[ Started: 2022-10-20 20:01:25 CEST ]
[ CARNIVAL v2.7.1 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 1.30.18), R 4.2.1 (2022-06-23)
Old packages: 'BiocParallel', 'GenomeInfoDb'
trying URL 'https://bioconductor.org/packages/3.16/bioc/src/contrib/BiocParallel_1.31.14.tar.gz'
Content type 'application/x-gzip' length 960806 bytes (938 KB)
==================================================
downloaded 938 KB

trying URL 'https://bioconductor.org/packages/3.16/bioc/src/contrib/GenomeInfoDb_1.33.13.tar.gz'
Content type 'application/x-gzip' length 3466260 bytes (3.3 MB)
==================================================
downloaded 3.3 MB

* installing *source* package ‘BiocParallel’ ...
** using staged installation
checking for gcc... gcc
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 we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking for shm_open in -lrt... yes
configure: creating ./config.status
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/BH/include' -I'/home/omnipath/local/R/4.2-3.16/cpp11/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/BH/include' -I'/home/omnipath/local/R/4.2-3.16/cpp11/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 ipcmutex.cpp -o ipcmutex.o
g++ -std=gnu++11 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o BiocParallel.so cpp11.o ipcmutex.o -lrt -L/usr/lib/R/lib -lR
installing to /home/omnipath/local/R/4.2-3.16/00LOCK-BiocParallel/00new/BiocParallel/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 (BiocParallel)
* installing *source* package ‘GenomeInfoDb’ ...
** 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 (GenomeInfoDb)

The downloaded source packages are in
	‘/tmp/RtmpgsBHEm/downloaded_packages’

Skipping 1 packages ahead of CRAN: BiocStyle
[ Finished: 2022-10-20 20:01:54 CEST ]