[ Started: 2022-11-07 01:00:30 CET ] [ 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" 'getOption("repos")' replaces Bioconductor standard repositories, see '?repositories' for details replacement repositories: CRAN: https://cloud.r-project.org Bioconductor version 3.16 (BiocManager 1.30.19), R 4.2.1 (2022-06-23) Old packages: 'future', 'ggrepel', 'lubridate' also installing the dependency ‘timechange’ trying URL 'https://cloud.r-project.org/src/contrib/timechange_0.1.1.tar.gz' Content type 'application/x-gzip' length 100502 bytes (98 KB) ================================================== downloaded 98 KB trying URL 'https://cloud.r-project.org/src/contrib/future_1.29.0.tar.gz' Content type 'application/x-gzip' length 367973 bytes (359 KB) ================================================== downloaded 359 KB trying URL 'https://cloud.r-project.org/src/contrib/ggrepel_0.9.2.tar.gz' Content type 'application/x-gzip' length 135988 bytes (132 KB) ================================================== downloaded 132 KB trying URL 'https://cloud.r-project.org/src/contrib/lubridate_1.9.0.tar.gz' Content type 'application/x-gzip' length 425481 bytes (415 KB) ================================================== downloaded 415 KB * installing *source* package ‘timechange’ ... ** package ‘timechange’ successfully unpacked and MD5 sums checked ** using staged installation ** libs g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -I. -I./cctz/src/ -I'/home/omnipath/local/R/4.2-3.16/cpp11/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c common.cpp -o common.o g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -I. -I./cctz/src/ -I'/home/omnipath/local/R/4.2-3.16/cpp11/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c cpp11.cpp -o cpp11.o g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -I. -I./cctz/src/ -I'/home/omnipath/local/R/4.2-3.16/cpp11/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c get.cpp -o get.o gcc -I"/usr/share/R/include" -DNDEBUG -I. -I./cctz/src/ -I'/home/omnipath/local/R/4.2-3.16/cpp11/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c parse.c -o parse.o g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -I. -I./cctz/src/ -I'/home/omnipath/local/R/4.2-3.16/cpp11/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c round.cpp -o round.o g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -I. -I./cctz/src/ -I'/home/omnipath/local/R/4.2-3.16/cpp11/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c tzone.cpp -o tzone.o g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -I. -I./cctz/src/ -I'/home/omnipath/local/R/4.2-3.16/cpp11/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c update.cpp -o update.o g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -I. -I./cctz/src/ -I'/home/omnipath/local/R/4.2-3.16/cpp11/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c cctz/src/time_zone_fixed.cc -o cctz/src/time_zone_fixed.o g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -I. -I./cctz/src/ -I'/home/omnipath/local/R/4.2-3.16/cpp11/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c cctz/src/time_zone_if.cc -o cctz/src/time_zone_if.o g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -I. -I./cctz/src/ -I'/home/omnipath/local/R/4.2-3.16/cpp11/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c cctz/src/time_zone_impl.cc -o cctz/src/time_zone_impl.o g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -I. -I./cctz/src/ -I'/home/omnipath/local/R/4.2-3.16/cpp11/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c cctz/src/time_zone_info.cc -o cctz/src/time_zone_info.o g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -I. -I./cctz/src/ -I'/home/omnipath/local/R/4.2-3.16/cpp11/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c cctz/src/time_zone_libc.cc -o cctz/src/time_zone_libc.o g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -I. -I./cctz/src/ -I'/home/omnipath/local/R/4.2-3.16/cpp11/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c cctz/src/time_zone_lookup.cc -o cctz/src/time_zone_lookup.o g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -I. -I./cctz/src/ -I'/home/omnipath/local/R/4.2-3.16/cpp11/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c cctz/src/time_zone_posix.cc -o cctz/src/time_zone_posix.o g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -I. -I./cctz/src/ -I'/home/omnipath/local/R/4.2-3.16/cpp11/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c cctz/src/zone_info_source.cc -o cctz/src/zone_info_source.o ar rcs libcctz.a ./cctz/src/time_zone_fixed.o ./cctz/src/time_zone_if.o ./cctz/src/time_zone_impl.o ./cctz/src/time_zone_info.o ./cctz/src/time_zone_libc.o ./cctz/src/time_zone_lookup.o ./cctz/src/time_zone_posix.o ./cctz/src/zone_info_source.o g++ -std=gnu++11 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o timechange.so common.o cpp11.o get.o parse.o round.o tzone.o update.o -L. -lcctz -L/usr/lib/R/lib -lR installing to /home/omnipath/local/R/4.2-3.16/00LOCK-timechange/00new/timechange/libs ** R ** 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 (timechange) * installing *source* package ‘future’ ... ** package ‘future’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** demo ** 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 ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (future) * installing *source* package ‘ggrepel’ ... ** package ‘ggrepel’ 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 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c RcppExports.cpp -o RcppExports.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 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c repel_boxes.cpp -o repel_boxes.o g++ -std=gnu++14 -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 /home/omnipath/local/R/4.2-3.16/00LOCK-ggrepel/00new/ggrepel/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 (ggrepel) * installing *source* package ‘lubridate’ ... ** package ‘lubridate’ successfully unpacked and MD5 sums checked ** using staged installation ** libs gcc -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c datetime.c -o datetime.o gcc -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -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 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c period.c -o period.o gcc -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c tparse.c -o tparse.o gcc -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c utils.c -o utils.o gcc -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o lubridate.so datetime.o init.o period.o tparse.o utils.o -L/usr/lib/R/lib -lR installing to /home/omnipath/local/R/4.2-3.16/00LOCK-lubridate/00new/lubridate/libs ** R ** data *** moving datasets to lazyload DB ** 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 (lubridate) The downloaded source packages are in ‘/tmp/RtmpkEkcTl/downloaded_packages’ Skipping 1 packages ahead of CRAN: lubridate [ Finished: 2022-11-07 01:01:19 CET ]