[ Started: 2022-11-19 01:01:37 CET ] [ CARNIVAL v2.7.2 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 1.30.19), R 4.2.1 (2022-06-23) Old packages: 'BiocCheck', 'insight', 'knitr', 'matrixStats', 'NMF' trying URL 'https://bioconductor.org/packages/3.16/bioc/src/contrib/BiocCheck_1.34.2.tar.gz' Content type 'application/x-gzip' length 4372102 bytes (4.2 MB) ================================================== downloaded 4.2 MB trying URL 'https://cloud.r-project.org/src/contrib/insight_0.18.7.tar.gz' Content type 'application/x-gzip' length 908220 bytes (886 KB) ================================================== downloaded 886 KB trying URL 'https://cloud.r-project.org/src/contrib/knitr_1.41.tar.gz' Content type 'application/x-gzip' length 890610 bytes (869 KB) ================================================== downloaded 869 KB trying URL 'https://cloud.r-project.org/src/contrib/matrixStats_0.63.0.tar.gz' Content type 'application/x-gzip' length 202957 bytes (198 KB) ================================================== downloaded 198 KB trying URL 'https://cloud.r-project.org/src/contrib/NMF_0.25.tar.gz' Content type 'application/x-gzip' length 1674534 bytes (1.6 MB) ================================================== downloaded 1.6 MB * installing *source* package ‘insight’ ... ** package ‘insight’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** data ** 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 ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (insight) * installing *source* package ‘knitr’ ... ** package ‘knitr’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** demo ** 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 (knitr) * installing *source* package ‘matrixStats’ ... ** package ‘matrixStats’ successfully unpacked and MD5 sums checked ** using staged installation ** libs gcc -I"/usr/share/R/include" -DNDEBUG -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 000.init.c -o 000.init.o gcc -I"/usr/share/R/include" -DNDEBUG -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 allocMatrix2.c -o allocMatrix2.o gcc -I"/usr/share/R/include" -DNDEBUG -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 anyMissing.c -o anyMissing.o gcc -I"/usr/share/R/include" -DNDEBUG -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 binCounts.c -o binCounts.o gcc -I"/usr/share/R/include" -DNDEBUG -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 binMeans.c -o binMeans.o gcc -I"/usr/share/R/include" -DNDEBUG -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 colCounts.c -o colCounts.o gcc -I"/usr/share/R/include" -DNDEBUG -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 colOrderStats.c -o colOrderStats.o gcc -I"/usr/share/R/include" -DNDEBUG -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 colRanges.c -o colRanges.o gcc -I"/usr/share/R/include" -DNDEBUG -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 diff2.c -o diff2.o gcc -I"/usr/share/R/include" -DNDEBUG -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 indexByRow.c -o indexByRow.o gcc -I"/usr/share/R/include" -DNDEBUG -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 logSumExp.c -o logSumExp.o gcc -I"/usr/share/R/include" -DNDEBUG -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 mean2.c -o mean2.o gcc -I"/usr/share/R/include" -DNDEBUG -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 naming.c -o naming.o gcc -I"/usr/share/R/include" -DNDEBUG -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 productExpSumLog.c -o productExpSumLog.o gcc -I"/usr/share/R/include" -DNDEBUG -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 psortKM.c -o psortKM.o gcc -I"/usr/share/R/include" -DNDEBUG -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 rowCounts.c -o rowCounts.o gcc -I"/usr/share/R/include" -DNDEBUG -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 rowCummaxs.c -o rowCummaxs.o gcc -I"/usr/share/R/include" -DNDEBUG -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 rowCummins.c -o rowCummins.o gcc -I"/usr/share/R/include" -DNDEBUG -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 rowCumprods.c -o rowCumprods.o gcc -I"/usr/share/R/include" -DNDEBUG -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 rowCumsums.c -o rowCumsums.o gcc -I"/usr/share/R/include" -DNDEBUG -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 rowDiffs.c -o rowDiffs.o gcc -I"/usr/share/R/include" -DNDEBUG -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 rowLogSumExp.c -o rowLogSumExp.o gcc -I"/usr/share/R/include" -DNDEBUG -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 rowMads.c -o rowMads.o gcc -I"/usr/share/R/include" -DNDEBUG -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 rowMeans2.c -o rowMeans2.o gcc -I"/usr/share/R/include" -DNDEBUG -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 rowMedians.c -o rowMedians.o gcc -I"/usr/share/R/include" -DNDEBUG -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 rowOrderStats.c -o rowOrderStats.o gcc -I"/usr/share/R/include" -DNDEBUG -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 rowRanges.c -o rowRanges.o gcc -I"/usr/share/R/include" -DNDEBUG -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 rowRanksWithTies.c -o rowRanksWithTies.o gcc -I"/usr/share/R/include" -DNDEBUG -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 rowSums2.c -o rowSums2.o gcc -I"/usr/share/R/include" -DNDEBUG -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 rowVars.c -o rowVars.o gcc -I"/usr/share/R/include" -DNDEBUG -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 signTabulate.c -o signTabulate.o gcc -I"/usr/share/R/include" -DNDEBUG -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 sum2.c -o sum2.o gcc -I"/usr/share/R/include" -DNDEBUG -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 validateIndices.c -o validateIndices.o gcc -I"/usr/share/R/include" -DNDEBUG -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 weightedMean.c -o weightedMean.o gcc -I"/usr/share/R/include" -DNDEBUG -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 weightedMedian.c -o weightedMedian.o gcc -I"/usr/share/R/include" -DNDEBUG -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 x_OP_y.c -o x_OP_y.o gcc -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o matrixStats.so 000.init.o allocMatrix2.o anyMissing.o binCounts.o binMeans.o colCounts.o colOrderStats.o colRanges.o diff2.o indexByRow.o logSumExp.o mean2.o naming.o productExpSumLog.o psortKM.o rowCounts.o rowCummaxs.o rowCummins.o rowCumprods.o rowCumsums.o rowDiffs.o rowLogSumExp.o rowMads.o rowMeans2.o rowMedians.o rowOrderStats.o rowRanges.o rowRanksWithTies.o rowSums2.o rowVars.o signTabulate.o sum2.o validateIndices.o weightedMean.o weightedMedian.o x_OP_y.o -L/usr/lib/R/lib -lR installing to /home/omnipath/local/R/4.2-3.16/00LOCK-matrixStats/00new/matrixStats/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 (matrixStats) * installing *source* package ‘NMF’ ... ** package ‘NMF’ successfully unpacked and MD5 sums checked ** using staged installation ** libs g++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG -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 distance.cpp -o distance.o g++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG -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 divergence.cpp -o divergence.o g++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG -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 euclidean.cpp -o euclidean.o gcc -I"/usr/share/R/include" -DNDEBUG -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 registerDynamicSymbol.c -o registerDynamicSymbol.o g++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG -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 utils.cpp -o utils.o g++ -std=gnu++14 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o NMF.so distance.o divergence.o euclidean.o registerDynamicSymbol.o utils.o -L/usr/lib/R/lib -lR installing to /home/omnipath/local/R/4.2-3.16/00LOCK-NMF/00new/NMF/libs ** R ** data ** demo ** inst ** byte-compile and prepare package for lazy loading Setting package specific options: package:NMF:logger (1 default option(s)) Setting package specific options: package:NMF (10 default option(s)) Creating a generic function for ‘plot’ from ‘graphics’ in package ‘NMF’ (from the saved implicit definition) Creating meta registry in package 'NMF' ... OK Creating registry 'extra_handler' in package 'NMF' ... OK Creating registry 'extra_action' in package 'NMF' ... OK Registering extra handler 'install.packages' [function] ... OK Creating registry 'algorithm' in package 'NMF' ... OK Registering NMF algorithm '.R#brunet' [NMFStrategyIterative] ... OK Registering NMF algorithm 'brunet' [NMFStrategyIterative] based on template '.R#brunet' ... OK Registering NMF algorithm 'KL' [NMFStrategyIterative] ... OK Registering NMF algorithm '.R#lee' [NMFStrategyIterative] ... OK Registering NMF algorithm 'lee' [NMFStrategyIterative] based on template '.R#lee' ... OK Registering NMF algorithm 'Frobenius' [NMFStrategyIterative] ... OK Registering NMF algorithm '.R#offset' [NMFStrategyIterative] ... OK Registering NMF algorithm 'offset' [NMFStrategyIterative] based on template '.R#offset' ... OK Registering NMF algorithm '.R#nsNMF' [NMFStrategyIterative] ... OK Registering NMF algorithm 'nsNMF' [NMFStrategyIterative] based on template '.R#nsNMF' ... OK Registering NMF algorithm 'ls-nmf' [NMFStrategyIterative] ... OK Registering NMF algorithm 'pe-nmf' [NMFStrategyIterative] ... OK Registering NMF algorithm '.siNMF' [NMFStrategyIterative] based on template 'lee' ... OK Registering NMF algorithm 'siNMF' [NMFStrategyIterative] based on template 'lee' ... OK Registering NMF algorithm 'snmf/r' [NMFStrategyFunction] ... OK Registering NMF algorithm 'snmf/l' [NMFStrategyFunction] ... OK Registering extra action 'bigmemory' for handler 'install.packages' ... OK Registering extra action 'synchronicity' for handler 'install.packages' ... OK Creating registry 'seed' in package 'NMF' ... OK Registering NMF seeding method 'none' [NMFSeed] ... OK Registering NMF seeding method 'random' [NMFSeed] ... OK Registering NMF seeding method 'ica' [NMFSeed] ... OK Registering NMF seeding method 'nndsvd' [NMFSeed] ... OK ** 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 (NMF) * 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) The downloaded source packages are in ‘/tmp/RtmpdWCUCw/downloaded_packages’ Skipping 1 packages ahead of CRAN: knitr [ Finished: 2022-11-19 01:02:33 CET ]