[ Started: 2023-04-29 23:48:02 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" Warning: unable to access index for repository https://cran.uni-muenster.de/src/contrib: cannot open URL 'https://cran.uni-muenster.de/src/contrib/PACKAGES' Warning: unable to access index for repository https://cran.uni-muenster.de/src/contrib: cannot open URL 'https://cran.uni-muenster.de/src/contrib/PACKAGES' Bioconductor version '3.16' is out-of-date; the current release version '3.17' is available with R version '4.3'; see https://bioconductor.org/install 'getOption("repos")' replaces Bioconductor standard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 1.30.20), R 4.2.3 (2023-03-15) Old packages: 'rlang', 'vroom' trying URL 'https://cloud.r-project.org/src/contrib/rlang_1.1.1.tar.gz' Content type 'application/x-gzip' length 762533 bytes (744 KB) ================================================== downloaded 744 KB trying URL 'https://cloud.r-project.org/src/contrib/vroom_1.6.3.tar.gz' Content type 'application/x-gzip' length 718863 bytes (702 KB) ================================================== downloaded 702 KB * installing *source* package ‘rlang’ ... ** package ‘rlang’ successfully unpacked and MD5 sums checked ** using staged installation ** libs gcc -I"/usr/share/R/include" -DNDEBUG -I./rlang/ -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 capture.c -o capture.o gcc -I"/usr/share/R/include" -DNDEBUG -I./rlang/ -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 internal.c -o internal.o gcc -I"/usr/share/R/include" -DNDEBUG -I./rlang/ -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 rlang.c -o rlang.o gcc -I"/usr/share/R/include" -DNDEBUG -I./rlang/ -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 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -o rlang.so capture.o internal.o rlang.o version.o -L/usr/lib/R/lib -lR installing to /home/omnipath/local/R/4.2-3.16/00LOCK-rlang/00new/rlang/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** 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 (rlang) * 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/RtmpQeeuaJ/downloaded_packages’ '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 1.30.20), 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' Skipping 17 packages not available: BiocManager, yaml, rmarkdown, knitr, bookdown, sessioninfo, testthat, covr, RefManageR, rjson, tidyr, tibble, dplyr, igraph, lpSolve, stringr, readr [ Finished: 2023-04-29 23:49:28 CEST ]