base.h:1079:48: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (dwRows * dwCols <= t_base::GetSize ()) ; ^ smat.base.h:1243:47: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (t_this::nrow () == t_this::m.nrow ()) ; ^ smat.base.h:1244:39: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (dwSource < t_this::m.ncol ()) ; ^ smat.base.h:1245:35: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (dwDest < t_this::ncol ()) ; ^ smat.base.h:1268:32: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (this->EqualDims (mat)) ; ^ smat.base.h:1286:46: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (t_this::ncol () == order.GetSize ()) ; ^ smat.base.h:1287:41: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (t_this::nrow () == mat.nrow ()) ; ^ smat.base.h:1363:66: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (ref.GetSize () <= dwRows * dwCols * dwSize * sizeof (T)) ; ^ smat.base.h:1388:70: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] tc_item &Item (t_size idx) const { THROW (idx < t_this::GetSize ()) ; return *m_apData [idx] ; } ^ In file included from smat.h:29:0, from smat.cpp:20: smat.elop.h:181:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.nrow () == c.size ()) ; ^ smat.elop.h:189:26: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.EqualDims (b)) ; ^ smat.elop.h:190:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.nrow () == c.size ()) ; ^ smat.elop.h:222:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.ncol () == c.size ()) ; ^ smat.elop.h:230:26: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.EqualDims (b)) ; ^ smat.elop.h:231:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.ncol () == c.size ()) ; ^ smat.elop.h:262:26: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.EqualDims (c)) ; ^ smat.elop.h:263:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (b.size () == c.nrow ()) ; ^ smat.elop.h:264:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (d.size () == c.ncol ()) ; ^ smat.elop.h:307:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.nrow () == b.size ()) ; ^ smat.elop.h:308:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.ncol () == c.size ()) ; ^ smat.elop.h:342:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.ncol () == b.ncol ()) ; ^ smat.elop.h:343:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (b.nrow () == c.size ()) ; ^ smat.elop.h:344:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (b.nrow () == d.size ()) ; ^ smat.elop.h:354:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.ncol () == b.ncol ()) ; ^ smat.elop.h:355:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (b.nrow () == c.size ()) ; ^ smat.elop.h:356:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (b.nrow () == d.size ()) ; ^ smat.elop.h:357:37: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (CountTrue (d) == a.nrow ()) ; ^ smat.elop.h:399:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.ncol () == b.ncol ()) ; ^ smat.elop.h:400:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (b.ncol () == c.size ()) ; ^ smat.elop.h:401:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (b.nrow () == d.size ()) ; ^ smat.elop.h:411:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.ncol () == b.ncol ()) ; ^ smat.elop.h:412:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (b.ncol () == c.size ()) ; ^ smat.elop.h:413:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (b.nrow () == d.size ()) ; ^ smat.elop.h:414:37: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (CountTrue (d) == a.nrow ()) ; ^ smat.elop.h:453:34: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (c.ncol () == b.nsize ()) ; ^ smat.elop.h:454:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (c.nrow () == e.size ()) ; ^ smat.elop.h:464:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.ncol () == c.ncol ()) ; ^ smat.elop.h:465:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.ncol () == b.size ()) ; ^ smat.elop.h:466:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (c.nrow () == e.size ()) ; ^ smat.elop.h:467:43: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (CountMatches (e, d) == a.nrow ()) ; ^ smat.elop.h:515:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (b.size () == c.ncol ()) ; ^ smat.elop.h:516:36: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (getMaxIdx (d) < c.nrow ()) ; ^ smat.elop.h:530:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.ncol () == c.ncol ()) ; ^ smat.elop.h:531:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.nrow () == d.size ()) ; ^ smat.elop.h:532:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (b.size () == c.ncol ()) ; ^ smat.elop.h:533:36: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (getMaxIdx (d) < c.nrow ()) ; ^ smat.elop.h:571:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.ncol () == b.size ()) ; ^ smat.elop.h:611:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (c.size () == d.size ()) ; ^ smat.elop.h:690:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (b.size () == c.size ()) ; ^ smat.elop.h:735:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (b.size () == c.size ()) ; ^ smat.elop.h:761:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (c.nrow () == e.size ()) ; ^ smat.elop.h:801:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (b.size () == c.ncol ()) ; ^ smat.elop.h:802:36: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (getMaxIdx (d) < c.nrow ()) ; ^ smat.elop.h:838:34: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.size () == b.size ()) ; ^ smat.elop.h:839:34: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.size () == c.size ()) ; ^ smat.elop.h:866:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.size () == b.nrow ()) ; ^ smat.elop.h:896:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.size () == b.nrow ()) ; ^ smat.elop.h:897:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (c.size () == b.ncol ()) ; ^ smat.elop.h:928:34: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.size () == b.ncols ()) ; ^ smat.elop.h:950:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.size () == b.ncol ()) ; ^ smat.elop.h:951:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (c.size () == b.nrow ()) ; ^ smat.elop.h:1010:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.size () == d.size ()) ; ^ smat.elop.h:1034:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (b.size () == d.size ()) ; ^ smat.elop.h:1056:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.size () == c.size ()) ; ^ smat.elop.h:1079:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.size () == b.ncol ()) ; ^ smat.elop.h:1108:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.size () == b.ncol ()) ; ^ smat.elop.h:1109:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (c.size () == b.nrow ()) ; ^ smat.elop.h:1110:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (d.size () == b.nrow ()) ; ^ smat.elop.h:1146:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (b.size () == c.size ()) ; ^ smat.elop.h:1147:37: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (CountTrue (c) == a.size ()) ; ^ smat.elop.h:1177:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.size () == b.size ()) ; ^ smat.elop.h:1203:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.size () == b.size ()) ; ^ smat.elop.h:1228:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.size () == b.size ()) ; ^ In file included from smat.h:31:0, from smat.cpp:20: smat.mem.h:25:24: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (c < b.nrow ()) ; ^ smat.mem.h:34:24: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (c < b.nrow ()) ; ^ smat.mem.h:35:31: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.size () == b.ncol()) ; ^ smat.mem.h:59:24: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (c < a.nrow ()) ; ^ smat.mem.h:60:32: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.ncol () == b.size ()) ; ^ smat.mem.h:84:24: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (c < a.nrow ()) ; ^ smat.mem.h:156:32: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.size () == b.size ()) ; ^ smat.mem.h:177:38: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (v.nsize () == m.GetMinDim ()) ; ^ smat.mem.h:193:27: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (dwCol < b.ncol ()) ; ^ smat.mem.h:207:26: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (dwStart <= dwEnd) ; ^ smat.mem.h:208:28: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (dwEnd <= b.ncol ()) ; ^ smat.mem.h:209:32: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.nrow () == b.nrow ()) ; ^ smat.mem.h:210:38: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.ncol () == dwEnd - dwStart) ; ^ In file included from smat.h:32:0, from smat.cpp:20: smat.matop.h:82:31: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.ncol() == b.size ()) ; ^ smat.matop.h:83:31: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.nrow() == b.size ()) ; ^ smat.matop.h:128:32: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.ncol () == a.nrow ()) ; ^ smat.matop.h:156:32: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.ncol () == a.nrow ()) ; ^ In file included from smat.h:33:0, from smat.cpp:20: smat.misc.h:32:16: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (l <= u) ; ^ In file included from smat.h:36:0, from smat.cpp:20: smat.stat.h:172:32: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.size () == b.ncol ()) ; ^ smat.stat.h:212:32: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.size () == b.ncol ()) ; ^ smat.cpp:143:20: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (IsOwner ()) ; ^ smat.cpp:324:32: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.ncol () == b.nrow ()) ; ^ smat.cpp:332:32: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.ncol () == b.nrow ()) ; ^ smat.cpp:333:58: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.nrow () == c.nrow () && c.ncol () == b.ncol ()) ; ^ smat.cpp:367:51: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.GetDim (!bTransA) == b.GetDim (bTransB)) ; ^ smat.cpp:368:77: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.GetDim (bTransA) == c.nrow () && c.ncol () == b.GetDim (!bTransB)) ; ^ smat.cpp:403:54: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (c.size () == ::sm_min (a.nrow (), a.ncol ())) ; ^ smat.cpp:499:24: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (p == A.ncol ()) ; ^ smat.cpp:509:24: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (p == A.ncol ()) ; ^ smat.cpp:510:27: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (vVal.size () == p) ; ^ smat.cpp:511:48: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (mVec.nrow () == p && mVec.ncol () == p) ; ^ smat.cpp:561:16: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (!nInfo) ; ^ smat.cpp:566:24: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (pd[2] == pd[1]) ; ^ smat.cpp:612:32: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.ncol () == b.size ()) ; ^ smat.cpp:619:32: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.ncol () == b.size ()) ; ^ smat.cpp:620:58: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (c.nrow () == a.nrow () && c.ncol () == a.nrow ()) ; ^ smat.cpp:638:32: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.nrow () == b.size ()) ; ^ smat.cpp:645:32: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.nrow () == b.size ()) ; ^ smat.cpp:646:58: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (c.nrow () == a.ncol () && c.ncol () == a.ncol ()) ; ^ smat.cpp:675:76: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (b.nrow () == b.GetDim (bTransA) && b.ncol () == a.GetDim (bTransA)) ; ^ smat.cpp:693:32: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (b.nrow () == b.ncol ()) ; ^ smat.cpp:694:42: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.GetDim (!bTransA) == b.nrow ()) ; ^ smat.cpp:701:32: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (b.nrow () == b.ncol ()) ; ^ smat.cpp:702:42: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.GetDim (!bTransA) == b.nrow ()) ; ^ smat.cpp:703:76: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (c.nrow () == a.GetDim (bTransA) && c.ncol () == a.GetDim (bTransA)) ; ^ smat.cpp:726:32: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.ncol () == b.nrow ()) ; ^ smat.cpp:733:32: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.ncol () == b.nrow ()) ; ^ smat.cpp:734:52: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (sm_min (a.nrow (), b.ncol ()) == c.size ()) ; ^ smat.cpp:793:32: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.ncol () == b.nrow ()) ; ^ smat.cpp:849:32: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (b.nrow () == c.nrow ()) ; ^ smat.cpp:877:32: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.nrow () == a.ncol ()) ; ^ smat.cpp:878:32: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.nrow () == b.ncol ()) ; ^ smat.cpp:963:32: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.size () == b.size ()) ; ^ smat.cpp:980:32: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] THROW (a.size () == b.size ()) ; ^ g++ -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o pcaPP.so L1Median_HoCr.o L1Median_VardiZhang.o ML_meal.o ML_package.o ML_passrng.o PCAgrid.o PCAproj.o R_meal.o R_meal_BLAS.o R_package.o cov.kendall.o hess.o l1median.o outSDo.o pcaPP.o pcaPP_init.o qnn.o smat.o -llapack -lblas -lgfortran -lm -lquadmath -L/usr/lib/R/lib -lR installing to /usr/local/lib/R/site-library/pcaPP/libs ** R ** inst ** preparing package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded * DONE (pcaPP) * installing *source* package 'htmlTable' ... ** package 'htmlTable' successfully unpacked and MD5 sums checked ** R ** data ** inst ** preparing package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded * DONE (htmlTable) * installing *source* package 'robustbase' ... ** package 'robustbase' successfully unpacked and MD5 sums checked ** libs gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c R-rng4ftn.c -o R-rng4ftn.o gfortran -fpic -g -O2 -fstack-protector-strong -c eigen.f -o eigen.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c init.c -o init.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c lmrob.c -o lmrob.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c mc.c -o mc.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c monitor.c -o monitor.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c qn_sn.c -o qn_sn.o gfortran -fpic -g -O2 -fstack-protector-strong -c rf-common.f -o rf-common.o gfortran -fpic -g -O2 -fstack-protector-strong -c rffastmcd.f -o rffastmcd.o gfortran -fpic -g -O2 -fstack-protector-strong -c rfltsreg.f -o rfltsreg.o gfortran -fpic -g -O2 -fstack-protector-strong -c rllarsbi.f -o rllarsbi.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c rob-utils.c -o rob-utils.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c rowMedians.c -o rowMedians.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c wgt_himed.c -o wgt_himed.o gcc -std=gnu99 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o robustbase.so R-rng4ftn.o eigen.o init.o lmrob.o mc.o monitor.o qn_sn.o rf-common.o rffastmcd.o rfltsreg.o rllarsbi.o rob-utils.o rowMedians.o wgt_himed.o -llapack -lblas -lgfortran -lm -lquadmath -lgfortran -lm -lquadmath -L/usr/lib/R/lib -lR installing to /usr/local/lib/R/site-library/robustbase/libs ** R ** data *** moving datasets to lazyload DB ** demo ** inst ** byte-compile and prepare package for lazy loading Creating a generic function from function 'chgDefaults' in package 'robustbase' ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded * DONE (robustbase) * installing *source* package 'ggbeeswarm' ... ** package 'ggbeeswarm' successfully unpacked and MD5 sums checked ** R ** inst ** preparing package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded * DONE (ggbeeswarm) * installing *source* package 'rrcov' ... ** package 'rrcov' successfully unpacked and MD5 sums checked ** libs gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c R-rng4ftn.c -o R-rng4ftn.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c covOPW.c -o covOPW.o gfortran -fpic -g -O2 -fstack-protector-strong -c ds11.f -o ds11.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c fast-mve.c -o fast-mve.o gfortran -fpic -g -O2 -fstack-protector-strong -c fsada.f -o fsada.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c sest.c -o sest.o gcc -std=gnu99 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o rrcov.so R-rng4ftn.o covOPW.o ds11.o fast-mve.o fsada.o sest.o -llapack -lblas -lgfortran -lm -lquadmath -lgfortran -lm -lquadmath -L/usr/lib/R/lib -lR installing to /usr/local/lib/R/site-library/rrcov/libs ** R ** data ** inst ** preparing package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded * DONE (rrcov) * installing *source* package 'Hmisc' ... ** package 'Hmisc' successfully unpacked and MD5 sums checked ** libs gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c Hmisc.c -o Hmisc.o gfortran -fpic -g -O2 -fstack-protector-strong -c cidxcn.f -o cidxcn.o gfortran -fpic -g -O2 -fstack-protector-strong -c cidxcp.f -o cidxcp.o gfortran -fpic -g -O2 -fstack-protector-strong -c hoeffd.f -o hoeffd.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c init.c -o init.o gfortran -fpic -g -O2 -fstack-protector-strong -c jacklins.f -o jacklins.o gfortran -fpic -g -O2 -fstack-protector-strong -c largrec.f -o largrec.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c mChoice.c -o mChoice.o gfortran -fpic -g -O2 -fstack-protector-strong -c maxempr.f -o maxempr.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c nstr.c -o nstr.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c ranksort.c -o ranksort.o gfortran -fpic -g -O2 -fstack-protector-strong -c rcorr.f -o rcorr.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c string_box.c -o string_box.o gfortran -fpic -g -O2 -fstack-protector-strong -c wclosest.f -o wclosest.o gcc -std=gnu99 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o Hmisc.so Hmisc.o cidxcn.o cidxcp.o hoeffd.o init.o jacklins.o largrec.o mChoice.o maxempr.o nstr.o ranksort.o rcorr.o string_box.o wclosest.o -lgfortran -lm -lquadmath -L/usr/lib/R/lib -lR installing to /usr/local/lib/R/site-library/Hmisc/libs ** R ** inst ** preparing package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded * DONE (Hmisc) * installing *source* package 'robust' ... ** package 'robust' successfully unpacked and MD5 sums checked ** libs gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c compatibility.c -o compatibility.o gfortran -fpic -g -O2 -fstack-protector-strong -c gamrob.f -o gamrob.o gfortran -fpic -g -O2 -fstack-protector-strong -c glmrob.f -o glmrob.o gfortran -fpic -g -O2 -fstack-protector-strong -c lmrobbi.f -o lmrobbi.o gfortran -fpic -g -O2 -fstack-protector-strong -c lmrobfs.f -o lmrobfs.o gfortran -fpic -g -O2 -fstack-protector-strong -c lmrobml.f -o lmrobml.o gfortran -fpic -g -O2 -fstack-protector-strong -c lmrobmm.f -o lmrobmm.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c mmprnt.c -o mmprnt.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c rb.c -o rb.o gfortran -fpic -g -O2 -fstack-protector-strong -c tdmean.f -o tdmean.o gfortran -fpic -g -O2 -fstack-protector-strong -c tmlfor.f -o tmlfor.o gfortran -fpic -g -O2 -fstack-protector-strong -c wblrob.f -o wblrob.o gcc -std=gnu99 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o robust.so compatibility.o gamrob.o glmrob.o lmrobbi.o lmrobfs.o lmrobml.o lmrobmm.o mmprnt.o rb.o tdmean.o tmlfor.o wblrob.o -llapack -lblas -lgfortran -lm -lquadmath -lgfortran -lm -lquadmath -L/usr/lib/R/lib -lR installing to /usr/local/lib/R/site-library/robust/libs ** R ** data ** inst ** preparing package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded * DONE (robust) * installing *source* package 'WGCNA' ... ** package 'WGCNA' successfully unpacked and MD5 sums checked ** libs gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DWITH_THREADS -I"/usr/local/lib/R/site-library/Rcpp/include" -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c corFunctions-common.c -o corFunctions-common.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DWITH_THREADS -I"/usr/local/lib/R/site-library/Rcpp/include" -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c corFunctions-unified.c -o corFunctions-unified.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DWITH_THREADS -I"/usr/local/lib/R/site-library/Rcpp/include" -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c networkFunctions.c -o networkFunctions.o g++ -I/usr/share/R/include -DNDEBUG -DWITH_THREADS -I"/usr/local/lib/R/site-library/Rcpp/include" -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c parallelQuantile.cc -o parallelQuantile.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DWITH_THREADS -I"/usr/local/lib/R/site-library/Rcpp/include" -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c pivot.c -o pivot.o g++ -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o WGCNA.so corFunctions-common.o corFunctions-unified.o networkFunctions.o parallelQuantile.o pivot.o -lpthread -L/usr/lib/R/lib -lR installing to /usr/local/lib/R/site-library/WGCNA/libs ** R ** data ** inst ** preparing package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded ========================================================================== * * Package WGCNA 1.61 loaded. * * Important note: It appears that your system supports multi-threading, * but it is not enabled within WGCNA in R. * To allow multi-threading within WGCNA with all available cores, use * * allowWGCNAThreads() * * within R. Use disableWGCNAThreads() to disable threading if necessary. * Alternatively, set the following environment variable on your system: * * ALLOW_WGCNA_THREADS= * * for example * * ALLOW_WGCNA_THREADS=2 * * To set the environment variable in linux bash shell, type * * export ALLOW_WGCNA_THREADS=2 * * before running R. Other operating systems or shells will * have a similar command to achieve the same aim. * ========================================================================== * DONE (WGCNA)  The downloaded source packages are in '/tmp/RtmpxNJ6sA/downloaded_packages' Downloading GitHub repo InouyeLab/NetRep@master from URL https://api.github.com/repos/InouyeLab/NetRep/zipball/master Installing NetRep trying URL 'https://cran.rstudio.com/src/contrib/RcppArmadillo_0.8.300.1.0.tar.gz' Content type 'application/x-gzip' length 1318517 bytes (1.3 MB) ================================================== downloaded 1.3 MB Installing RcppArmadillo '/usr/lib/R/bin/R' --no-site-file --no-environ --no-save --no-restore --quiet \ CMD INSTALL '/tmp/RtmpxNJ6sA/devtools73b21a59e/RcppArmadillo' \ --library='/usr/local/lib/R/site-library' --install-tests * installing *source* package 'RcppArmadillo' ... ** package 'RcppArmadillo' successfully unpacked and MD5 sums checked checking whether the C++ compiler works... yes checking for C++ compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C++ compiler... yes checking whether g++ accepts -g... yes checking how to run the C++ preprocessor... g++ -E checking whether we are using the GNU C++ compiler... (cached) yes checking whether g++ accepts -g... (cached) yes checking whether g++ version is sufficient... almost configure: WARNING: Compiler self-identifies as being compliant with GNUC extensions but is not g++. checking LAPACK_LIBS... system LAPACK found checking for macOS... not found as on Linux configure: creating ./config.status config.status: creating inst/include/RcppArmadilloConfigGenerated.h config.status: creating src/Makevars ** libs g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG -I"/usr/local/lib/R/site-library/Rcpp/include" -I../inst/include -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c RcppArmadillo.cpp -o RcppArmadillo.o g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG -I"/usr/local/lib/R/site-library/Rcpp/include" -I../inst/include -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG -I"/usr/local/lib/R/site-library/Rcpp/include" -I../inst/include -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c fastLm.cpp -o fastLm.o g++ -std=gnu++11 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o RcppArmadillo.so RcppArmadillo.o RcppExports.o fastLm.o -llapack -lblas -lgfortran -lm -lquadmath -L/usr/lib/R/lib -lR installing to /usr/local/lib/R/site-library/RcppArmadillo/libs ** R ** inst ** tests ** preparing package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded * DONE (RcppArmadillo) trying URL 'https://cran.rstudio.com/src/contrib/ref_0.99.tar.gz' Content type 'application/x-gzip' length 26310 bytes (25 KB) ================================================== downloaded 25 KB Installing ref '/usr/lib/R/bin/R' --no-site-file --no-environ --no-save --no-restore --quiet \ CMD INSTALL '/tmp/RtmpxNJ6sA/devtools737cc6413/ref' \ --library='/usr/local/lib/R/site-library' --install-tests  * installing *source* package 'ref' ... ** package 'ref' successfully unpacked and MD5 sums checked ** R ** exec ** inst ** preparing package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded * DONE (ref) trying URL 'https://cran.rstudio.com/src/contrib/RhpcBLASctl_0.15-148.tar.gz' Content type 'application/x-gzip' length 39916 bytes (38 KB) ================================================== downloaded 38 KB Installing RhpcBLASctl '/usr/lib/R/bin/R' --no-site-file --no-environ --no-save --no-restore --quiet \ CMD INSTALL '/tmp/RtmpxNJ6sA/devtools71d99036b/RhpcBLASctl' \ --library='/usr/local/lib/R/site-library' --install-tests  * installing *source* package 'RhpcBLASctl' ... ** package 'RhpcBLASctl' successfully unpacked and MD5 sums checked checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking how to run the C preprocessor... gcc -E checking for grep that handles long lines and -e... /bin/grep checking for egrep... /bin/grep -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking sys/sysctl.h usability... yes checking sys/sysctl.h presence... yes checking for sys/sysctl.h... yes checking for sysctl... yes checking for sysctlbyname... no checking sys/sysinfo.h usability... yes checking sys/sysinfo.h presence... yes checking for sys/sysinfo.h... yes checking for get_nprocs... yes configure: creating ./config.status config.status: creating src/Makevars config.status: creating src/config.h ** libs gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c blasctl.c -o blasctl.o blasctl.c: In function 'get_num_cores': blasctl.c:161:7: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets(pbuf,sizeof(pbuf),pfd); ^ blasctl.c:162:7: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets(cbuf,sizeof(cbuf),cfd); ^ gcc -std=gnu99 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o RhpcBLASctl.so blasctl.o -ldl -fopenmp -L/usr/lib/R/lib -lR installing to /usr/local/lib/R/site-library/RhpcBLASctl/libs ** R ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded * DONE (RhpcBLASctl) '/usr/lib/R/bin/R' --no-site-file --no-environ --no-save --no-restore --quiet \ CMD INSTALL '/tmp/RtmpxNJ6sA/devtools724f8df6b/InouyeLab-NetRep-956c821' \ --library='/usr/local/lib/R/site-library' --install-tests  * installing *source* package 'NetRep' ... ** libs g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/BH/include" -I"/usr/local/lib/R/site-library/RcppArmadillo/include" -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/BH/include" -I"/usr/local/lib/R/site-library/RcppArmadillo/include" -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c checkFinite.cpp -o checkFinite.o g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/BH/include" -I"/usr/local/lib/R/site-library/RcppArmadillo/include" -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c discProps.cpp -o discProps.o g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/BH/include" -I"/usr/local/lib/R/site-library/RcppArmadillo/include" -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c interrupt.cpp -o interrupt.o g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/BH/include" -I"/usr/local/lib/R/site-library/RcppArmadillo/include" -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c netStats.cpp -o netStats.o g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/BH/include" -I"/usr/local/lib/R/site-library/RcppArmadillo/include" -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c permutations.cpp -o permutations.o g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/BH/include" -I"/usr/local/lib/R/site-library/RcppArmadillo/include" -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c permutationsNoData.cpp -o permutationsNoData.o g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/BH/include" -I"/usr/local/lib/R/site-library/RcppArmadillo/include" -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c properties.cpp -o properties.o g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/BH/include" -I"/usr/local/lib/R/site-library/RcppArmadillo/include" -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c scale.cpp -o scale.o g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/BH/include" -I"/usr/local/lib/R/site-library/RcppArmadillo/include" -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c thread-utils.cpp -o thread-utils.o g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/BH/include" -I"/usr/local/lib/R/site-library/RcppArmadillo/include" -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c utils.cpp -o utils.o g++ -std=gnu++11 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o NetRep.so RcppExports.o checkFinite.o discProps.o interrupt.o netStats.o permutations.o permutationsNoData.o properties.o scale.o thread-utils.o utils.o -llapack -lblas -lgfortran -lm -lquadmath -L/usr/lib/R/lib -lR installing to /usr/local/lib/R/site-library/NetRep/libs ** R ** data ** inst ** tests ** preparing package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded * DONE (NetRep) Running analyze_mouse_wt.R... Loading required package: AnnotationDbi Loading required package: methods Loading required package: stats4 Loading required package: BiocGenerics Loading required package: parallel  Attaching package: 'BiocGenerics' The following objects are masked from 'package:parallel': clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, clusterExport, clusterMap, parApply, parCapply, parLapply, parLapplyLB, parRapply, parSapply, parSapplyLB The following objects are masked from 'package:stats': IQR, mad, sd, var, xtabs The following objects are masked from 'package:base': Filter, Find, Map, Position, Reduce, anyDuplicated, append, as.data.frame, cbind, colMeans, colSums, colnames, do.call, duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply, setdiff, sort, table, tapply, union, unique, unsplit, which, which.max, which.min Loading required package: Biobase Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. Loading required package: IRanges Loading required package: S4Vectors  Attaching package: 'S4Vectors' The following object is masked from 'package:base': expand.grid Loading required package: XML  Attaching package: 'gridExtra' The following object is masked from 'package:Biobase': combine The following object is masked from 'package:BiocGenerics': combine -- Attaching packages --------------------------------------- tidyverse 1.2.1 --  ggplot2 2.2.1 purrr 0.2.4 tibble 1.4.1 dplyr 0.7.4 tidyr 0.7.2 stringr 1.2.0 readr 1.1.1 forcats 0.2.0 -- Conflicts ------------------------------------------ tidyverse_conflicts() -- x ggplot2::Position() masks BiocGenerics::Position(), base::Position() x dplyr::collapse() masks IRanges::collapse() x dplyr::combine() masks gridExtra::combine(), Biobase::combine(), BiocGenerics::combine() x dplyr::desc() masks IRanges::desc() x tidyr::expand() masks S4Vectors::expand() x dplyr::filter() masks stats::filter() x dplyr::first() masks S4Vectors::first() x dplyr::lag() masks stats::lag() x purrr::reduce() masks IRanges::reduce() x dplyr::rename() masks S4Vectors::rename() x dplyr::select() masks AnnotationDbi::select() x dplyr::slice() masks IRanges::slice()  Attaching package: 'cowplot' The following object is masked from 'package:ggplot2': ggsave Loading required package: foreach  Attaching package: 'foreach' The following objects are masked from 'package:purrr': accumulate, when Loading required package: iterators Loading required package: rngtools Loading required package: pkgmaker Loading required package: registry  Attaching package: 'pkgmaker' The following object is masked from 'package:S4Vectors': new2 The following object is masked from 'package:base': isNamespaceLoaded  Attaching package: 'lubridate' The following object is masked from 'package:IRanges': %within% The following objects are masked from 'package:S4Vectors': second, second<- The following object is masked from 'package:base': date Joining, by = c("study", "tissue") # A tibble: 1 x 1 nPair 1 59 Joining, by = c("study", "ztGroup") Joining, by = c("study", "ztGroup") Joining, by = c("study", "ztGroup") Joining, by = c("study", "ztGroup") Joining, by = c("study", "ztGroup") Joining, by = c("study", "ztGroup") Running analyze_human.R... Loading required package: AnnotationDbi Loading required package: methods Loading required package: stats4 Loading required package: BiocGenerics Loading required package: parallel  Attaching package: 'BiocGenerics' The following objects are masked from 'package:parallel': clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, clusterExport, clusterMap, parApply, parCapply, parLapply, parLapplyLB, parRapply, parSapply, parSapplyLB The following objects are masked from 'package:stats': IQR, mad, sd, var, xtabs The following objects are masked from 'package:base': Filter, Find, Map, Position, Reduce, anyDuplicated, append, as.data.frame, cbind, colMeans, colSums, colnames, do.call, duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply, setdiff, sort, table, tapply, union, unique, unsplit, which, which.max, which.min Loading required package: Biobase Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. Loading required package: IRanges Loading required package: S4Vectors  Attaching package: 'S4Vectors' The following object is masked from 'package:base': expand.grid Loading required package: XML  Attaching package: 'gridExtra' The following object is masked from 'package:Biobase': combine The following object is masked from 'package:BiocGenerics': combine -- Attaching packages --------------------------------------- tidyverse 1.2.1 --  ggplot2 2.2.1 purrr 0.2.4 tibble 1.4.1 dplyr 0.7.4 tidyr 0.7.2 stringr 1.2.0 readr 1.1.1 forcats 0.2.0 -- Conflicts ------------------------------------------ tidyverse_conflicts() -- x ggplot2::Position() masks BiocGenerics::Position(), base::Position() x dplyr::collapse() masks IRanges::collapse() x dplyr::combine() masks gridExtra::combine(), Biobase::combine(), BiocGenerics::combine() x dplyr::desc() masks IRanges::desc() x tidyr::expand() masks S4Vectors::expand() x dplyr::filter() masks stats::filter() x dplyr::first() masks S4Vectors::first() x dplyr::lag() masks stats::lag() x purrr::reduce() masks IRanges::reduce() x dplyr::rename() masks S4Vectors::rename() x dplyr::select() masks AnnotationDbi::select() x dplyr::slice() masks IRanges::slice()  Attaching package: 'cowplot' The following object is masked from 'package:ggplot2': ggsave Loading required package: foreach  Attaching package: 'foreach' The following objects are masked from 'package:purrr': accumulate, when Loading required package: iterators Loading required package: rngtools Loading required package: pkgmaker Loading required package: registry  Attaching package: 'pkgmaker' The following object is masked from 'package:S4Vectors': new2 The following object is masked from 'package:base': isNamespaceLoaded  Attaching package: 'lubridate' The following object is masked from 'package:IRanges': %within% The following objects are masked from 'package:S4Vectors': second, second<- The following object is masked from 'package:base': date Joining, by = c("study", "tissue", "site") Warning message: In calcCcd(ref, ematList[[dfStudy$study[ii]]][, sampleNamesNow]) : 1 gene(s) in reference is/are not in the expression matrix. Warning message: Column `clock_time` has different attributes on LHS and RHS of join Found18batches Adjusting for0covariate(s) or covariate level(s) Standardizing Data across genes Fitting L/S model and finding priors Finding parametric adjustments Adjusting the Data Joining, by = "clock_time" Joining, by = "clock_time" Joining, by = "clock_time" Running analyze_mouse_wt_human.R... Loading required package: AnnotationDbi Loading required package: methods Loading required package: stats4 Loading required package: BiocGenerics Loading required package: parallel  Attaching package: 'BiocGenerics' The following objects are masked from 'package:parallel': clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, clusterExport, clusterMap, parApply, parCapply, parLapply, parLapplyLB, parRapply, parSapply, parSapplyLB The following objects are masked from 'package:stats': IQR, mad, sd, var, xtabs The following objects are masked from 'package:base': Filter, Find, Map, Position, Reduce, anyDuplicated, append, as.data.frame, cbind, colMeans, colSums, colnames, do.call, duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply, setdiff, sort, table, tapply, union, unique, unsplit, which, which.max, which.min Loading required package: Biobase Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. Loading required package: IRanges Loading required package: S4Vectors  Attaching package: 'S4Vectors' The following object is masked from 'package:base': expand.grid Loading required package: XML  Attaching package: 'gridExtra' The following object is masked from 'package:Biobase': combine The following object is masked from 'package:BiocGenerics': combine -- Attaching packages --------------------------------------- tidyverse 1.2.1 --  ggplot2 2.2.1 purrr 0.2.4 tibble 1.4.1 dplyr 0.7.4 tidyr 0.7.2 stringr 1.2.0 readr 1.1.1 forcats 0.2.0 -- Conflicts ------------------------------------------ tidyverse_conflicts() -- x ggplot2::Position() masks BiocGenerics::Position(), base::Position() x dplyr::collapse() masks IRanges::collapse() x dplyr::combine() masks gridExtra::combine(), Biobase::combine(), BiocGenerics::combine() x dplyr::desc() masks IRanges::desc() x tidyr::expand() masks S4Vectors::expand() x dplyr::filter() masks stats::filter() x dplyr::first() masks S4Vectors::first() x dplyr::lag() masks stats::lag() x purrr::reduce() masks IRanges::reduce() x dplyr::rename() masks S4Vectors::rename() x dplyr::select() masks AnnotationDbi::select() x dplyr::slice() masks IRanges::slice()  Attaching package: 'cowplot' The following object is masked from 'package:ggplot2': ggsave Loading required package: foreach  Attaching package: 'foreach' The following objects are masked from 'package:purrr': accumulate, when Loading required package: iterators Loading required package: rngtools Loading required package: pkgmaker Loading required package: registry  Attaching package: 'pkgmaker' The following object is masked from 'package:S4Vectors': new2 The following object is masked from 'package:base': isNamespaceLoaded  Attaching package: 'lubridate' The following object is masked from 'package:IRanges': %within% The following objects are masked from 'package:S4Vectors': second, second<- The following object is masked from 'package:base': date Warning message: The plyr::rename operation has created duplicates for the following name(s): (`size`) Running analyze_cancer.R... Loading required package: AnnotationDbi Loading required package: methods Loading required package: stats4 Loading required package: BiocGenerics Loading required package: parallel  Attaching package: 'BiocGenerics' The following objects are masked from 'package:parallel': clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, clusterExport, clusterMap, parApply, parCapply, parLapply, parLapplyLB, parRapply, parSapply, parSapplyLB The following objects are masked from 'package:stats': IQR, mad, sd, var, xtabs The following objects are masked from 'package:base': Filter, Find, Map, Position, Reduce, anyDuplicated, append, as.data.frame, cbind, colMeans, colSums, colnames, do.call, duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply, setdiff, sort, table, tapply, union, unique, unsplit, which, which.max, which.min Loading required package: Biobase Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. Loading required package: IRanges Loading required package: S4Vectors  Attaching package: 'S4Vectors' The following object is masked from 'package:base': expand.grid Loading required package: XML  Attaching package: 'gridExtra' The following object is masked from 'package:Biobase': combine The following object is masked from 'package:BiocGenerics': combine -- Attaching packages --------------------------------------- tidyverse 1.2.1 --  ggplot2 2.2.1 purrr 0.2.4 tibble 1.4.1 dplyr 0.7.4 tidyr 0.7.2 stringr 1.2.0 readr 1.1.1 forcats 0.2.0 -- Conflicts ------------------------------------------ tidyverse_conflicts() -- x ggplot2::Position() masks BiocGenerics::Position(), base::Position() x dplyr::collapse() masks IRanges::collapse() x dplyr::combine() masks gridExtra::combine(), Biobase::combine(), BiocGenerics::combine() x dplyr::desc() masks IRanges::desc() x tidyr::expand() masks S4Vectors::expand() x dplyr::filter() masks stats::filter() x dplyr::first() masks S4Vectors::first() x dplyr::lag() masks stats::lag() x purrr::reduce() masks IRanges::reduce() x dplyr::rename() masks S4Vectors::rename() x dplyr::select() masks AnnotationDbi::select() x dplyr::slice() masks IRanges::slice()  Attaching package: 'cowplot' The following object is masked from 'package:ggplot2': ggsave Loading required package: foreach  Attaching package: 'foreach' The following objects are masked from 'package:purrr': accumulate, when Loading required package: iterators Loading required package: rngtools Loading required package: pkgmaker Loading required package: registry  Attaching package: 'pkgmaker' The following object is masked from 'package:S4Vectors': new2 The following object is masked from 'package:base': isNamespaceLoaded  Attaching package: 'lubridate' The following object is masked from 'package:IRanges': %within% The following objects are masked from 'package:S4Vectors': second, second<- The following object is masked from 'package:base': date Joining, by = c("study", "condition", "category") Joining, by = c("study", "condition", "category") Joining, by = c("study", "condition", "category") Joining, by = c("study", "condition", "category") Joining, by = c("study", "condition", "category") Joining, by = c("study", "condition", "category") Joining, by = c("study", "condition", "category") Joining, by = c("study", "condition", "category") Joining, by = c("study", "condition", "category") Joining, by = c("study", "condition", "category") Joining, by = c("study", "condition", "category") Joining, by = c("study", "condition", "category") Joining, by = c("study", "condition", "category") Joining, by = c("study", "condition", "category") Joining, by = c("study", "condition", "category") Joining, by = c("study", "condition", "category") Joining, by = c("study", "condition", "category") Joining, by = c("study", "condition", "category") Joining, by = c("study", "condition", "category") Joining, by = c("study", "condition", "category") Joining, by = c("study", "condition", "category") Joining, by = c("study", "condition", "category") Joining, by = c("study", "condition", "category") Joining, by = c("study", "condition", "category") Joining, by = c("study", "condition", "category") Joining, by = c("study", "condition", "category") Joining, by = c("study", "condition", "category") Joining, by = c("study", "condition", "category") Joining, by = c("study", "condition", "category") Joining, by = c("study", "condition", "category") Joining, by = c("study", "condition", "category") Joining, by = c("study", "condition", "category") Joining, by = c("study", "condition", "category") Joining, by = c("study", "condition", "category") Joining, by = c("study", "condition", "category") Joining, by = c("study", "condition", "category") Joining, by = c("study", "condition", "category") Joining, by = c("study", "condition", "category") Joining, by = c("study", "condition", "category") Joining, by = c("study", "condition", "category") Joining, by = c("study", "category") Joining, by = c("study", "category") Joining, by = c("study", "category") Joining, by = c("study", "category") Joining, by = c("study", "category") Joining, by = c("study", "category") Joining, by = c("study", "category") Joining, by = c("study", "category") Joining, by = c("study", "category") Joining, by = c("study", "category") Joining, by = c("study", "category") Joining, by = c("study", "category") Joining, by = c("study", "category") Joining, by = c("study", "category") Joining, by = c("study", "category") Joining, by = c("study", "category") Joining, by = c("study", "category") Joining, by = c("study", "category") Joining, by = c("study", "category") Joining, by = c("study", "category") Warning messages: 1: Removed 2 rows containing missing values (geom_point). 2: Removed 2 rows containing missing values (geom_point). Running analyze_cancer_supp.R... Loading required package: AnnotationDbi Loading required package: methods Loading required package: stats4 Loading required package: BiocGenerics Loading required package: parallel  Attaching package: 'BiocGenerics' The following objects are masked from 'package:parallel': clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, clusterExport, clusterMap, parApply, parCapply, parLapply, parLapplyLB, parRapply, parSapply, parSapplyLB The following objects are masked from 'package:stats': IQR, mad, sd, var, xtabs The following objects are masked from 'package:base': Filter, Find, Map, Position, Reduce, anyDuplicated, append, as.data.frame, cbind, colMeans, colSums, colnames, do.call, duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply, setdiff, sort, table, tapply, union, unique, unsplit, which, which.max, which.min Loading required package: Biobase Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. Loading required package: IRanges Loading required package: S4Vectors  Attaching package: 'S4Vectors' The following object is masked from 'package:base': expand.grid Loading required package: XML  Attaching package: 'gridExtra' The following object is masked from 'package:Biobase': combine The following object is masked from 'package:BiocGenerics': combine -- Attaching packages --------------------------------------- tidyverse 1.2.1 --  ggplot2 2.2.1 purrr 0.2.4 tibble 1.4.1 dplyr 0.7.4 tidyr 0.7.2 stringr 1.2.0 readr 1.1.1 forcats 0.2.0 -- Conflicts ------------------------------------------ tidyverse_conflicts() -- x ggplot2::Position() masks BiocGenerics::Position(), base::Position() x dplyr::collapse() masks IRanges::collapse() x dplyr::combine() masks gridExtra::combine(), Biobase::combine(), BiocGenerics::combine() x dplyr::desc() masks IRanges::desc() x tidyr::expand() masks S4Vectors::expand() x dplyr::filter() masks stats::filter() x dplyr::first() masks S4Vectors::first() x dplyr::lag() masks stats::lag() x purrr::reduce() masks IRanges::reduce() x dplyr::rename() masks S4Vectors::rename() x dplyr::select() masks AnnotationDbi::select() x dplyr::slice() masks IRanges::slice()  Attaching package: 'cowplot' The following object is masked from 'package:ggplot2': ggsave Loading required package: foreach  Attaching package: 'foreach' The following objects are masked from 'package:purrr': accumulate, when Loading required package: iterators Loading required package: rngtools Loading required package: pkgmaker Loading required package: registry  Attaching package: 'pkgmaker' The following object is masked from 'package:S4Vectors': new2 The following object is masked from 'package:base': isNamespaceLoaded  Attaching package: 'lubridate' The following object is masked from 'package:IRanges': %within% The following objects are masked from 'package:S4Vectors': second, second<- The following object is masked from 'package:base': date Joining, by = c("cancerType", "condition") Joining, by = "cancerType" Joining, by = c("cancerType", "condition") Joining, by = "cancerType" Joining, by = c("cancerType", "condition") Joining, by = "cancerType" Joining, by = c("cancerType", "condition") Joining, by = "cancerType" Joining, by = c("cancerType", "condition") Joining, by = "cancerType" Joining, by = c("cancerType", "condition") Joining, by = "cancerType" Joining, by = c("cancerType", "condition") Joining, by = "cancerType" Joining, by = c("cancerType", "condition") Joining, by = "cancerType" Joining, by = c("cancerType", "condition") Joining, by = "cancerType" Joining, by = c("cancerType", "condition") Joining, by = "cancerType" Joining, by = c("cancerType", "condition") Joining, by = "cancerType" Running analyze_mouse_mutant.R... Loading required package: AnnotationDbi Loading required package: methods Loading required package: stats4 Loading required package: BiocGenerics Loading required package: parallel  Attaching package: 'BiocGenerics' The following objects are masked from 'package:parallel': clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, clusterExport, clusterMap, parApply, parCapply, parLapply, parLapplyLB, parRapply, parSapply, parSapplyLB The following objects are masked from 'package:stats': IQR, mad, sd, var, xtabs The following objects are masked from 'package:base': Filter, Find, Map, Position, Reduce, anyDuplicated, append, as.data.frame, cbind, colMeans, colSums, colnames, do.call, duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply, setdiff, sort, table, tapply, union, unique, unsplit, which, which.max, which.min Loading required package: Biobase Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. Loading required package: IRanges Loading required package: S4Vectors  Attaching package: 'S4Vectors' The following object is masked from 'package:base': expand.grid Loading required package: XML  Attaching package: 'gridExtra' The following object is masked from 'package:Biobase': combine The following object is masked from 'package:BiocGenerics': combine -- Attaching packages --------------------------------------- tidyverse 1.2.1 --  ggplot2 2.2.1 purrr 0.2.4 tibble 1.4.1 dplyr 0.7.4 tidyr 0.7.2 stringr 1.2.0 readr 1.1.1 forcats 0.2.0 -- Conflicts ------------------------------------------ tidyverse_conflicts() -- x ggplot2::Position() masks BiocGenerics::Position(), base::Position() x dplyr::collapse() masks IRanges::collapse() x dplyr::combine() masks gridExtra::combine(), Biobase::combine(), BiocGenerics::combine() x dplyr::desc() masks IRanges::desc() x tidyr::expand() masks S4Vectors::expand() x dplyr::filter() masks stats::filter() x dplyr::first() masks S4Vectors::first() x dplyr::lag() masks stats::lag() x purrr::reduce() masks IRanges::reduce() x dplyr::rename() masks S4Vectors::rename() x dplyr::select() masks AnnotationDbi::select() x dplyr::slice() masks IRanges::slice()  Attaching package: 'cowplot' The following object is masked from 'package:ggplot2': ggsave Loading required package: foreach  Attaching package: 'foreach' The following objects are masked from 'package:purrr': accumulate, when Loading required package: iterators Loading required package: rngtools Loading required package: pkgmaker Loading required package: registry  Attaching package: 'pkgmaker' The following object is masked from 'package:S4Vectors': new2 The following object is masked from 'package:base': isNamespaceLoaded  Attaching package: 'lubridate' The following object is masked from 'package:IRanges': %within% The following objects are masked from 'package:S4Vectors': second, second<- The following object is masked from 'package:base': date Joining, by = c("study", "condition", "label") Joining, by = c("study", "condition", "label") Joining, by = c("study", "condition", "label") Joining, by = c("study", "condition", "label") Joining, by = c("study", "condition", "label") Joining, by = c("study", "condition", "label") Joining, by = c("study", "condition", "label") Joining, by = c("study", "condition", "label") Joining, by = c("study", "condition", "label") Joining, by = c("study", "condition", "label") Joining, by = c("study", "condition", "label") Joining, by = c("study", "condition", "label") Joining, by = c("study", "condition", "label") Joining, by = c("study", "condition", "label") Joining, by = c("study", "label") Joining, by = c("study", "label") Joining, by = c("study", "label") Joining, by = c("study", "label") Joining, by = c("study", "label") Joining, by = c("study", "label") Joining, by = c("study", "label") Warning message: Removed 3 rows containing missing values (geom_point). Joining, by = c("category", "study") Joining, by = c("category", "study") Joining, by = c("category", "study") Joining, by = c("category", "study") Joining, by = c("category", "study") Joining, by = c("category", "study") Joining, by = c("category", "study") Joining, by = c("category", "study") Joining, by = c("category", "study") Joining, by = c("category", "study") Joining, by = c("category", "study") Joining, by = c("category", "study") Joining, by = c("category", "study") Joining, by = c("category", "study") Joining, by = c("category", "study") Joining, by = c("category", "study") Joining, by = c("category", "study") Joining, by = c("category", "study") Joining, by = c("category", "study") Joining, by = c("category", "study") Joining, by = "study" Joining, by = "study" Joining, by = "study" Joining, by = "study" Joining, by = "study" Joining, by = "study" Joining, by = "study" Running analyze_human_lung.R... Loading required package: AnnotationDbi Loading required package: methods Loading required package: stats4 Loading required package: BiocGenerics Loading required package: parallel  Attaching package: 'BiocGenerics' The following objects are masked from 'package:parallel': clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, clusterExport, clusterMap, parApply, parCapply, parLapply, parLapplyLB, parRapply, parSapply, parSapplyLB The following objects are masked from 'package:stats': IQR, mad, sd, var, xtabs The following objects are masked from 'package:base': Filter, Find, Map, Position, Reduce, anyDuplicated, append, as.data.frame, cbind, colMeans, colSums, colnames, do.call, duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply, setdiff, sort, table, tapply, union, unique, unsplit, which, which.max, which.min Loading required package: Biobase Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. Loading required package: IRanges Loading required package: S4Vectors  Attaching package: 'S4Vectors' The following object is masked from 'package:base': expand.grid Loading required package: XML  Attaching package: 'gridExtra' The following object is masked from 'package:Biobase': combine The following object is masked from 'package:BiocGenerics': combine -- Attaching packages --------------------------------------- tidyverse 1.2.1 --  ggplot2 2.2.1 purrr 0.2.4 tibble 1.4.1 dplyr 0.7.4 tidyr 0.7.2 stringr 1.2.0 readr 1.1.1 forcats 0.2.0 -- Conflicts ------------------------------------------ tidyverse_conflicts() -- x ggplot2::Position() masks BiocGenerics::Position(), base::Position() x dplyr::collapse() masks IRanges::collapse() x dplyr::combine() masks gridExtra::combine(), Biobase::combine(), BiocGenerics::combine() x dplyr::desc() masks IRanges::desc() x tidyr::expand() masks S4Vectors::expand() x dplyr::filter() masks stats::filter() x dplyr::first() masks S4Vectors::first() x dplyr::lag() masks stats::lag() x purrr::reduce() masks IRanges::reduce() x dplyr::rename() masks S4Vectors::rename() x dplyr::select() masks AnnotationDbi::select() x dplyr::slice() masks IRanges::slice()  Attaching package: 'cowplot' The following object is masked from 'package:ggplot2': ggsave Loading required package: foreach  Attaching package: 'foreach' The following objects are masked from 'package:purrr': accumulate, when Loading required package: iterators Loading required package: rngtools Loading required package: pkgmaker Loading required package: registry  Attaching package: 'pkgmaker' The following object is masked from 'package:S4Vectors': new2 The following object is masked from 'package:base': isNamespaceLoaded  Attaching package: 'lubridate' The following object is masked from 'package:IRanges': %within% The following objects are masked from 'package:S4Vectors': second, second<- The following object is masked from 'package:base': date Found2batches Adjusting for0covariate(s) or covariate level(s) Standardizing Data across genes Fitting L/S model and finding priors Finding parametric adjustments Adjusting the Data  null device 1 Joining, by = c("study", "module", "statName")  ---> 147245aa110d Removing intermediate container 2333050b8389 Successfully built 147245aa110d Successfully tagged circadian_clock_cancer:latest