[ Started: 2023-02-23 01:00:45 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 4.2.2 Patched (2022-11-10 r83330) Old packages: 'ggalluvial', 'gh', 'RcppArmadillo', 'tidyverse' also installing the dependencies ‘httr2’, ‘conflicted’ trying URL 'https://cloud.r-project.org/src/contrib/httr2_0.2.2.tar.gz' Content type 'application/x-gzip' length 121360 bytes (118 KB) ================================================== downloaded 118 KB trying URL 'https://cloud.r-project.org/src/contrib/conflicted_1.2.0.tar.gz' Content type 'application/x-gzip' length 17071 bytes (16 KB) ================================================== downloaded 16 KB trying URL 'https://cloud.r-project.org/src/contrib/ggalluvial_0.12.5.tar.gz' Content type 'application/x-gzip' length 2850813 bytes (2.7 MB) ================================================== downloaded 2.7 MB trying URL 'https://cloud.r-project.org/src/contrib/gh_1.4.0.tar.gz' Content type 'application/x-gzip' length 41214 bytes (40 KB) ================================================== downloaded 40 KB trying URL 'https://cloud.r-project.org/src/contrib/RcppArmadillo_0.12.0.1.0.tar.gz' Content type 'application/x-gzip' length 1366502 bytes (1.3 MB) ================================================== downloaded 1.3 MB trying URL 'https://cloud.r-project.org/src/contrib/tidyverse_2.0.0.tar.gz' Content type 'application/x-gzip' length 704618 bytes (688 KB) ================================================== downloaded 688 KB * installing *source* package ‘httr2’ ... ** package ‘httr2’ 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 (httr2) * installing *source* package ‘conflicted’ ... ** package ‘conflicted’ successfully unpacked and MD5 sums checked ** using staged installation ** 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 ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (conflicted) * installing *source* package ‘ggalluvial’ ... ** package ‘ggalluvial’ successfully unpacked and MD5 sums checked ** using staged installation ** 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 ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (ggalluvial) * 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++14 -I"/usr/share/R/include" -DNDEBUG -I../inst/include -I'/home/omnipath/local/R/4.2-3.16/Rcpp/include' -fopenmp -fpic -g -O2 -fdebug-prefix-map=/build/r-base-a3XuZ5/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c RcppArmadillo.cpp -o RcppArmadillo.o g++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG -I../inst/include -I'/home/omnipath/local/R/4.2-3.16/Rcpp/include' -fopenmp -fpic -g -O2 -fdebug-prefix-map=/build/r-base-a3XuZ5/r-base-4.2.2.20221110=. -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../inst/include -I'/home/omnipath/local/R/4.2-3.16/Rcpp/include' -fopenmp -fpic -g -O2 -fdebug-prefix-map=/build/r-base-a3XuZ5/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c fastLm.cpp -o fastLm.o g++ -std=gnu++14 -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 ‘gh’ ... ** package ‘gh’ 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 ** 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 (gh) * installing *source* package ‘tidyverse’ ... ** package ‘tidyverse’ 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 (tidyverse) The downloaded source packages are in ‘/tmp/RtmpqcyyT2/downloaded_packages’ [ Finished: 2023-02-23 01:01:28 CET ]