[ Started: 2023-10-10 12:46:03 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" trying URL 'https://cran.uni-muenster.de/src/contrib/systemfonts_1.0.5.tar.gz' Content type 'application/x-gzip' length 80638 bytes (78 KB) ================================================== downloaded 78 KB trying URL 'https://cran.uni-muenster.de/src/contrib/textshaping_0.3.7.tar.gz' Content type 'application/x-gzip' length 35100 bytes (34 KB) ================================================== downloaded 34 KB * installing *source* package ‘systemfonts’ ... ** package ‘systemfonts’ successfully unpacked and MD5 sums checked ** using staged installation Found pkg-config cflags and libs! Using PKG_CFLAGS=-I/usr/local/include/freetype2 -I/usr/include/uuid -I/usr/include/libpng16 -I/usr/include/harfbuzz -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include Using PKG_LIBS=-L/usr/local/lib -lfontconfig -lfreetype ** libs using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ rm -f systemfonts.so caches.o cpp11.o dev_metrics.o font_matching.o font_registry.o ft_cache.o string_shape.o font_metrics.o font_fallback.o string_metrics.o emoji.o cache_store.o init.o unix/FontManagerLinux.o g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include/freetype2 -I/usr/include/uuid -I/usr/include/libpng16 -I/usr/include/harfbuzz -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I'/home/omnipath/local/R/4.3-3.17/cpp11/include' -I/usr/local/include -fpic -g -O2 -c caches.cpp -o caches.o g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include/freetype2 -I/usr/include/uuid -I/usr/include/libpng16 -I/usr/include/harfbuzz -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/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++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include/freetype2 -I/usr/include/uuid -I/usr/include/libpng16 -I/usr/include/harfbuzz -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I'/home/omnipath/local/R/4.3-3.17/cpp11/include' -I/usr/local/include -fpic -g -O2 -c dev_metrics.cpp -o dev_metrics.o g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include/freetype2 -I/usr/include/uuid -I/usr/include/libpng16 -I/usr/include/harfbuzz -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I'/home/omnipath/local/R/4.3-3.17/cpp11/include' -I/usr/local/include -fpic -g -O2 -c font_matching.cpp -o font_matching.o g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include/freetype2 -I/usr/include/uuid -I/usr/include/libpng16 -I/usr/include/harfbuzz -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I'/home/omnipath/local/R/4.3-3.17/cpp11/include' -I/usr/local/include -fpic -g -O2 -c font_registry.cpp -o font_registry.o g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include/freetype2 -I/usr/include/uuid -I/usr/include/libpng16 -I/usr/include/harfbuzz -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I'/home/omnipath/local/R/4.3-3.17/cpp11/include' -I/usr/local/include -fpic -g -O2 -c ft_cache.cpp -o ft_cache.o g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include/freetype2 -I/usr/include/uuid -I/usr/include/libpng16 -I/usr/include/harfbuzz -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I'/home/omnipath/local/R/4.3-3.17/cpp11/include' -I/usr/local/include -fpic -g -O2 -c string_shape.cpp -o string_shape.o g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include/freetype2 -I/usr/include/uuid -I/usr/include/libpng16 -I/usr/include/harfbuzz -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I'/home/omnipath/local/R/4.3-3.17/cpp11/include' -I/usr/local/include -fpic -g -O2 -c font_metrics.cpp -o font_metrics.o g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include/freetype2 -I/usr/include/uuid -I/usr/include/libpng16 -I/usr/include/harfbuzz -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I'/home/omnipath/local/R/4.3-3.17/cpp11/include' -I/usr/local/include -fpic -g -O2 -c font_fallback.cpp -o font_fallback.o g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include/freetype2 -I/usr/include/uuid -I/usr/include/libpng16 -I/usr/include/harfbuzz -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I'/home/omnipath/local/R/4.3-3.17/cpp11/include' -I/usr/local/include -fpic -g -O2 -c string_metrics.cpp -o string_metrics.o g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include/freetype2 -I/usr/include/uuid -I/usr/include/libpng16 -I/usr/include/harfbuzz -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I'/home/omnipath/local/R/4.3-3.17/cpp11/include' -I/usr/local/include -fpic -g -O2 -c emoji.cpp -o emoji.o g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include/freetype2 -I/usr/include/uuid -I/usr/include/libpng16 -I/usr/include/harfbuzz -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I'/home/omnipath/local/R/4.3-3.17/cpp11/include' -I/usr/local/include -fpic -g -O2 -c cache_store.cpp -o cache_store.o g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include/freetype2 -I/usr/include/uuid -I/usr/include/libpng16 -I/usr/include/harfbuzz -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I'/home/omnipath/local/R/4.3-3.17/cpp11/include' -I/usr/local/include -fpic -g -O2 -c init.cpp -o init.o g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include/freetype2 -I/usr/include/uuid -I/usr/include/libpng16 -I/usr/include/harfbuzz -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I'/home/omnipath/local/R/4.3-3.17/cpp11/include' -I/usr/local/include -fpic -g -O2 -c unix/FontManagerLinux.cpp -o unix/FontManagerLinux.o g++ -std=gnu++17 -shared -L/usr/local/lib -o systemfonts.so caches.o cpp11.o dev_metrics.o font_matching.o font_registry.o ft_cache.o string_shape.o font_metrics.o font_fallback.o string_metrics.o emoji.o cache_store.o init.o unix/FontManagerLinux.o -L/usr/local/lib -lfontconfig -lfreetype installing to /home/omnipath/local/R/4.3-3.17/00LOCK-systemfonts/00new/systemfonts/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 (systemfonts) * installing *source* package ‘textshaping’ ... ** package ‘textshaping’ successfully unpacked and MD5 sums checked ** using staged installation Found pkg-config cflags and libs! Using PKG_CFLAGS=-I/usr/local/include/freetype2 -I/usr/include/libpng16 -I/usr/include/harfbuzz -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/fribidi Using PKG_LIBS=-L/usr/local/lib -lharfbuzz -lfreetype -lfribidi ** libs using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ rm -f textshaping.so cpp11.o face_feature.o hb_shaper.o init.o string_bidi.o string_metrics.o string_shape.o g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -DNDEBUG -I/usr/local/include/freetype2 -I/usr/include/libpng16 -I/usr/include/harfbuzz -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/fribidi -I'/home/omnipath/local/R/4.3-3.17/cpp11/include' -I'/home/omnipath/local/R/4.3-3.17/systemfonts/include' -I/usr/local/include -fpic -g -O2 -c cpp11.cpp -o cpp11.o g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -DNDEBUG -I/usr/local/include/freetype2 -I/usr/include/libpng16 -I/usr/include/harfbuzz -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/fribidi -I'/home/omnipath/local/R/4.3-3.17/cpp11/include' -I'/home/omnipath/local/R/4.3-3.17/systemfonts/include' -I/usr/local/include -fpic -g -O2 -c face_feature.cpp -o face_feature.o g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -DNDEBUG -I/usr/local/include/freetype2 -I/usr/include/libpng16 -I/usr/include/harfbuzz -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/fribidi -I'/home/omnipath/local/R/4.3-3.17/cpp11/include' -I'/home/omnipath/local/R/4.3-3.17/systemfonts/include' -I/usr/local/include -fpic -g -O2 -c hb_shaper.cpp -o hb_shaper.o g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -DNDEBUG -I/usr/local/include/freetype2 -I/usr/include/libpng16 -I/usr/include/harfbuzz -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/fribidi -I'/home/omnipath/local/R/4.3-3.17/cpp11/include' -I'/home/omnipath/local/R/4.3-3.17/systemfonts/include' -I/usr/local/include -fpic -g -O2 -c init.cpp -o init.o g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -DNDEBUG -I/usr/local/include/freetype2 -I/usr/include/libpng16 -I/usr/include/harfbuzz -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/fribidi -I'/home/omnipath/local/R/4.3-3.17/cpp11/include' -I'/home/omnipath/local/R/4.3-3.17/systemfonts/include' -I/usr/local/include -fpic -g -O2 -c string_bidi.cpp -o string_bidi.o g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -DNDEBUG -I/usr/local/include/freetype2 -I/usr/include/libpng16 -I/usr/include/harfbuzz -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/fribidi -I'/home/omnipath/local/R/4.3-3.17/cpp11/include' -I'/home/omnipath/local/R/4.3-3.17/systemfonts/include' -I/usr/local/include -fpic -g -O2 -c string_metrics.cpp -o string_metrics.o g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -DNDEBUG -I/usr/local/include/freetype2 -I/usr/include/libpng16 -I/usr/include/harfbuzz -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/fribidi -I'/home/omnipath/local/R/4.3-3.17/cpp11/include' -I'/home/omnipath/local/R/4.3-3.17/systemfonts/include' -I/usr/local/include -fpic -g -O2 -c string_shape.cpp -o string_shape.o g++ -std=gnu++17 -shared -L/usr/local/lib -o textshaping.so cpp11.o face_feature.o hb_shaper.o init.o string_bidi.o string_metrics.o string_shape.o -L/usr/local/lib -lharfbuzz -lfreetype -lfribidi installing to /home/omnipath/local/R/4.3-3.17/00LOCK-textshaping/00new/textshaping/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 (textshaping) The downloaded source packages are in ‘/tmp/RtmprHc9fo/downloaded_packages’ Bioconductor version 3.17 (BiocManager 1.30.22), R 4.3.0 (2023-04-21) Old packages: 'GenomicRanges', 'markdown', 'ragg' trying URL 'https://bioconductor.org/packages/3.17/bioc/src/contrib/GenomicRanges_1.52.1.tar.gz' Content type 'application/x-gzip' length 1139904 bytes (1.1 MB) ================================================== downloaded 1.1 MB trying URL 'https://cloud.r-project.org/src/contrib/markdown_1.10.tar.gz' Content type 'application/x-gzip' length 109827 bytes (107 KB) ================================================== downloaded 107 KB trying URL 'https://cloud.r-project.org/src/contrib/ragg_1.2.6.tar.gz' Content type 'application/x-gzip' length 425391 bytes (415 KB) ================================================== downloaded 415 KB * installing *source* package ‘GenomicRanges’ ... ** using staged installation ** libs using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.3-3.17/S4Vectors/include' -I'/home/omnipath/local/R/4.3-3.17/IRanges/include' -I/usr/local/include -fpic -g -O2 -c IRanges_stubs.c -o IRanges_stubs.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.3-3.17/S4Vectors/include' -I'/home/omnipath/local/R/4.3-3.17/IRanges/include' -I/usr/local/include -fpic -g -O2 -c R_init_GenomicRanges.c -o R_init_GenomicRanges.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.3-3.17/S4Vectors/include' -I'/home/omnipath/local/R/4.3-3.17/IRanges/include' -I/usr/local/include -fpic -g -O2 -c S4Vectors_stubs.c -o S4Vectors_stubs.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.3-3.17/S4Vectors/include' -I'/home/omnipath/local/R/4.3-3.17/IRanges/include' -I/usr/local/include -fpic -g -O2 -c transcript_utils.c -o transcript_utils.o gcc -shared -L/usr/local/lib -o GenomicRanges.so IRanges_stubs.o R_init_GenomicRanges.o S4Vectors_stubs.o transcript_utils.o installing to /home/omnipath/local/R/4.3-3.17/00LOCK-GenomicRanges/00new/GenomicRanges/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 (GenomicRanges) * installing *source* package ‘markdown’ ... ** package ‘markdown’ 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 (markdown) * 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/local/include/freetype2 -I/usr/include/harfbuzz -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/libpng16 -I/usr/include/x86_64-linux-gnu Using PKG_LIBS=-L/usr/local/lib -lfreetype -lpng16 -lz -ltiff -ljpeg -ljpeg ** libs using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I./agg/include -I/usr/local/include/freetype2 -I/usr/include/harfbuzz -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/libpng16 -I/usr/include/x86_64-linux-gnu -I'/home/omnipath/local/R/4.3-3.17/systemfonts/include' -I'/home/omnipath/local/R/4.3-3.17/textshaping/include' -I/usr/local/include -fpic -g -O2 -c capture_dev.cpp -o capture_dev.o g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I./agg/include -I/usr/local/include/freetype2 -I/usr/include/harfbuzz -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/libpng16 -I/usr/include/x86_64-linux-gnu -I'/home/omnipath/local/R/4.3-3.17/systemfonts/include' -I'/home/omnipath/local/R/4.3-3.17/textshaping/include' -I/usr/local/include -fpic -g -O2 -c init.cpp -o init.o g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I./agg/include -I/usr/local/include/freetype2 -I/usr/include/harfbuzz -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/libpng16 -I/usr/include/x86_64-linux-gnu -I'/home/omnipath/local/R/4.3-3.17/systemfonts/include' -I'/home/omnipath/local/R/4.3-3.17/textshaping/include' -I/usr/local/include -fpic -g -O2 -c jpeg_dev.cpp -o jpeg_dev.o g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I./agg/include -I/usr/local/include/freetype2 -I/usr/include/harfbuzz -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/libpng16 -I/usr/include/x86_64-linux-gnu -I'/home/omnipath/local/R/4.3-3.17/systemfonts/include' -I'/home/omnipath/local/R/4.3-3.17/textshaping/include' -I/usr/local/include -fpic -g -O2 -c png_dev.cpp -o png_dev.o g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I./agg/include -I/usr/local/include/freetype2 -I/usr/include/harfbuzz -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/libpng16 -I/usr/include/x86_64-linux-gnu -I'/home/omnipath/local/R/4.3-3.17/systemfonts/include' -I'/home/omnipath/local/R/4.3-3.17/textshaping/include' -I/usr/local/include -fpic -g -O2 -c ppm_dev.cpp -o ppm_dev.o g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I./agg/include -I/usr/local/include/freetype2 -I/usr/include/harfbuzz -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/libpng16 -I/usr/include/x86_64-linux-gnu -I'/home/omnipath/local/R/4.3-3.17/systemfonts/include' -I'/home/omnipath/local/R/4.3-3.17/textshaping/include' -I/usr/local/include -fpic -g -O2 -c tiff_dev.cpp -o tiff_dev.o g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I./agg/include -I/usr/local/include/freetype2 -I/usr/include/harfbuzz -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/libpng16 -I/usr/include/x86_64-linux-gnu -I'/home/omnipath/local/R/4.3-3.17/systemfonts/include' -I'/home/omnipath/local/R/4.3-3.17/textshaping/include' -I/usr/local/include -fpic -g -O2 -c agg/src/agg_curves.cpp -o agg/src/agg_curves.o g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I./agg/include -I/usr/local/include/freetype2 -I/usr/include/harfbuzz -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/libpng16 -I/usr/include/x86_64-linux-gnu -I'/home/omnipath/local/R/4.3-3.17/systemfonts/include' -I'/home/omnipath/local/R/4.3-3.17/textshaping/include' -I/usr/local/include -fpic -g -O2 -c agg/src/agg_font_freetype.cpp -o agg/src/agg_font_freetype.o g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I./agg/include -I/usr/local/include/freetype2 -I/usr/include/harfbuzz -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/libpng16 -I/usr/include/x86_64-linux-gnu -I'/home/omnipath/local/R/4.3-3.17/systemfonts/include' -I'/home/omnipath/local/R/4.3-3.17/textshaping/include' -I/usr/local/include -fpic -g -O2 -c agg/src/agg_image_filters.cpp -o agg/src/agg_image_filters.o g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I./agg/include -I/usr/local/include/freetype2 -I/usr/include/harfbuzz -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/libpng16 -I/usr/include/x86_64-linux-gnu -I'/home/omnipath/local/R/4.3-3.17/systemfonts/include' -I'/home/omnipath/local/R/4.3-3.17/textshaping/include' -I/usr/local/include -fpic -g -O2 -c agg/src/agg_trans_affine.cpp -o agg/src/agg_trans_affine.o g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I./agg/include -I/usr/local/include/freetype2 -I/usr/include/harfbuzz -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/libpng16 -I/usr/include/x86_64-linux-gnu -I'/home/omnipath/local/R/4.3-3.17/systemfonts/include' -I'/home/omnipath/local/R/4.3-3.17/textshaping/include' -I/usr/local/include -fpic -g -O2 -c agg/src/agg_vcgen_dash.cpp -o agg/src/agg_vcgen_dash.o g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I./agg/include -I/usr/local/include/freetype2 -I/usr/include/harfbuzz -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/libpng16 -I/usr/include/x86_64-linux-gnu -I'/home/omnipath/local/R/4.3-3.17/systemfonts/include' -I'/home/omnipath/local/R/4.3-3.17/textshaping/include' -I/usr/local/include -fpic -g -O2 -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/local/lib -o ragg.so capture_dev.o init.o jpeg_dev.o png_dev.o ppm_dev.o tiff_dev.o -Lagg -lstatagg -L/usr/local/lib -lfreetype -lpng16 -lz -ltiff -ljpeg -ljpeg installing to /home/omnipath/local/R/4.3-3.17/00LOCK-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/RtmprHc9fo/downloaded_packages’ Bioconductor version 3.17 (BiocManager 1.30.22), R 4.3.0 (2023-04-21) Warning message: package(s) not installed when version(s) same as or greater than current; use `force = TRUE` to re-install: 'BiocCheck' [ Finished: 2023-10-10 12:48:11 CEST ]