[ Started: 2024-09-12 15:31:08 CEST ] [ CARNIVAL v2.7.2 for BioC-3.20 from https://github.com/saezlab/CARNIVAL@master (2b8887a 2023-12-06 13:18:32) ] [1] "Libraries: " "/home/omnipath/local/R/4.4-3.20" [3] "/home/omnipath/local/R/4.4" "/usr/lib/R/library" trying URL 'https://cran.uni-muenster.de/src/contrib/ragg_1.3.3.tar.gz' Content type 'application/x-gzip' length 428945 bytes (418 KB) ================================================== downloaded 418 KB * installing *source* package ‘ragg’ ... ** package ‘ragg’ successfully unpacked and MD5 sums checked ** using staged installation Found pkg-config cflags and libs! Using PKG_CFLAGS=-I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/x86_64-linux-gnu -I/usr/include/webp Using PKG_LIBS=-lfreetype -lpng16 -ltiff -ljpeg ** libs using C++ compiler: ‘g++ (Ubuntu 13.2.0-23ubuntu4) 13.2.0’ g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I./agg/include -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/x86_64-linux-gnu -I/usr/include/webp -I'/home/omnipath/local/R/4.4-3.20/systemfonts/include' -I'/home/omnipath/local/R/4.4-3.20/textshaping/include' -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c capture_dev.cpp -o capture_dev.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I./agg/include -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/x86_64-linux-gnu -I/usr/include/webp -I'/home/omnipath/local/R/4.4-3.20/systemfonts/include' -I'/home/omnipath/local/R/4.4-3.20/textshaping/include' -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c init.cpp -o init.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I./agg/include -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/x86_64-linux-gnu -I/usr/include/webp -I'/home/omnipath/local/R/4.4-3.20/systemfonts/include' -I'/home/omnipath/local/R/4.4-3.20/textshaping/include' -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c jpeg_dev.cpp -o jpeg_dev.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I./agg/include -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/x86_64-linux-gnu -I/usr/include/webp -I'/home/omnipath/local/R/4.4-3.20/systemfonts/include' -I'/home/omnipath/local/R/4.4-3.20/textshaping/include' -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c png_dev.cpp -o png_dev.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I./agg/include -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/x86_64-linux-gnu -I/usr/include/webp -I'/home/omnipath/local/R/4.4-3.20/systemfonts/include' -I'/home/omnipath/local/R/4.4-3.20/textshaping/include' -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c ppm_dev.cpp -o ppm_dev.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I./agg/include -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/x86_64-linux-gnu -I/usr/include/webp -I'/home/omnipath/local/R/4.4-3.20/systemfonts/include' -I'/home/omnipath/local/R/4.4-3.20/textshaping/include' -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c tiff_dev.cpp -o tiff_dev.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I./agg/include -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/x86_64-linux-gnu -I/usr/include/webp -I'/home/omnipath/local/R/4.4-3.20/systemfonts/include' -I'/home/omnipath/local/R/4.4-3.20/textshaping/include' -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c agg/src/agg_curves.cpp -o agg/src/agg_curves.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I./agg/include -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/x86_64-linux-gnu -I/usr/include/webp -I'/home/omnipath/local/R/4.4-3.20/systemfonts/include' -I'/home/omnipath/local/R/4.4-3.20/textshaping/include' -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c agg/src/agg_font_freetype.cpp -o agg/src/agg_font_freetype.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I./agg/include -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/x86_64-linux-gnu -I/usr/include/webp -I'/home/omnipath/local/R/4.4-3.20/systemfonts/include' -I'/home/omnipath/local/R/4.4-3.20/textshaping/include' -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c agg/src/agg_image_filters.cpp -o agg/src/agg_image_filters.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I./agg/include -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/x86_64-linux-gnu -I/usr/include/webp -I'/home/omnipath/local/R/4.4-3.20/systemfonts/include' -I'/home/omnipath/local/R/4.4-3.20/textshaping/include' -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c agg/src/agg_trans_affine.cpp -o agg/src/agg_trans_affine.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I./agg/include -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/x86_64-linux-gnu -I/usr/include/webp -I'/home/omnipath/local/R/4.4-3.20/systemfonts/include' -I'/home/omnipath/local/R/4.4-3.20/textshaping/include' -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c agg/src/agg_vcgen_dash.cpp -o agg/src/agg_vcgen_dash.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I./agg/include -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/x86_64-linux-gnu -I/usr/include/webp -I'/home/omnipath/local/R/4.4-3.20/systemfonts/include' -I'/home/omnipath/local/R/4.4-3.20/textshaping/include' -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c agg/src/agg_vcgen_stroke.cpp -o agg/src/agg_vcgen_stroke.o ar rcs agg/libstatagg.a agg/src/agg_curves.o agg/src/agg_font_freetype.o agg/src/agg_image_filters.o agg/src/agg_trans_affine.o agg/src/agg_vcgen_dash.o agg/src/agg_vcgen_stroke.o g++ -std=gnu++17 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -o ragg.so capture_dev.o init.o jpeg_dev.o png_dev.o ppm_dev.o tiff_dev.o -Lagg -lstatagg -lfreetype -lpng16 -ltiff -ljpeg -L/usr/lib/R/lib -lR installing to /home/omnipath/local/R/4.4-3.20/00LOCK-ragg/00new/ragg/libs ** R ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** 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 (ragg) The downloaded source packages are in ‘/tmp/Rtmp9Q9spc/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 3.20 (BiocManager 1.30.25), R 4.4.1 (2024-06-14) Old packages: 'BiocCheck', 'RcppArmadillo' trying URL 'https://bioconductor.org/packages/3.20/bioc/src/contrib/BiocCheck_1.41.17.tar.gz' Content type 'application/x-gzip' length 317381 bytes (309 KB) ================================================== downloaded 309 KB trying URL 'https://cloud.r-project.org/src/contrib/RcppArmadillo_14.0.2-1.tar.gz' Content type 'application/x-gzip' length 1392764 bytes (1.3 MB) ================================================== downloaded 1.3 MB * installing *source* package ‘BiocCheck’ ... ** package ‘BiocCheck’ successfully unpacked and MD5 sums checked ** 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 ‘RcppArmadillo’ ... ** package ‘RcppArmadillo’ successfully unpacked and MD5 sums checked ** 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 how to run the C++ preprocessor... g++ -std=gnu++17 -E checking whether the compiler supports GNU C++... (cached) yes checking whether g++ -std=gnu++17 accepts -g... (cached) yes checking for g++ -std=gnu++17 option to enable C++11 features... (cached) none needed checking whether we have a suitable tempdir... /tmp checking whether R CMD SHLIB can already compile programs using OpenMP... yes checking LAPACK_LIBS... system LAPACK found configure: creating ./config.status config.status: creating inst/include/RcppArmadillo/config/RcppArmadilloConfigGenerated.h config.status: creating src/Makevars ** libs using C++ compiler: ‘g++ (Ubuntu 13.2.0-23ubuntu4) 13.2.0’ g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I../inst/include -I'/home/omnipath/local/R/4.4-3.20/Rcpp/include' -fopenmp -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c RcppArmadillo.cpp -o RcppArmadillo.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I../inst/include -I'/home/omnipath/local/R/4.4-3.20/Rcpp/include' -fopenmp -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I../inst/include -I'/home/omnipath/local/R/4.4-3.20/Rcpp/include' -fopenmp -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c fastLm.cpp -o fastLm.o g++ -std=gnu++17 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -o RcppArmadillo.so RcppArmadillo.o RcppExports.o fastLm.o -fopenmp -llapack -lblas -lgfortran -lm -lquadmath -L/usr/lib/R/lib -lR installing to /home/omnipath/local/R/4.4-3.20/00LOCK-RcppArmadillo/00new/RcppArmadillo/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 (RcppArmadillo) The downloaded source packages are in ‘/tmp/Rtmp9Q9spc/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 3.20 (BiocManager 1.30.25), R 4.4.1 (2024-06-14) 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: BiocStyle [ Finished: 2024-09-12 15:34:16 CEST ]