[ Started: 2023-05-07 00:45:10 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"     
Bioconductor version 3.17 (BiocManager 1.30.20), R 4.3.0 (2023-04-21)
Old packages: 'BiocParallel', 'DelayedArray'
trying URL 'https://bioconductor.org/packages/3.17/bioc/src/contrib/BiocParallel_1.34.1.tar.gz'
Content type 'application/x-gzip' length 997511 bytes (974 KB)
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downloaded 974 KB

trying URL 'https://bioconductor.org/packages/3.17/bioc/src/contrib/DelayedArray_0.26.2.tar.gz'
Content type 'application/x-gzip' length 625314 bytes (610 KB)
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downloaded 610 KB

* installing *source* package ‘BiocParallel’ ...
** 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++17 accepts -g... yes
checking for g++ -std=gnu++17 option to enable C++11 features... none needed
checking for library containing shm_open... none required
checking for stdio.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for strings.h... yes
checking for sys/stat.h... yes
checking for sys/types.h... yes
checking for unistd.h... yes
checking for sys/mman.h... yes
configure: creating ./config.status
config.status: creating src/Makevars
** libs
using C++ compiler: ‘g++ (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’
using C++11
g++ -std=gnu++11 -I"/opt/R-devel/lib/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.3-3.17/BH/include' -I'/home/omnipath/local/R/4.3-3.17/cpp11/include' -I/usr/local/include    -fpic  -g -O2  -c cpp11.cpp -o cpp11.o
g++ -std=gnu++11 -I"/opt/R-devel/lib/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.3-3.17/BH/include' -I'/home/omnipath/local/R/4.3-3.17/cpp11/include' -I/usr/local/include    -fpic  -g -O2  -c ipcmutex.cpp -o ipcmutex.o
g++ -std=gnu++11 -shared -L/usr/local/lib -o BiocParallel.so cpp11.o ipcmutex.o
installing to /home/omnipath/local/R/4.3-3.17/00LOCK-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 ‘DelayedArray’ ...
** 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'/home/omnipath/local/R/4.3-3.17/S4Vectors/include' -I/usr/local/include    -fpic  -g -O2  -c R_init_DelayedArray.c -o R_init_DelayedArray.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.3-3.17/S4Vectors/include' -I/usr/local/include    -fpic  -g -O2  -c S4Vectors_stubs.c -o S4Vectors_stubs.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.3-3.17/S4Vectors/include' -I/usr/local/include    -fpic  -g -O2  -c compress_atomic_vector.c -o compress_atomic_vector.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.3-3.17/S4Vectors/include' -I/usr/local/include    -fpic  -g -O2  -c sparseMatrix_utils.c -o sparseMatrix_utils.o
gcc -shared -L/usr/local/lib -o DelayedArray.so R_init_DelayedArray.o S4Vectors_stubs.o compress_atomic_vector.o sparseMatrix_utils.o
installing to /home/omnipath/local/R/4.3-3.17/00LOCK-DelayedArray/00new/DelayedArray/libs
** R
** inst
** byte-compile and prepare package for lazy loading
Creating a new generic function for ‘apply’ in package ‘DelayedArray’
Creating a new generic function for ‘sweep’ in package ‘DelayedArray’
Creating a new generic function for ‘scale’ in package ‘DelayedArray’
Creating a generic function for ‘dnorm’ from package ‘stats’ in package ‘DelayedArray’
Creating a generic function for ‘pnorm’ from package ‘stats’ in package ‘DelayedArray’
Creating a generic function for ‘qnorm’ from package ‘stats’ in package ‘DelayedArray’
Creating a generic function for ‘dbinom’ from package ‘stats’ in package ‘DelayedArray’
Creating a generic function for ‘pbinom’ from package ‘stats’ in package ‘DelayedArray’
Creating a generic function for ‘qbinom’ from package ‘stats’ in package ‘DelayedArray’
Creating a generic function for ‘dpois’ from package ‘stats’ in package ‘DelayedArray’
Creating a generic function for ‘ppois’ from package ‘stats’ in package ‘DelayedArray’
Creating a generic function for ‘qpois’ from package ‘stats’ in package ‘DelayedArray’
Creating a generic function for ‘dlogis’ from package ‘stats’ in package ‘DelayedArray’
Creating a generic function for ‘plogis’ from package ‘stats’ in package ‘DelayedArray’
Creating a generic function for ‘qlogis’ from package ‘stats’ in package ‘DelayedArray’
** 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 (DelayedArray)

The downloaded source packages are in
	‘/tmp/RtmpNQMVj8/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' 

[ Finished: 2023-05-07 00:45:47 CEST ]