[ Started: 2023-04-21 00:14:55 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-beta/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 RC (2023-04-13 r84266)
Old packages: 'dplyr', 'S4Vectors', 'xfun'
trying URL 'https://cloud.r-project.org/src/contrib/dplyr_1.1.2.tar.gz'
Content type 'application/x-gzip' length 1083348 bytes (1.0 MB)
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downloaded 1.0 MB

trying URL 'https://bioconductor.org/packages/3.17/bioc/src/contrib/S4Vectors_0.37.7.tar.gz'
Content type 'application/x-gzip' length 838936 bytes (819 KB)
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downloaded 819 KB

trying URL 'https://cloud.r-project.org/src/contrib/xfun_0.39.tar.gz'
Content type 'application/x-gzip' length 135480 bytes (132 KB)
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downloaded 132 KB

* installing *source* package ‘dplyr’ ...
** package ‘dplyr’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: ‘g++ (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’
g++ -std=gnu++17 -I"/opt/R-beta/lib/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -c chop.cpp -o chop.o
g++ -std=gnu++17 -I"/opt/R-beta/lib/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -c filter.cpp -o filter.o
g++ -std=gnu++17 -I"/opt/R-beta/lib/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -c funs.cpp -o funs.o
g++ -std=gnu++17 -I"/opt/R-beta/lib/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -c group_by.cpp -o group_by.o
g++ -std=gnu++17 -I"/opt/R-beta/lib/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -c group_data.cpp -o group_data.o
g++ -std=gnu++17 -I"/opt/R-beta/lib/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -c imports.cpp -o imports.o
g++ -std=gnu++17 -I"/opt/R-beta/lib/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -c init.cpp -o init.o
g++ -std=gnu++17 -I"/opt/R-beta/lib/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -c mask.cpp -o mask.o
g++ -std=gnu++17 -I"/opt/R-beta/lib/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -c mutate.cpp -o mutate.o
g++ -std=gnu++17 -I"/opt/R-beta/lib/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -c slice.cpp -o slice.o
g++ -std=gnu++17 -I"/opt/R-beta/lib/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -c summarise.cpp -o summarise.o
g++ -std=gnu++17 -shared -L/usr/local/lib -o dplyr.so chop.o filter.o funs.o group_by.o group_data.o imports.o init.o mask.o mutate.o slice.o summarise.o
installing to /home/omnipath/local/R/4.3-3.17/00LOCK-dplyr/00new/dplyr/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 (dplyr)
* installing *source* package ‘S4Vectors’ ...
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’
gcc -I"/opt/R-beta/lib/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -c AEbufs.c -o AEbufs.o
gcc -I"/opt/R-beta/lib/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -c DataFrame_class.c -o DataFrame_class.o
gcc -I"/opt/R-beta/lib/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -c Hits_class.c -o Hits_class.o
gcc -I"/opt/R-beta/lib/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -c LLint_class.c -o LLint_class.o
gcc -I"/opt/R-beta/lib/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -c List_class.c -o List_class.o
gcc -I"/opt/R-beta/lib/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -c R_init_S4Vectors.c -o R_init_S4Vectors.o
gcc -I"/opt/R-beta/lib/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -c Rle_class.c -o Rle_class.o
gcc -I"/opt/R-beta/lib/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -c Rle_utils.c -o Rle_utils.o
gcc -I"/opt/R-beta/lib/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -c SEXP_utils.c -o SEXP_utils.o
gcc -I"/opt/R-beta/lib/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -c SimpleList_class.c -o SimpleList_class.o
gcc -I"/opt/R-beta/lib/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -c anyMissing.c -o anyMissing.o
gcc -I"/opt/R-beta/lib/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -c character_utils.c -o character_utils.o
gcc -I"/opt/R-beta/lib/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -c eval_utils.c -o eval_utils.o
gcc -I"/opt/R-beta/lib/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -c hash_utils.c -o hash_utils.o
gcc -I"/opt/R-beta/lib/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -c integer_utils.c -o integer_utils.o
gcc -I"/opt/R-beta/lib/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -c logical_utils.c -o logical_utils.o
gcc -I"/opt/R-beta/lib/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -c map_ranges_to_runs.c -o map_ranges_to_runs.o
gcc -I"/opt/R-beta/lib/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -c raw_utils.c -o raw_utils.o
gcc -I"/opt/R-beta/lib/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -c safe_arithm.c -o safe_arithm.o
gcc -I"/opt/R-beta/lib/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -c sort_utils.c -o sort_utils.o
gcc -I"/opt/R-beta/lib/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -c subsetting_utils.c -o subsetting_utils.o
gcc -I"/opt/R-beta/lib/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -c vector_utils.c -o vector_utils.o
gcc -shared -L/usr/local/lib -o S4Vectors.so AEbufs.o DataFrame_class.o Hits_class.o LLint_class.o List_class.o R_init_S4Vectors.o Rle_class.o Rle_utils.o SEXP_utils.o SimpleList_class.o anyMissing.o character_utils.o eval_utils.o hash_utils.o integer_utils.o logical_utils.o map_ranges_to_runs.o raw_utils.o safe_arithm.o sort_utils.o subsetting_utils.o vector_utils.o
installing to /home/omnipath/local/R/4.3-3.17/00LOCK-S4Vectors/00new/S4Vectors/libs
** R
** inst
** byte-compile and prepare package for lazy loading
in method for ‘normalizeSingleBracketReplacementValue’ with signature ‘"List"’: no definition for class “List”
Creating a new generic function for ‘unname’ in package ‘S4Vectors’
Creating a new generic function for ‘expand.grid’ in package ‘S4Vectors’
Creating a new generic function for ‘findMatches’ in package ‘S4Vectors’
Creating a generic function for ‘setequal’ from package ‘base’ in package ‘S4Vectors’
in method for ‘coerce’ with signature ‘"Hits","DFrame"’: no definition for class “DFrame”
Creating a generic function for ‘as.factor’ from package ‘base’ in package ‘S4Vectors’
Creating a generic function for ‘tabulate’ from package ‘base’ in package ‘S4Vectors’
Creating a generic function for ‘cov’ from package ‘stats’ in package ‘S4Vectors’
Creating a generic function for ‘cor’ from package ‘stats’ in package ‘S4Vectors’
Creating a generic function for ‘smoothEnds’ from package ‘stats’ in package ‘S4Vectors’
Creating a generic function for ‘runmed’ from package ‘stats’ in package ‘S4Vectors’
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
Creating a generic function for ‘substr’ from package ‘base’ in package ‘S4Vectors’
Creating a generic function for ‘substring’ from package ‘base’ in package ‘S4Vectors’
Creating a generic function for ‘chartr’ from package ‘base’ in package ‘S4Vectors’
Creating a generic function for ‘tolower’ from package ‘base’ in package ‘S4Vectors’
Creating a generic function for ‘toupper’ from package ‘base’ in package ‘S4Vectors’
Creating a generic function for ‘sub’ from package ‘base’ in package ‘S4Vectors’
Creating a generic function for ‘gsub’ from package ‘base’ in package ‘S4Vectors’
Creating a generic function for ‘nlevels’ from package ‘base’ in package ‘S4Vectors’
in method for ‘coerce’ with signature ‘"data.table","DFrame"’: no definition for class “data.table”
Creating a generic function for ‘complete.cases’ from package ‘stats’ in package ‘S4Vectors’
** 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 (S4Vectors)
* installing *source* package ‘xfun’ ...
** package ‘xfun’ 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-beta/lib/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -c base64.c -o base64.o
gcc -I"/opt/R-beta/lib/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -c init.c -o init.o
gcc -shared -L/usr/local/lib -o xfun.so base64.o init.o
installing to /home/omnipath/local/R/4.3-3.17/00LOCK-xfun/00new/xfun/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 (xfun)

The downloaded source packages are in
	‘/tmp/RtmpnO3hcq/downloaded_packages’
Bioconductor version 3.17 (BiocManager 1.30.20), R 4.3.0 RC (2023-04-13 r84266)
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: 2023-04-21 00:15:31 CEST ]