[ Started: 2023-03-30 12:28:37 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 Under development (unstable)
  (2023-03-16 r83996)
Old packages: 'BiocGenerics', 'BiocParallel', 'biomaRt', 'graph', 'limma',
  'MatrixGenerics', 'rhdf5'
trying URL 'https://bioconductor.org/packages/3.17/bioc/src/contrib/BiocGenerics_0.45.3.tar.gz'
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* installing *source* package ‘BiocGenerics’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
Creating a new generic function for ‘aperm’ in package ‘BiocGenerics’
Creating a new generic function for ‘append’ in package ‘BiocGenerics’
Creating a new generic function for ‘as.data.frame’ in package ‘BiocGenerics’
Creating a new generic function for ‘cbind’ in package ‘BiocGenerics’
Creating a new generic function for ‘rbind’ in package ‘BiocGenerics’
Creating a new generic function for ‘do.call’ in package ‘BiocGenerics’
Creating a new generic function for ‘duplicated’ in package ‘BiocGenerics’
Creating a new generic function for ‘anyDuplicated’ in package ‘BiocGenerics’
Creating a new generic function for ‘eval’ in package ‘BiocGenerics’
Creating a new generic function for ‘pmax’ in package ‘BiocGenerics’
Creating a new generic function for ‘pmin’ in package ‘BiocGenerics’
Creating a new generic function for ‘pmax.int’ in package ‘BiocGenerics’
Creating a new generic function for ‘pmin.int’ in package ‘BiocGenerics’
Creating a new generic function for ‘Reduce’ in package ‘BiocGenerics’
Creating a new generic function for ‘Filter’ in package ‘BiocGenerics’
Creating a new generic function for ‘Find’ in package ‘BiocGenerics’
Creating a new generic function for ‘Map’ in package ‘BiocGenerics’
Creating a new generic function for ‘Position’ in package ‘BiocGenerics’
Creating a new generic function for ‘get’ in package ‘BiocGenerics’
Creating a new generic function for ‘mget’ in package ‘BiocGenerics’
Creating a new generic function for ‘grep’ in package ‘BiocGenerics’
Creating a new generic function for ‘grepl’ in package ‘BiocGenerics’
Creating a new generic function for ‘is.unsorted’ in package ‘BiocGenerics’
Creating a new generic function for ‘lapply’ in package ‘BiocGenerics’
Creating a new generic function for ‘sapply’ in package ‘BiocGenerics’
Creating a new generic function for ‘mapply’ in package ‘BiocGenerics’
Creating a new generic function for ‘match’ in package ‘BiocGenerics’
Creating a new generic function for ‘order’ in package ‘BiocGenerics’
Creating a new generic function for ‘paste’ in package ‘BiocGenerics’
Creating a new generic function for ‘rank’ in package ‘BiocGenerics’
Creating a new generic function for ‘rownames’ in package ‘BiocGenerics’
Creating a new generic function for ‘colnames’ in package ‘BiocGenerics’
Creating a new generic function for ‘union’ in package ‘BiocGenerics’
Creating a new generic function for ‘intersect’ in package ‘BiocGenerics’
Creating a new generic function for ‘setdiff’ in package ‘BiocGenerics’
Creating a new generic function for ‘sort’ in package ‘BiocGenerics’
Creating a new generic function for ‘table’ in package ‘BiocGenerics’
Creating a new generic function for ‘tapply’ in package ‘BiocGenerics’
Creating a new generic function for ‘unique’ in package ‘BiocGenerics’
Creating a new generic function for ‘unsplit’ in package ‘BiocGenerics’
Creating a new generic function for ‘var’ in package ‘BiocGenerics’
Creating a new generic function for ‘sd’ in package ‘BiocGenerics’
Creating a new generic function for ‘which.min’ in package ‘BiocGenerics’
Creating a new generic function for ‘which.max’ in package ‘BiocGenerics’
Creating a new generic function for ‘IQR’ in package ‘BiocGenerics’
Creating a new generic function for ‘mad’ in package ‘BiocGenerics’
Creating a new generic function for ‘xtabs’ in package ‘BiocGenerics’
Creating a new generic function for ‘basename’ in package ‘BiocGenerics’
Creating a new generic function for ‘dirname’ in package ‘BiocGenerics’
** help
*** installing help indices
** building package indices
** 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 (BiocGenerics)
* 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 ‘biomaRt’ ...
** 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 (biomaRt)
* installing *source* package ‘limma’ ...
** 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 init.c -o init.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -c normexp.c -o normexp.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -c weighted_lowess.c -o weighted_lowess.o
gcc -shared -L/usr/local/lib -o limma.so init.o normexp.o weighted_lowess.o
installing to /home/omnipath/local/R/4.3-3.17/00LOCK-limma/00new/limma/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 (limma)
* installing *source* package ‘MatrixGenerics’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
Creating a new generic function for ‘rowAlls’ in package ‘MatrixGenerics’
Creating a new generic function for ‘colAlls’ in package ‘MatrixGenerics’
Creating a new generic function for ‘rowAnyNAs’ in package ‘MatrixGenerics’
Creating a new generic function for ‘colAnyNAs’ in package ‘MatrixGenerics’
Creating a new generic function for ‘rowAnys’ in package ‘MatrixGenerics’
Creating a new generic function for ‘colAnys’ in package ‘MatrixGenerics’
Creating a new generic function for ‘rowAvgsPerColSet’ in package ‘MatrixGenerics’
Creating a new generic function for ‘colAvgsPerRowSet’ in package ‘MatrixGenerics’
Creating a new generic function for ‘rowCollapse’ in package ‘MatrixGenerics’
Creating a new generic function for ‘colCollapse’ in package ‘MatrixGenerics’
Creating a new generic function for ‘rowCounts’ in package ‘MatrixGenerics’
Creating a new generic function for ‘colCounts’ in package ‘MatrixGenerics’
Creating a new generic function for ‘rowCummaxs’ in package ‘MatrixGenerics’
Creating a new generic function for ‘colCummaxs’ in package ‘MatrixGenerics’
Creating a new generic function for ‘rowCummins’ in package ‘MatrixGenerics’
Creating a new generic function for ‘colCummins’ in package ‘MatrixGenerics’
Creating a new generic function for ‘rowCumprods’ in package ‘MatrixGenerics’
Creating a new generic function for ‘colCumprods’ in package ‘MatrixGenerics’
Creating a new generic function for ‘rowCumsums’ in package ‘MatrixGenerics’
Creating a new generic function for ‘colCumsums’ in package ‘MatrixGenerics’
Creating a new generic function for ‘rowDiffs’ in package ‘MatrixGenerics’
Creating a new generic function for ‘colDiffs’ in package ‘MatrixGenerics’
Creating a new generic function for ‘rowIQRDiffs’ in package ‘MatrixGenerics’
Creating a new generic function for ‘colIQRDiffs’ in package ‘MatrixGenerics’
Creating a new generic function for ‘rowIQRs’ in package ‘MatrixGenerics’
Creating a new generic function for ‘colIQRs’ in package ‘MatrixGenerics’
Creating a new generic function for ‘rowLogSumExps’ in package ‘MatrixGenerics’
Creating a new generic function for ‘colLogSumExps’ in package ‘MatrixGenerics’
Creating a new generic function for ‘rowMadDiffs’ in package ‘MatrixGenerics’
Creating a new generic function for ‘colMadDiffs’ in package ‘MatrixGenerics’
Creating a new generic function for ‘rowMads’ in package ‘MatrixGenerics’
Creating a new generic function for ‘colMads’ in package ‘MatrixGenerics’
Creating a new generic function for ‘rowMaxs’ in package ‘MatrixGenerics’
Creating a new generic function for ‘colMaxs’ in package ‘MatrixGenerics’
Creating a new generic function for ‘rowMeans2’ in package ‘MatrixGenerics’
Creating a new generic function for ‘colMeans2’ in package ‘MatrixGenerics’
Creating a new generic function for ‘rowMedians’ in package ‘MatrixGenerics’
Creating a new generic function for ‘colMedians’ in package ‘MatrixGenerics’
Creating a new generic function for ‘rowMins’ in package ‘MatrixGenerics’
Creating a new generic function for ‘colMins’ in package ‘MatrixGenerics’
Creating a new generic function for ‘rowOrderStats’ in package ‘MatrixGenerics’
Creating a new generic function for ‘colOrderStats’ in package ‘MatrixGenerics’
Creating a new generic function for ‘rowProds’ in package ‘MatrixGenerics’
Creating a new generic function for ‘colProds’ in package ‘MatrixGenerics’
Creating a new generic function for ‘rowQuantiles’ in package ‘MatrixGenerics’
Creating a new generic function for ‘colQuantiles’ in package ‘MatrixGenerics’
Creating a new generic function for ‘rowRanges’ in package ‘MatrixGenerics’
Creating a new generic function for ‘colRanges’ in package ‘MatrixGenerics’
Creating a new generic function for ‘rowRanks’ in package ‘MatrixGenerics’
Creating a new generic function for ‘colRanks’ in package ‘MatrixGenerics’
Creating a new generic function for ‘rowSdDiffs’ in package ‘MatrixGenerics’
Creating a new generic function for ‘colSdDiffs’ in package ‘MatrixGenerics’
Creating a new generic function for ‘rowSds’ in package ‘MatrixGenerics’
Creating a new generic function for ‘colSds’ in package ‘MatrixGenerics’
Creating a new generic function for ‘rowSums2’ in package ‘MatrixGenerics’
Creating a new generic function for ‘colSums2’ in package ‘MatrixGenerics’
Creating a new generic function for ‘rowTabulates’ in package ‘MatrixGenerics’
Creating a new generic function for ‘colTabulates’ in package ‘MatrixGenerics’
Creating a new generic function for ‘rowVarDiffs’ in package ‘MatrixGenerics’
Creating a new generic function for ‘colVarDiffs’ in package ‘MatrixGenerics’
Creating a new generic function for ‘rowVars’ in package ‘MatrixGenerics’
Creating a new generic function for ‘colVars’ in package ‘MatrixGenerics’
Creating a new generic function for ‘rowWeightedMads’ in package ‘MatrixGenerics’
Creating a new generic function for ‘colWeightedMads’ in package ‘MatrixGenerics’
Creating a new generic function for ‘rowWeightedMeans’ in package ‘MatrixGenerics’
Creating a new generic function for ‘colWeightedMeans’ in package ‘MatrixGenerics’
Creating a new generic function for ‘rowWeightedMedians’ in package ‘MatrixGenerics’
Creating a new generic function for ‘colWeightedMedians’ in package ‘MatrixGenerics’
Creating a new generic function for ‘rowWeightedSds’ in package ‘MatrixGenerics’
Creating a new generic function for ‘colWeightedSds’ in package ‘MatrixGenerics’
Creating a new generic function for ‘rowWeightedVars’ in package ‘MatrixGenerics’
Creating a new generic function for ‘colWeightedVars’ in package ‘MatrixGenerics’
** help
*** installing help indices
** building package indices
** 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 (MatrixGenerics)
* installing *source* package ‘rhdf5’ ...
** using staged installation
configure: creating ./config.status
config.status: creating src/external_filters.h
** 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’
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.3-3.17/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -c H5.c -o H5.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.3-3.17/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -c H5A.c -o H5A.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.3-3.17/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -c H5D.c -o H5D.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.3-3.17/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -c H5E.c -o H5E.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.3-3.17/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -c H5F.c -o H5F.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.3-3.17/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -c H5G.c -o H5G.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.3-3.17/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -c H5I.c -o H5I.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.3-3.17/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -c H5L.c -o H5L.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.3-3.17/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -c H5O.c -o H5O.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.3-3.17/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -c H5P.c -o H5P.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.3-3.17/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -c H5R.c -o H5R.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.3-3.17/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -c H5S.c -o H5S.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.3-3.17/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -c H5S_extras.c -o H5S_extras.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.3-3.17/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -c H5T.c -o H5T.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.3-3.17/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -c H5Z.c -o H5Z.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.3-3.17/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -c H5constants.c -o H5constants.o
g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.3-3.17/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -c HandleList.cpp -o HandleList.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.3-3.17/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -c HandleListWrap.c -o HandleListWrap.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.3-3.17/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -c bit64conversion.c -o bit64conversion.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.3-3.17/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -c external_filters.c -o external_filters.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.3-3.17/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -c h5dump.c -o h5dump.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.3-3.17/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -c h5ls.c -o h5ls.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.3-3.17/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -c h5testLock.c -o h5testLock.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.3-3.17/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -c h5writeDataFrame.c -o h5writeDataFrame.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.3-3.17/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -c printdatatype.c -o printdatatype.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.3-3.17/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -c utils.c -o utils.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.3-3.17/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -c wrap.c -o wrap.o
g++ -std=gnu++17 -shared -L/usr/local/lib -o rhdf5.so H5.o H5A.o H5D.o H5E.o H5F.o H5G.o H5I.o H5L.o H5O.o H5P.o H5R.o H5S.o H5S_extras.o H5T.o H5Z.o H5constants.o HandleList.o HandleListWrap.o bit64conversion.o external_filters.o h5dump.o h5ls.o h5testLock.o h5writeDataFrame.o printdatatype.o utils.o wrap.o /home/omnipath/local/R/4.3-3.17/Rhdf5lib/lib/libhdf5.a -lcrypto -lcurl -lsz -laec -lz -ldl -lm
installing to /home/omnipath/local/R/4.3-3.17/00LOCK-rhdf5/00new/rhdf5/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 (rhdf5)
* installing *source* package ‘graph’ ...
** 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 graph.c -o graph.o
gcc -shared -L/usr/local/lib -o graph.so graph.o
mv graph.so BioC_graph.so
installing to /home/omnipath/local/R/4.3-3.17/00LOCK-graph/00new/graph/libs
** R
** data
** 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 (graph)

The downloaded source packages are in
	‘/tmp/Rtmp5kbk7x/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' 

[ Finished: 2023-03-30 12:29:40 CEST ]