[ Started: 2024-02-16 11:51:15 CET ] [ CARNIVAL v2.7.2 for BioC-3.18 from https://github.com/saezlab/CARNIVAL@master ] [1] "Libraries: " "/home/omnipath/local/R/4.3-3.18" [3] "/home/omnipath/local/R/4.3" "/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 3.18 (BiocManager 1.30.22), R 4.3.1 (2023-06-16) Old packages: 'beachmat', 'HDF5Array' trying URL 'https://bioconductor.org/packages/3.18/bioc/src/contrib/beachmat_2.18.1.tar.gz' Content type 'application/x-gzip' length 512143 bytes (500 KB) ================================================== downloaded 500 KB trying URL 'https://bioconductor.org/packages/3.18/bioc/src/contrib/HDF5Array_1.30.1.tar.gz' Content type 'application/x-gzip' length 8098441 bytes (7.7 MB) ================================================== downloaded 7.7 MB * installing *source* package ‘beachmat’ ... ** using staged installation ** libs using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ using C++17 g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I../inst/include -I'/home/omnipath/local/R/4.3-3.18/Rcpp/include' -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I../inst/include -I'/home/omnipath/local/R/4.3-3.18/Rcpp/include' -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c delayed_isometric_binary.cpp -o delayed_isometric_binary.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I../inst/include -I'/home/omnipath/local/R/4.3-3.18/Rcpp/include' -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c delayed_isometric_math.cpp -o delayed_isometric_math.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I../inst/include -I'/home/omnipath/local/R/4.3-3.18/Rcpp/include' -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c delayed_isometric_unary.cpp -o delayed_isometric_unary.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I../inst/include -I'/home/omnipath/local/R/4.3-3.18/Rcpp/include' -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c delayed_other.cpp -o delayed_other.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I../inst/include -I'/home/omnipath/local/R/4.3-3.18/Rcpp/include' -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c dense_matrix.cpp -o dense_matrix.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I../inst/include -I'/home/omnipath/local/R/4.3-3.18/Rcpp/include' -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c fragment_sparse_rows.cpp -o fragment_sparse_rows.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I../inst/include -I'/home/omnipath/local/R/4.3-3.18/Rcpp/include' -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c sparse_matrix.cpp -o sparse_matrix.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I../inst/include -I'/home/omnipath/local/R/4.3-3.18/Rcpp/include' -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c tatami_utils.cpp -o tatami_utils.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I../inst/include -I'/home/omnipath/local/R/4.3-3.18/Rcpp/include' -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c unknown_matrix.cpp -o unknown_matrix.o g++ -std=gnu++17 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -o beachmat.so RcppExports.o delayed_isometric_binary.o delayed_isometric_math.o delayed_isometric_unary.o delayed_other.o dense_matrix.o fragment_sparse_rows.o sparse_matrix.o tatami_utils.o unknown_matrix.o -L/usr/lib/R/lib -lR installing to /home/omnipath/local/R/4.3-3.18/00LOCK-beachmat/00new/beachmat/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 (beachmat) * installing *source* package ‘HDF5Array’ ... ** using staged installation ** libs using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.3-3.18/S4Vectors/include' -I'/home/omnipath/local/R/4.3-3.18/Rhdf5lib/include' -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c S4Vectors_stubs.c -o S4Vectors_stubs.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.3-3.18/S4Vectors/include' -I'/home/omnipath/local/R/4.3-3.18/Rhdf5lib/include' -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c H5File.c -o H5File.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.3-3.18/S4Vectors/include' -I'/home/omnipath/local/R/4.3-3.18/Rhdf5lib/include' -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c global_errmsg_buf.c -o global_errmsg_buf.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.3-3.18/S4Vectors/include' -I'/home/omnipath/local/R/4.3-3.18/Rhdf5lib/include' -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c H5DSetDescriptor.c -o H5DSetDescriptor.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.3-3.18/S4Vectors/include' -I'/home/omnipath/local/R/4.3-3.18/Rhdf5lib/include' -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c h5dimscales.c -o h5dimscales.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.3-3.18/S4Vectors/include' -I'/home/omnipath/local/R/4.3-3.18/Rhdf5lib/include' -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c uaselection.c -o uaselection.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.3-3.18/S4Vectors/include' -I'/home/omnipath/local/R/4.3-3.18/Rhdf5lib/include' -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c h5mread_helpers.c -o h5mread_helpers.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.3-3.18/S4Vectors/include' -I'/home/omnipath/local/R/4.3-3.18/Rhdf5lib/include' -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c h5mread_startscounts.c -o h5mread_startscounts.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.3-3.18/S4Vectors/include' -I'/home/omnipath/local/R/4.3-3.18/Rhdf5lib/include' -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c ChunkIterator.c -o ChunkIterator.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.3-3.18/S4Vectors/include' -I'/home/omnipath/local/R/4.3-3.18/Rhdf5lib/include' -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c h5mread_index.c -o h5mread_index.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.3-3.18/S4Vectors/include' -I'/home/omnipath/local/R/4.3-3.18/Rhdf5lib/include' -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c h5mread_sparse.c -o h5mread_sparse.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.3-3.18/S4Vectors/include' -I'/home/omnipath/local/R/4.3-3.18/Rhdf5lib/include' -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c h5mread.c -o h5mread.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.3-3.18/S4Vectors/include' -I'/home/omnipath/local/R/4.3-3.18/Rhdf5lib/include' -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c h5summarize.c -o h5summarize.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.3-3.18/S4Vectors/include' -I'/home/omnipath/local/R/4.3-3.18/Rhdf5lib/include' -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c R_init_HDF5Array.c -o R_init_HDF5Array.o gcc -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -o HDF5Array.so S4Vectors_stubs.o H5File.o global_errmsg_buf.o H5DSetDescriptor.o h5dimscales.o uaselection.o h5mread_helpers.o h5mread_startscounts.o ChunkIterator.o h5mread_index.o h5mread_sparse.o h5mread.o h5summarize.o R_init_HDF5Array.o /home/omnipath/local/R/4.3-3.18/Rhdf5lib/lib/libhdf5_hl.a /home/omnipath/local/R/4.3-3.18/Rhdf5lib/lib/libhdf5.a -lcrypto -lcurl -lsz -laec -lz -ldl -lm -L/usr/lib/R/lib -lR installing to /home/omnipath/local/R/4.3-3.18/00LOCK-HDF5Array/00new/HDF5Array/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** 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 (HDF5Array) The downloaded source packages are in ‘/tmp/RtmpLRjiTa/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 3.18 (BiocManager 1.30.22), R 4.3.1 (2023-06-16) Warning message: package(s) not installed when version(s) same as or greater than current; use `force = TRUE` to re-install: 'BiocCheck' [ Finished: 2024-02-16 11:55:40 CET ]