[ Started: 2023-04-29 23:45:38 CEST ]
[ CARNIVAL v2.7.2 for BioC-3.17 from https://github.com/saezlab/CARNIVAL@master ]

[1] "Libraries: "                     "/home/omnipath/local/R/4.3-3.17"
[3] "/home/omnipath/local/R/4.3"      "/opt/R-devel/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 3.17 (BiocManager 1.30.20), R 4.3.0 (2023-04-21)
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)
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downloaded 702 KB

* installing *source* package ‘rlang’ ...
** package ‘rlang’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I./rlang/  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -c capture.c -o capture.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I./rlang/  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -c internal.c -o internal.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I./rlang/  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -c rlang.c -o rlang.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I./rlang/  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -c version.c -o version.o
gcc -shared -L/usr/local/lib -o rlang.so capture.o internal.o rlang.o version.o
installing to /home/omnipath/local/R/4.3-3.17/00LOCK-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
using C compiler: ‘gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’
using C++ compiler: ‘g++ (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’
g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -Imio/include -DWIN32_LEAN_AND_MEAN -Ispdlog/include -DFMT_HEADER_ONLY -I'/home/omnipath/local/R/4.3-3.17/cpp11/include' -I'/home/omnipath/local/R/4.3-3.17/progress/include' -I'/home/omnipath/local/R/4.3-3.17/tzdb/include' -I/usr/local/include    -fpic  -g -O2  -c Iconv.cpp -o Iconv.o
g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -Imio/include -DWIN32_LEAN_AND_MEAN -Ispdlog/include -DFMT_HEADER_ONLY -I'/home/omnipath/local/R/4.3-3.17/cpp11/include' -I'/home/omnipath/local/R/4.3-3.17/progress/include' -I'/home/omnipath/local/R/4.3-3.17/tzdb/include' -I/usr/local/include    -fpic  -g -O2  -c LocaleInfo.cpp -o LocaleInfo.o
g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -Imio/include -DWIN32_LEAN_AND_MEAN -Ispdlog/include -DFMT_HEADER_ONLY -I'/home/omnipath/local/R/4.3-3.17/cpp11/include' -I'/home/omnipath/local/R/4.3-3.17/progress/include' -I'/home/omnipath/local/R/4.3-3.17/tzdb/include' -I/usr/local/include    -fpic  -g -O2  -c altrep.cc -o altrep.o
g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -Imio/include -DWIN32_LEAN_AND_MEAN -Ispdlog/include -DFMT_HEADER_ONLY -I'/home/omnipath/local/R/4.3-3.17/cpp11/include' -I'/home/omnipath/local/R/4.3-3.17/progress/include' -I'/home/omnipath/local/R/4.3-3.17/tzdb/include' -I/usr/local/include    -fpic  -g -O2  -c cpp11.cpp -o cpp11.o
g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -Imio/include -DWIN32_LEAN_AND_MEAN -Ispdlog/include -DFMT_HEADER_ONLY -I'/home/omnipath/local/R/4.3-3.17/cpp11/include' -I'/home/omnipath/local/R/4.3-3.17/progress/include' -I'/home/omnipath/local/R/4.3-3.17/tzdb/include' -I/usr/local/include    -fpic  -g -O2  -c delimited_index.cc -o delimited_index.o
g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -Imio/include -DWIN32_LEAN_AND_MEAN -Ispdlog/include -DFMT_HEADER_ONLY -I'/home/omnipath/local/R/4.3-3.17/cpp11/include' -I'/home/omnipath/local/R/4.3-3.17/progress/include' -I'/home/omnipath/local/R/4.3-3.17/tzdb/include' -I/usr/local/include    -fpic  -g -O2  -c delimited_index_connection.cc -o delimited_index_connection.o
g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -Imio/include -DWIN32_LEAN_AND_MEAN -Ispdlog/include -DFMT_HEADER_ONLY -I'/home/omnipath/local/R/4.3-3.17/cpp11/include' -I'/home/omnipath/local/R/4.3-3.17/progress/include' -I'/home/omnipath/local/R/4.3-3.17/tzdb/include' -I/usr/local/include    -fpic  -g -O2  -c fixed_width_index_connection.cc -o fixed_width_index_connection.o
g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -Imio/include -DWIN32_LEAN_AND_MEAN -Ispdlog/include -DFMT_HEADER_ONLY -I'/home/omnipath/local/R/4.3-3.17/cpp11/include' -I'/home/omnipath/local/R/4.3-3.17/progress/include' -I'/home/omnipath/local/R/4.3-3.17/tzdb/include' -I/usr/local/include    -fpic  -g -O2  -c gen.cc -o gen.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -Imio/include -DWIN32_LEAN_AND_MEAN -Ispdlog/include -DFMT_HEADER_ONLY -I'/home/omnipath/local/R/4.3-3.17/cpp11/include' -I'/home/omnipath/local/R/4.3-3.17/progress/include' -I'/home/omnipath/local/R/4.3-3.17/tzdb/include' -I/usr/local/include    -fpic  -g -O2  -c grisu3.c -o grisu3.o
g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -Imio/include -DWIN32_LEAN_AND_MEAN -Ispdlog/include -DFMT_HEADER_ONLY -I'/home/omnipath/local/R/4.3-3.17/cpp11/include' -I'/home/omnipath/local/R/4.3-3.17/progress/include' -I'/home/omnipath/local/R/4.3-3.17/tzdb/include' -I/usr/local/include    -fpic  -g -O2  -c guess_type.cc -o guess_type.o
g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -Imio/include -DWIN32_LEAN_AND_MEAN -Ispdlog/include -DFMT_HEADER_ONLY -I'/home/omnipath/local/R/4.3-3.17/cpp11/include' -I'/home/omnipath/local/R/4.3-3.17/progress/include' -I'/home/omnipath/local/R/4.3-3.17/tzdb/include' -I/usr/local/include    -fpic  -g -O2  -c iconv_file.cc -o iconv_file.o
g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -Imio/include -DWIN32_LEAN_AND_MEAN -Ispdlog/include -DFMT_HEADER_ONLY -I'/home/omnipath/local/R/4.3-3.17/cpp11/include' -I'/home/omnipath/local/R/4.3-3.17/progress/include' -I'/home/omnipath/local/R/4.3-3.17/tzdb/include' -I/usr/local/include    -fpic  -g -O2  -c index_collection.cc -o index_collection.o
g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -Imio/include -DWIN32_LEAN_AND_MEAN -Ispdlog/include -DFMT_HEADER_ONLY -I'/home/omnipath/local/R/4.3-3.17/cpp11/include' -I'/home/omnipath/local/R/4.3-3.17/progress/include' -I'/home/omnipath/local/R/4.3-3.17/tzdb/include' -I/usr/local/include    -fpic  -g -O2  -c vroom.cc -o vroom.o
g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -Imio/include -DWIN32_LEAN_AND_MEAN -Ispdlog/include -DFMT_HEADER_ONLY -I'/home/omnipath/local/R/4.3-3.17/cpp11/include' -I'/home/omnipath/local/R/4.3-3.17/progress/include' -I'/home/omnipath/local/R/4.3-3.17/tzdb/include' -I/usr/local/include    -fpic  -g -O2  -c vroom_big_int.cc -o vroom_big_int.o
g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -Imio/include -DWIN32_LEAN_AND_MEAN -Ispdlog/include -DFMT_HEADER_ONLY -I'/home/omnipath/local/R/4.3-3.17/cpp11/include' -I'/home/omnipath/local/R/4.3-3.17/progress/include' -I'/home/omnipath/local/R/4.3-3.17/tzdb/include' -I/usr/local/include    -fpic  -g -O2  -c vroom_chr.cc -o vroom_chr.o
g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -Imio/include -DWIN32_LEAN_AND_MEAN -Ispdlog/include -DFMT_HEADER_ONLY -I'/home/omnipath/local/R/4.3-3.17/cpp11/include' -I'/home/omnipath/local/R/4.3-3.17/progress/include' -I'/home/omnipath/local/R/4.3-3.17/tzdb/include' -I/usr/local/include    -fpic  -g -O2  -c vroom_date.cc -o vroom_date.o
g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -Imio/include -DWIN32_LEAN_AND_MEAN -Ispdlog/include -DFMT_HEADER_ONLY -I'/home/omnipath/local/R/4.3-3.17/cpp11/include' -I'/home/omnipath/local/R/4.3-3.17/progress/include' -I'/home/omnipath/local/R/4.3-3.17/tzdb/include' -I/usr/local/include    -fpic  -g -O2  -c vroom_dbl.cc -o vroom_dbl.o
g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -Imio/include -DWIN32_LEAN_AND_MEAN -Ispdlog/include -DFMT_HEADER_ONLY -I'/home/omnipath/local/R/4.3-3.17/cpp11/include' -I'/home/omnipath/local/R/4.3-3.17/progress/include' -I'/home/omnipath/local/R/4.3-3.17/tzdb/include' -I/usr/local/include    -fpic  -g -O2  -c vroom_dttm.cc -o vroom_dttm.o
g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -Imio/include -DWIN32_LEAN_AND_MEAN -Ispdlog/include -DFMT_HEADER_ONLY -I'/home/omnipath/local/R/4.3-3.17/cpp11/include' -I'/home/omnipath/local/R/4.3-3.17/progress/include' -I'/home/omnipath/local/R/4.3-3.17/tzdb/include' -I/usr/local/include    -fpic  -g -O2  -c vroom_errors.cpp -o vroom_errors.o
g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -Imio/include -DWIN32_LEAN_AND_MEAN -Ispdlog/include -DFMT_HEADER_ONLY -I'/home/omnipath/local/R/4.3-3.17/cpp11/include' -I'/home/omnipath/local/R/4.3-3.17/progress/include' -I'/home/omnipath/local/R/4.3-3.17/tzdb/include' -I/usr/local/include    -fpic  -g -O2  -c vroom_fct.cc -o vroom_fct.o
g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -Imio/include -DWIN32_LEAN_AND_MEAN -Ispdlog/include -DFMT_HEADER_ONLY -I'/home/omnipath/local/R/4.3-3.17/cpp11/include' -I'/home/omnipath/local/R/4.3-3.17/progress/include' -I'/home/omnipath/local/R/4.3-3.17/tzdb/include' -I/usr/local/include    -fpic  -g -O2  -c vroom_fwf.cc -o vroom_fwf.o
g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -Imio/include -DWIN32_LEAN_AND_MEAN -Ispdlog/include -DFMT_HEADER_ONLY -I'/home/omnipath/local/R/4.3-3.17/cpp11/include' -I'/home/omnipath/local/R/4.3-3.17/progress/include' -I'/home/omnipath/local/R/4.3-3.17/tzdb/include' -I/usr/local/include    -fpic  -g -O2  -c vroom_int.cc -o vroom_int.o
g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -Imio/include -DWIN32_LEAN_AND_MEAN -Ispdlog/include -DFMT_HEADER_ONLY -I'/home/omnipath/local/R/4.3-3.17/cpp11/include' -I'/home/omnipath/local/R/4.3-3.17/progress/include' -I'/home/omnipath/local/R/4.3-3.17/tzdb/include' -I/usr/local/include    -fpic  -g -O2  -c vroom_num.cc -o vroom_num.o
g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -Imio/include -DWIN32_LEAN_AND_MEAN -Ispdlog/include -DFMT_HEADER_ONLY -I'/home/omnipath/local/R/4.3-3.17/cpp11/include' -I'/home/omnipath/local/R/4.3-3.17/progress/include' -I'/home/omnipath/local/R/4.3-3.17/tzdb/include' -I/usr/local/include    -fpic  -g -O2  -c vroom_rle.cc -o vroom_rle.o
g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -Imio/include -DWIN32_LEAN_AND_MEAN -Ispdlog/include -DFMT_HEADER_ONLY -I'/home/omnipath/local/R/4.3-3.17/cpp11/include' -I'/home/omnipath/local/R/4.3-3.17/progress/include' -I'/home/omnipath/local/R/4.3-3.17/tzdb/include' -I/usr/local/include    -fpic  -g -O2  -c vroom_time.cc -o vroom_time.o
g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -Imio/include -DWIN32_LEAN_AND_MEAN -Ispdlog/include -DFMT_HEADER_ONLY -I'/home/omnipath/local/R/4.3-3.17/cpp11/include' -I'/home/omnipath/local/R/4.3-3.17/progress/include' -I'/home/omnipath/local/R/4.3-3.17/tzdb/include' -I/usr/local/include    -fpic  -g -O2  -c vroom_write.cc -o vroom_write.o
g++ -std=gnu++17 -shared -L/usr/local/lib -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
installing to /home/omnipath/local/R/4.3-3.17/00LOCK-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/RtmpT8SD2m/downloaded_packages’
Bioconductor version 3.17 (BiocManager 1.30.20), R 4.3.0 (2023-04-21)
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 23:47:05 CEST ]