[ Started: 2023-10-03 07:41:50 CEST ] [ CARNIVAL v2.7.2 for BioC-3.16 from https://github.com/saezlab/CARNIVAL@master ] [1] "Libraries: " "/home/omnipath/local/R/4.2-3.16" [3] "/home/omnipath/local/R/4.2" "/usr/lib/R/library" trying URL 'https://cran.uni-muenster.de/src/contrib/curl_5.1.0.tar.gz' Content type 'application/x-gzip' length 714157 bytes (697 KB) ================================================== downloaded 697 KB trying URL 'https://cran.uni-muenster.de/src/contrib/plyr_1.8.9.tar.gz' Content type 'application/x-gzip' length 401488 bytes (392 KB) ================================================== downloaded 392 KB trying URL 'https://cran.uni-muenster.de/src/contrib/sp_2.1-0.tar.gz' Content type 'application/x-gzip' length 1244682 bytes (1.2 MB) ================================================== downloaded 1.2 MB trying URL 'https://cran.uni-muenster.de/src/contrib/vroom_1.6.4.tar.gz' Content type 'application/x-gzip' length 750198 bytes (732 KB) ================================================== downloaded 732 KB * installing *source* package ‘curl’ ... ** package ‘curl’ successfully unpacked and MD5 sums checked ** using staged installation Found pkg-config cflags and libs! Using PKG_CFLAGS=-I/usr/local/include Using PKG_LIBS=-L/usr/local/lib -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 options.o reflist.o split.o ssl.o typechecking.o utils.o version.o winidn.o writer.o gcc -I"/usr/share/R/include" -DNDEBUG -I/usr/local/include -DSTRICT_R_HEADERS -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-LhKvHL/r-base-4.2.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c callbacks.c -o callbacks.o gcc -I"/usr/share/R/include" -DNDEBUG -I/usr/local/include -DSTRICT_R_HEADERS -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-LhKvHL/r-base-4.2.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c curl.c -o curl.o gcc -I"/usr/share/R/include" -DNDEBUG -I/usr/local/include -DSTRICT_R_HEADERS -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-LhKvHL/r-base-4.2.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c download.c -o download.o gcc -I"/usr/share/R/include" -DNDEBUG -I/usr/local/include -DSTRICT_R_HEADERS -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-LhKvHL/r-base-4.2.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c escape.c -o escape.o gcc -I"/usr/share/R/include" -DNDEBUG -I/usr/local/include -DSTRICT_R_HEADERS -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-LhKvHL/r-base-4.2.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c fetch.c -o fetch.o gcc -I"/usr/share/R/include" -DNDEBUG -I/usr/local/include -DSTRICT_R_HEADERS -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-LhKvHL/r-base-4.2.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c form.c -o form.o gcc -I"/usr/share/R/include" -DNDEBUG -I/usr/local/include -DSTRICT_R_HEADERS -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-LhKvHL/r-base-4.2.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c getdate.c -o getdate.o gcc -I"/usr/share/R/include" -DNDEBUG -I/usr/local/include -DSTRICT_R_HEADERS -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-LhKvHL/r-base-4.2.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c handle.c -o handle.o gcc -I"/usr/share/R/include" -DNDEBUG -I/usr/local/include -DSTRICT_R_HEADERS -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-LhKvHL/r-base-4.2.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c ieproxy.c -o ieproxy.o gcc -I"/usr/share/R/include" -DNDEBUG -I/usr/local/include -DSTRICT_R_HEADERS -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-LhKvHL/r-base-4.2.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c init.c -o init.o gcc -I"/usr/share/R/include" -DNDEBUG -I/usr/local/include -DSTRICT_R_HEADERS -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-LhKvHL/r-base-4.2.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c interrupt.c -o interrupt.o gcc -I"/usr/share/R/include" -DNDEBUG -I/usr/local/include -DSTRICT_R_HEADERS -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-LhKvHL/r-base-4.2.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c multi.c -o multi.o gcc -I"/usr/share/R/include" -DNDEBUG -I/usr/local/include -DSTRICT_R_HEADERS -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-LhKvHL/r-base-4.2.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c nslookup.c -o nslookup.o gcc -I"/usr/share/R/include" -DNDEBUG -I/usr/local/include -DSTRICT_R_HEADERS -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-LhKvHL/r-base-4.2.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c options.c -o options.o gcc -I"/usr/share/R/include" -DNDEBUG -I/usr/local/include -DSTRICT_R_HEADERS -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-LhKvHL/r-base-4.2.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c reflist.c -o reflist.o gcc -I"/usr/share/R/include" -DNDEBUG -I/usr/local/include -DSTRICT_R_HEADERS -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-LhKvHL/r-base-4.2.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c split.c -o split.o gcc -I"/usr/share/R/include" -DNDEBUG -I/usr/local/include -DSTRICT_R_HEADERS -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-LhKvHL/r-base-4.2.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c ssl.c -o ssl.o gcc -I"/usr/share/R/include" -DNDEBUG -I/usr/local/include -DSTRICT_R_HEADERS -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-LhKvHL/r-base-4.2.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c typechecking.c -o typechecking.o gcc -I"/usr/share/R/include" -DNDEBUG -I/usr/local/include -DSTRICT_R_HEADERS -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-LhKvHL/r-base-4.2.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c utils.c -o utils.o gcc -I"/usr/share/R/include" -DNDEBUG -I/usr/local/include -DSTRICT_R_HEADERS -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-LhKvHL/r-base-4.2.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c version.c -o version.o gcc -I"/usr/share/R/include" -DNDEBUG -I/usr/local/include -DSTRICT_R_HEADERS -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-LhKvHL/r-base-4.2.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c winidn.c -o winidn.o gcc -I"/usr/share/R/include" -DNDEBUG -I/usr/local/include -DSTRICT_R_HEADERS -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-LhKvHL/r-base-4.2.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c writer.c -o writer.o gcc -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -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 options.o reflist.o split.o ssl.o typechecking.o utils.o version.o winidn.o writer.o -L/usr/local/lib -lcurl -L/usr/lib/R/lib -lR installing to /home/omnipath/local/R/4.2-3.16/00LOCK-curl/00new/curl/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 from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (curl) * installing *source* package ‘plyr’ ... ** package ‘plyr’ successfully unpacked and MD5 sums checked ** using staged installation ** libs g++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.2-3.16/Rcpp/include' -fpic -g -O2 -ffile-prefix-map=/build/r-base-LhKvHL/r-base-4.2.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c RcppExports.cpp -o RcppExports.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.2-3.16/Rcpp/include' -fpic -g -O2 -ffile-prefix-map=/build/r-base-LhKvHL/r-base-4.2.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c loop_apply.c -o loop_apply.o g++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.2-3.16/Rcpp/include' -fpic -g -O2 -ffile-prefix-map=/build/r-base-LhKvHL/r-base-4.2.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c split-numeric.cpp -o split-numeric.o g++ -std=gnu++14 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -o plyr.so RcppExports.o loop_apply.o split-numeric.o -L/usr/lib/R/lib -lR installing to /home/omnipath/local/R/4.2-3.16/00LOCK-plyr/00new/plyr/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 from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (plyr) * installing *source* package ‘sp’ ... ** package ‘sp’ successfully unpacked and MD5 sums checked ** using staged installation ** libs gcc -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -ffile-prefix-map=/build/r-base-LhKvHL/r-base-4.2.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c Rcentroid.c -o Rcentroid.o gcc -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -ffile-prefix-map=/build/r-base-LhKvHL/r-base-4.2.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c gcdist.c -o gcdist.o gcc -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -ffile-prefix-map=/build/r-base-LhKvHL/r-base-4.2.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c init.c -o init.o gcc -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -ffile-prefix-map=/build/r-base-LhKvHL/r-base-4.2.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c pip.c -o pip.o gcc -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -ffile-prefix-map=/build/r-base-LhKvHL/r-base-4.2.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c pip2.c -o pip2.o gcc -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -ffile-prefix-map=/build/r-base-LhKvHL/r-base-4.2.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c sp_xports.c -o sp_xports.o gcc -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -ffile-prefix-map=/build/r-base-LhKvHL/r-base-4.2.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c surfaceArea.c -o surfaceArea.o gcc -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -ffile-prefix-map=/build/r-base-LhKvHL/r-base-4.2.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c zerodist.c -o zerodist.o gcc -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -o sp.so Rcentroid.o gcdist.o init.o pip.o pip2.o sp_xports.o surfaceArea.o zerodist.o -L/usr/lib/R/lib -lR installing to /home/omnipath/local/R/4.2-3.16/00LOCK-sp/00new/sp/libs ** R ** data ** demo ** 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 from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (sp) * installing *source* package ‘vroom’ ... ** package ‘vroom’ successfully unpacked and MD5 sums checked ** using staged installation ** libs g++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG -Imio/include -DWIN32_LEAN_AND_MEAN -Ispdlog/include -DFMT_HEADER_ONLY -I'/home/omnipath/local/R/4.2-3.16/cpp11/include' -I'/home/omnipath/local/R/4.2-3.16/progress/include' -I'/home/omnipath/local/R/4.2-3.16/tzdb/include' -fpic -g -O2 -ffile-prefix-map=/build/r-base-LhKvHL/r-base-4.2.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c Iconv.cpp -o Iconv.o g++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG -Imio/include -DWIN32_LEAN_AND_MEAN -Ispdlog/include -DFMT_HEADER_ONLY -I'/home/omnipath/local/R/4.2-3.16/cpp11/include' -I'/home/omnipath/local/R/4.2-3.16/progress/include' -I'/home/omnipath/local/R/4.2-3.16/tzdb/include' -fpic -g -O2 -ffile-prefix-map=/build/r-base-LhKvHL/r-base-4.2.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c LocaleInfo.cpp -o LocaleInfo.o g++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG -Imio/include -DWIN32_LEAN_AND_MEAN -Ispdlog/include -DFMT_HEADER_ONLY -I'/home/omnipath/local/R/4.2-3.16/cpp11/include' -I'/home/omnipath/local/R/4.2-3.16/progress/include' -I'/home/omnipath/local/R/4.2-3.16/tzdb/include' -fpic -g -O2 -ffile-prefix-map=/build/r-base-LhKvHL/r-base-4.2.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c altrep.cc -o altrep.o g++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG -Imio/include -DWIN32_LEAN_AND_MEAN -Ispdlog/include -DFMT_HEADER_ONLY -I'/home/omnipath/local/R/4.2-3.16/cpp11/include' -I'/home/omnipath/local/R/4.2-3.16/progress/include' -I'/home/omnipath/local/R/4.2-3.16/tzdb/include' -fpic -g -O2 -ffile-prefix-map=/build/r-base-LhKvHL/r-base-4.2.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c cpp11.cpp -o cpp11.o g++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG -Imio/include -DWIN32_LEAN_AND_MEAN -Ispdlog/include -DFMT_HEADER_ONLY -I'/home/omnipath/local/R/4.2-3.16/cpp11/include' -I'/home/omnipath/local/R/4.2-3.16/progress/include' -I'/home/omnipath/local/R/4.2-3.16/tzdb/include' -fpic -g -O2 -ffile-prefix-map=/build/r-base-LhKvHL/r-base-4.2.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c delimited_index.cc -o delimited_index.o g++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG -Imio/include -DWIN32_LEAN_AND_MEAN -Ispdlog/include -DFMT_HEADER_ONLY -I'/home/omnipath/local/R/4.2-3.16/cpp11/include' -I'/home/omnipath/local/R/4.2-3.16/progress/include' -I'/home/omnipath/local/R/4.2-3.16/tzdb/include' -fpic -g -O2 -ffile-prefix-map=/build/r-base-LhKvHL/r-base-4.2.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c delimited_index_connection.cc -o delimited_index_connection.o g++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG -Imio/include -DWIN32_LEAN_AND_MEAN -Ispdlog/include -DFMT_HEADER_ONLY -I'/home/omnipath/local/R/4.2-3.16/cpp11/include' -I'/home/omnipath/local/R/4.2-3.16/progress/include' -I'/home/omnipath/local/R/4.2-3.16/tzdb/include' -fpic -g -O2 -ffile-prefix-map=/build/r-base-LhKvHL/r-base-4.2.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c fixed_width_index_connection.cc -o fixed_width_index_connection.o g++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG -Imio/include -DWIN32_LEAN_AND_MEAN -Ispdlog/include -DFMT_HEADER_ONLY -I'/home/omnipath/local/R/4.2-3.16/cpp11/include' -I'/home/omnipath/local/R/4.2-3.16/progress/include' -I'/home/omnipath/local/R/4.2-3.16/tzdb/include' -fpic -g -O2 -ffile-prefix-map=/build/r-base-LhKvHL/r-base-4.2.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c gen.cc -o gen.o gcc -I"/usr/share/R/include" -DNDEBUG -Imio/include -DWIN32_LEAN_AND_MEAN -Ispdlog/include -DFMT_HEADER_ONLY -I'/home/omnipath/local/R/4.2-3.16/cpp11/include' -I'/home/omnipath/local/R/4.2-3.16/progress/include' -I'/home/omnipath/local/R/4.2-3.16/tzdb/include' -fpic -g -O2 -ffile-prefix-map=/build/r-base-LhKvHL/r-base-4.2.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c grisu3.c -o grisu3.o g++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG -Imio/include -DWIN32_LEAN_AND_MEAN -Ispdlog/include -DFMT_HEADER_ONLY -I'/home/omnipath/local/R/4.2-3.16/cpp11/include' -I'/home/omnipath/local/R/4.2-3.16/progress/include' -I'/home/omnipath/local/R/4.2-3.16/tzdb/include' -fpic -g -O2 -ffile-prefix-map=/build/r-base-LhKvHL/r-base-4.2.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c guess_type.cc -o guess_type.o g++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG -Imio/include -DWIN32_LEAN_AND_MEAN -Ispdlog/include -DFMT_HEADER_ONLY -I'/home/omnipath/local/R/4.2-3.16/cpp11/include' -I'/home/omnipath/local/R/4.2-3.16/progress/include' -I'/home/omnipath/local/R/4.2-3.16/tzdb/include' -fpic -g -O2 -ffile-prefix-map=/build/r-base-LhKvHL/r-base-4.2.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c iconv_file.cc -o iconv_file.o g++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG -Imio/include -DWIN32_LEAN_AND_MEAN -Ispdlog/include -DFMT_HEADER_ONLY -I'/home/omnipath/local/R/4.2-3.16/cpp11/include' -I'/home/omnipath/local/R/4.2-3.16/progress/include' -I'/home/omnipath/local/R/4.2-3.16/tzdb/include' -fpic -g -O2 -ffile-prefix-map=/build/r-base-LhKvHL/r-base-4.2.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c index_collection.cc -o index_collection.o g++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG -Imio/include -DWIN32_LEAN_AND_MEAN -Ispdlog/include -DFMT_HEADER_ONLY -I'/home/omnipath/local/R/4.2-3.16/cpp11/include' -I'/home/omnipath/local/R/4.2-3.16/progress/include' -I'/home/omnipath/local/R/4.2-3.16/tzdb/include' -fpic -g -O2 -ffile-prefix-map=/build/r-base-LhKvHL/r-base-4.2.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c vroom.cc -o vroom.o g++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG -Imio/include -DWIN32_LEAN_AND_MEAN -Ispdlog/include -DFMT_HEADER_ONLY -I'/home/omnipath/local/R/4.2-3.16/cpp11/include' -I'/home/omnipath/local/R/4.2-3.16/progress/include' -I'/home/omnipath/local/R/4.2-3.16/tzdb/include' -fpic -g -O2 -ffile-prefix-map=/build/r-base-LhKvHL/r-base-4.2.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c vroom_big_int.cc -o vroom_big_int.o g++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG -Imio/include -DWIN32_LEAN_AND_MEAN -Ispdlog/include -DFMT_HEADER_ONLY -I'/home/omnipath/local/R/4.2-3.16/cpp11/include' -I'/home/omnipath/local/R/4.2-3.16/progress/include' -I'/home/omnipath/local/R/4.2-3.16/tzdb/include' -fpic -g -O2 -ffile-prefix-map=/build/r-base-LhKvHL/r-base-4.2.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c vroom_chr.cc -o vroom_chr.o g++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG -Imio/include -DWIN32_LEAN_AND_MEAN -Ispdlog/include -DFMT_HEADER_ONLY -I'/home/omnipath/local/R/4.2-3.16/cpp11/include' -I'/home/omnipath/local/R/4.2-3.16/progress/include' -I'/home/omnipath/local/R/4.2-3.16/tzdb/include' -fpic -g -O2 -ffile-prefix-map=/build/r-base-LhKvHL/r-base-4.2.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c vroom_date.cc -o vroom_date.o g++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG -Imio/include -DWIN32_LEAN_AND_MEAN -Ispdlog/include -DFMT_HEADER_ONLY -I'/home/omnipath/local/R/4.2-3.16/cpp11/include' -I'/home/omnipath/local/R/4.2-3.16/progress/include' -I'/home/omnipath/local/R/4.2-3.16/tzdb/include' -fpic -g -O2 -ffile-prefix-map=/build/r-base-LhKvHL/r-base-4.2.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c vroom_dbl.cc -o vroom_dbl.o g++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG -Imio/include -DWIN32_LEAN_AND_MEAN -Ispdlog/include -DFMT_HEADER_ONLY -I'/home/omnipath/local/R/4.2-3.16/cpp11/include' -I'/home/omnipath/local/R/4.2-3.16/progress/include' -I'/home/omnipath/local/R/4.2-3.16/tzdb/include' -fpic -g -O2 -ffile-prefix-map=/build/r-base-LhKvHL/r-base-4.2.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c vroom_dttm.cc -o vroom_dttm.o g++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG -Imio/include -DWIN32_LEAN_AND_MEAN -Ispdlog/include -DFMT_HEADER_ONLY -I'/home/omnipath/local/R/4.2-3.16/cpp11/include' -I'/home/omnipath/local/R/4.2-3.16/progress/include' -I'/home/omnipath/local/R/4.2-3.16/tzdb/include' -fpic -g -O2 -ffile-prefix-map=/build/r-base-LhKvHL/r-base-4.2.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c vroom_errors.cpp -o vroom_errors.o g++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG -Imio/include -DWIN32_LEAN_AND_MEAN -Ispdlog/include -DFMT_HEADER_ONLY -I'/home/omnipath/local/R/4.2-3.16/cpp11/include' -I'/home/omnipath/local/R/4.2-3.16/progress/include' -I'/home/omnipath/local/R/4.2-3.16/tzdb/include' -fpic -g -O2 -ffile-prefix-map=/build/r-base-LhKvHL/r-base-4.2.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c vroom_fct.cc -o vroom_fct.o g++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG -Imio/include -DWIN32_LEAN_AND_MEAN -Ispdlog/include -DFMT_HEADER_ONLY -I'/home/omnipath/local/R/4.2-3.16/cpp11/include' -I'/home/omnipath/local/R/4.2-3.16/progress/include' -I'/home/omnipath/local/R/4.2-3.16/tzdb/include' -fpic -g -O2 -ffile-prefix-map=/build/r-base-LhKvHL/r-base-4.2.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c vroom_fwf.cc -o vroom_fwf.o g++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG -Imio/include -DWIN32_LEAN_AND_MEAN -Ispdlog/include -DFMT_HEADER_ONLY -I'/home/omnipath/local/R/4.2-3.16/cpp11/include' -I'/home/omnipath/local/R/4.2-3.16/progress/include' -I'/home/omnipath/local/R/4.2-3.16/tzdb/include' -fpic -g -O2 -ffile-prefix-map=/build/r-base-LhKvHL/r-base-4.2.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c vroom_int.cc -o vroom_int.o g++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG -Imio/include -DWIN32_LEAN_AND_MEAN -Ispdlog/include -DFMT_HEADER_ONLY -I'/home/omnipath/local/R/4.2-3.16/cpp11/include' -I'/home/omnipath/local/R/4.2-3.16/progress/include' -I'/home/omnipath/local/R/4.2-3.16/tzdb/include' -fpic -g -O2 -ffile-prefix-map=/build/r-base-LhKvHL/r-base-4.2.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c vroom_num.cc -o vroom_num.o g++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG -Imio/include -DWIN32_LEAN_AND_MEAN -Ispdlog/include -DFMT_HEADER_ONLY -I'/home/omnipath/local/R/4.2-3.16/cpp11/include' -I'/home/omnipath/local/R/4.2-3.16/progress/include' -I'/home/omnipath/local/R/4.2-3.16/tzdb/include' -fpic -g -O2 -ffile-prefix-map=/build/r-base-LhKvHL/r-base-4.2.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c vroom_rle.cc -o vroom_rle.o g++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG -Imio/include -DWIN32_LEAN_AND_MEAN -Ispdlog/include -DFMT_HEADER_ONLY -I'/home/omnipath/local/R/4.2-3.16/cpp11/include' -I'/home/omnipath/local/R/4.2-3.16/progress/include' -I'/home/omnipath/local/R/4.2-3.16/tzdb/include' -fpic -g -O2 -ffile-prefix-map=/build/r-base-LhKvHL/r-base-4.2.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c vroom_time.cc -o vroom_time.o g++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG -Imio/include -DWIN32_LEAN_AND_MEAN -Ispdlog/include -DFMT_HEADER_ONLY -I'/home/omnipath/local/R/4.2-3.16/cpp11/include' -I'/home/omnipath/local/R/4.2-3.16/progress/include' -I'/home/omnipath/local/R/4.2-3.16/tzdb/include' -fpic -g -O2 -ffile-prefix-map=/build/r-base-LhKvHL/r-base-4.2.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c vroom_write.cc -o vroom_write.o g++ -std=gnu++14 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -o vroom.so Iconv.o LocaleInfo.o altrep.o cpp11.o delimited_index.o delimited_index_connection.o fixed_width_index_connection.o gen.o grisu3.o guess_type.o iconv_file.o index_collection.o vroom.o vroom_big_int.o vroom_chr.o vroom_date.o vroom_dbl.o vroom_dttm.o vroom_errors.o vroom_fct.o vroom_fwf.o vroom_int.o vroom_num.o vroom_rle.o vroom_time.o vroom_write.o -L/usr/lib/R/lib -lR installing to /home/omnipath/local/R/4.2-3.16/00LOCK-vroom/00new/vroom/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (vroom) The downloaded source packages are in ‘/tmp/RtmpcMvvNN/downloaded_packages’ Bioconductor version '3.16' is out-of-date; the current release version '3.17' is available with R version '4.3'; see https://bioconductor.org/install 'getOption("repos")' replaces Bioconductor standard repositories, see 'help("repositories", package = "BiocManager")' for details. Replacement repositories: CRAN: https://cloud.r-project.org Bioconductor version 3.16 (BiocManager 1.30.22), R 4.2.3 (2023-03-15) 'getOption("repos")' replaces Bioconductor standard repositories, see 'help("repositories", package = "BiocManager")' for details. Replacement repositories: CRAN: https://cloud.r-project.org Bioconductor version 3.16 (BiocManager 1.30.22), R 4.2.3 (2023-03-15) Warning message: package(s) not installed when version(s) same as or greater than current; use `force = TRUE` to re-install: 'BiocCheck' [ Finished: 2023-10-03 07:43:32 CEST ]