[ Started: 2023-03-20 18:01:31 CET ] [ progeny v1.17.3 for BioC-3.16 from https://github.com/saezlab/progeny@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 'help("repositories", package = "BiocManager")' for details. Replacement repositories: CRAN: https://cloud.r-project.org Bioconductor version 3.16 (BiocManager 1.30.20), R 4.2.2 Patched (2022-11-10 r83330) Old packages: 'BiocParallel', 'NMF', 'SingleCellExperiment' trying URL 'https://bioconductor.org/packages/3.16/bioc/src/contrib/BiocParallel_1.32.6.tar.gz' Content type 'application/x-gzip' length 978897 bytes (955 KB) ================================================== downloaded 955 KB trying URL 'https://cloud.r-project.org/src/contrib/NMF_0.26.tar.gz' Content type 'application/x-gzip' length 1672812 bytes (1.6 MB) ================================================== downloaded 1.6 MB trying URL 'https://bioconductor.org/packages/3.16/bioc/src/contrib/SingleCellExperiment_1.20.1.tar.gz' Content type 'application/x-gzip' length 939265 bytes (917 KB) ================================================== downloaded 917 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++14 accepts -g... yes checking for g++ -std=gnu++14 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 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 -ffile-prefix-map=/build/r-base-Faorqz/r-base-4.2.2.20221110=. -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 -ffile-prefix-map=/build/r-base-Faorqz/r-base-4.2.2.20221110=. -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 -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -o BiocParallel.so cpp11.o ipcmutex.o -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 ‘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 -ffile-prefix-map=/build/r-base-Faorqz/r-base-4.2.2.20221110=. -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 -ffile-prefix-map=/build/r-base-Faorqz/r-base-4.2.2.20221110=. -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 -ffile-prefix-map=/build/r-base-Faorqz/r-base-4.2.2.20221110=. -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 -ffile-prefix-map=/build/r-base-Faorqz/r-base-4.2.2.20221110=. -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 -ffile-prefix-map=/build/r-base-Faorqz/r-base-4.2.2.20221110=. -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 -flto=auto -ffat-lto-objects -flto=auto -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 ‘SingleCellExperiment’ ... ** 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 (SingleCellExperiment) The downloaded source packages are in ‘/tmp/RtmpCcBvdT/downloaded_packages’ 'getOption("repos")' replaces Bioconductor standard repositories, see 'help("repositories", package = "BiocManager")' for details. Replacement repositories: CRAN: https://cloud.r-project.org Bioconductor version 3.16 (BiocManager 1.30.20), R 4.2.2 Patched (2022-11-10 r83330) Warning message: package(s) not installed when version(s) same as or greater than current; use `force = TRUE` to re-install: 'BiocCheck' Skipping 2 packages ahead of CRAN: tibble, FNN [ Finished: 2023-03-20 18:02:23 CET ]