[ Started: 2023-03-24 22:11:16 CET ]
[ 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 Under development (unstable)
  (2023-03-16 r83996)
Old packages: 'BiocCheck', 'BiocParallel', 'xfun'
trying URL 'https://bioconductor.org/packages/3.17/bioc/src/contrib/BiocCheck_1.35.15.tar.gz'
Content type 'application/x-gzip' length 4373870 bytes (4.2 MB)
==================================================
downloaded 4.2 MB

trying URL 'https://bioconductor.org/packages/3.17/bioc/src/contrib/BiocParallel_1.33.11.tar.gz'
Content type 'application/x-gzip' length 996294 bytes (972 KB)
==================================================
downloaded 972 KB

trying URL 'https://cloud.r-project.org/src/contrib/xfun_0.38.tar.gz'
Content type 'application/x-gzip' length 133925 bytes (130 KB)
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downloaded 130 KB

* installing *source* package ‘BiocCheck’ ...
** 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 (BiocCheck)
* 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 ‘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-devel/lib/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -c base64.c -o base64.o
gcc -I"/opt/R-devel/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/RtmpL2pZ1O/downloaded_packages’
Bioconductor version 3.17 (BiocManager 1.30.20), R Under development (unstable)
  (2023-03-16 r83996)
Warning message:
package(s) not installed when version(s) same as or greater than current; use
  `force = TRUE` to re-install: 'BiocCheck' 

Skipping 1 packages ahead of CRAN: xfun
[ Finished: 2023-03-24 22:11:44 CET ]