[ Started: 2022-11-10 01:01:36 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: 'bookdown', 'RcppArmadillo', 'recipes', 'rmarkdown', 'rstatix' also installing the dependency ‘clock’ trying URL 'https://cloud.r-project.org/src/contrib/clock_0.6.1.tar.gz' Content type 'application/x-gzip' length 501028 bytes (489 KB) ================================================== downloaded 489 KB trying URL 'https://cloud.r-project.org/src/contrib/bookdown_0.30.tar.gz' Content type 'application/x-gzip' length 854822 bytes (834 KB) ================================================== downloaded 834 KB trying URL 'https://cloud.r-project.org/src/contrib/RcppArmadillo_0.11.4.2.1.tar.gz' Content type 'application/x-gzip' length 1372103 bytes (1.3 MB) ================================================== downloaded 1.3 MB trying URL 'https://cloud.r-project.org/src/contrib/recipes_1.0.3.tar.gz' Content type 'application/x-gzip' length 797377 bytes (778 KB) ================================================== downloaded 778 KB trying URL 'https://cloud.r-project.org/src/contrib/rmarkdown_2.18.tar.gz' Content type 'application/x-gzip' length 3243612 bytes (3.1 MB) ================================================== downloaded 3.1 MB trying URL 'https://cloud.r-project.org/src/contrib/rstatix_0.7.1.tar.gz' Content type 'application/x-gzip' length 403999 bytes (394 KB) ================================================== downloaded 394 KB * installing *source* package ‘clock’ ... ** package ‘clock’ successfully unpacked and MD5 sums checked ** using staged installation ** libs g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.2-3.16/cpp11/include' -I'/home/omnipath/local/R/4.2-3.16/tzdb/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'/home/omnipath/local/R/4.2-3.16/cpp11/include' -I'/home/omnipath/local/R/4.2-3.16/tzdb/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 duration.cpp -o duration.o g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.2-3.16/cpp11/include' -I'/home/omnipath/local/R/4.2-3.16/tzdb/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 enums.cpp -o enums.o g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.2-3.16/cpp11/include' -I'/home/omnipath/local/R/4.2-3.16/tzdb/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 format.cpp -o format.o g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.2-3.16/cpp11/include' -I'/home/omnipath/local/R/4.2-3.16/tzdb/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 gregorian-year-day.cpp -o gregorian-year-day.o g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.2-3.16/cpp11/include' -I'/home/omnipath/local/R/4.2-3.16/tzdb/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 gregorian-year-month-day.cpp -o gregorian-year-month-day.o g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.2-3.16/cpp11/include' -I'/home/omnipath/local/R/4.2-3.16/tzdb/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 gregorian-year-month-weekday.cpp -o gregorian-year-month-weekday.o g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.2-3.16/cpp11/include' -I'/home/omnipath/local/R/4.2-3.16/tzdb/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 iso-year-week-day.cpp -o iso-year-week-day.o g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.2-3.16/cpp11/include' -I'/home/omnipath/local/R/4.2-3.16/tzdb/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 naive-time.cpp -o naive-time.o g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.2-3.16/cpp11/include' -I'/home/omnipath/local/R/4.2-3.16/tzdb/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 quarterly-year-quarter-day.cpp -o quarterly-year-quarter-day.o g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.2-3.16/cpp11/include' -I'/home/omnipath/local/R/4.2-3.16/tzdb/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 rcrd.cpp -o rcrd.o g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.2-3.16/cpp11/include' -I'/home/omnipath/local/R/4.2-3.16/tzdb/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 sys-time.cpp -o sys-time.o g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.2-3.16/cpp11/include' -I'/home/omnipath/local/R/4.2-3.16/tzdb/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 time-point.cpp -o time-point.o g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.2-3.16/cpp11/include' -I'/home/omnipath/local/R/4.2-3.16/tzdb/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 utils.cpp -o utils.o g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.2-3.16/cpp11/include' -I'/home/omnipath/local/R/4.2-3.16/tzdb/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 weekday.cpp -o weekday.o g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.2-3.16/cpp11/include' -I'/home/omnipath/local/R/4.2-3.16/tzdb/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 zone.cpp -o zone.o g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.2-3.16/cpp11/include' -I'/home/omnipath/local/R/4.2-3.16/tzdb/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 zoned-time.cpp -o zoned-time.o g++ -std=gnu++11 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o clock.so cpp11.o duration.o enums.o format.o gregorian-year-day.o gregorian-year-month-day.o gregorian-year-month-weekday.o iso-year-week-day.o naive-time.o quarterly-year-quarter-day.o rcrd.o sys-time.o time-point.o utils.o weekday.o zone.o zoned-time.o -L/usr/lib/R/lib -lR installing to /home/omnipath/local/R/4.2-3.16/00LOCK-clock/00new/clock/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 (clock) * installing *source* package ‘RcppArmadillo’ ... ** package ‘RcppArmadillo’ successfully unpacked and MD5 sums checked ** using staged installation 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 the compiler supports GNU C++... yes checking whether g++ -std=gnu++14 accepts -g... yes checking for g++ -std=gnu++14 option to enable C++11 features... none needed checking how to run the C++ preprocessor... g++ -std=gnu++14 -E checking whether the compiler supports GNU C++... (cached) yes checking whether g++ -std=gnu++14 accepts -g... (cached) yes checking for g++ -std=gnu++14 option to enable C++11 features... (cached) none needed checking whether we have a suitable tempdir... /tmp checking whether R CMD SHLIB can already compile programs using OpenMP... yes checking LAPACK_LIBS... system LAPACK found configure: creating ./config.status config.status: creating inst/include/RcppArmadillo/config/RcppArmadilloConfigGenerated.h config.status: creating src/Makevars ** libs g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.2-3.16/Rcpp/include' -I../inst/include -fopenmp -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 RcppArmadillo.cpp -o RcppArmadillo.o g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.2-3.16/Rcpp/include' -I../inst/include -fopenmp -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++11 -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.2-3.16/Rcpp/include' -I../inst/include -fopenmp -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 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 -fopenmp -llapack -lblas -lgfortran -lm -lquadmath -L/usr/lib/R/lib -lR installing to /home/omnipath/local/R/4.2-3.16/00LOCK-RcppArmadillo/00new/RcppArmadillo/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 (RcppArmadillo) * installing *source* package ‘rmarkdown’ ... ** package ‘rmarkdown’ successfully unpacked and MD5 sums checked ** using staged installation ** 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 ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (rmarkdown) * installing *source* package ‘rstatix’ ... ** package ‘rstatix’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** 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 ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (rstatix) * installing *source* package ‘bookdown’ ... ** package ‘bookdown’ successfully unpacked and MD5 sums checked ** using staged installation ** 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 ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (bookdown) * installing *source* package ‘recipes’ ... ** package ‘recipes’ successfully unpacked and MD5 sums checked ** using staged installation ** 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 ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (recipes) The downloaded source packages are in ‘/tmp/Rtmp7oQlNs/downloaded_packages’ Skipping 2 packages ahead of CRAN: rmarkdown, bookdown [ Finished: 2022-11-10 01:04:55 CET ]