[ Started: 2025-01-20 12:21:12 CET ] [ CARNIVAL v2.14.0 for BioC-3.19 from https://git.bioconductor.org/packages/CARNIVAL@RELEASE_3_19 (bcf3cbc 2024-04-30 11:23:36) ] [1] "Libraries: " "/home/omnipath/local/R/4.4-3.19" [3] "/home/omnipath/local/R/4.4" "/usr/lib/R/library" Bioconductor version '3.19' is out-of-date; the current release version '3.20' is available with R version '4.4'; see https://bioconductor.org/install 'getOption("repos")' replaces Bioconductor standard repositories, see 'help("repositories", package = "BiocManager")' for details. Replacement repositories: CRAN: https://cloud.r-project.org Bioconductor version 3.19 (BiocManager 1.30.25), R 4.4.1 (2024-06-14) Old packages: 'systemfonts', 'textshaping' trying URL 'https://cloud.r-project.org/src/contrib/systemfonts_1.2.1.tar.gz' Content type 'application/x-gzip' length 101773 bytes (99 KB) ================================================== downloaded 99 KB trying URL 'https://cloud.r-project.org/src/contrib/textshaping_1.0.0.tar.gz' Content type 'application/x-gzip' length 75510 bytes (73 KB) ================================================== downloaded 73 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/include/freetype2 -I/usr/include/libpng16 Using PKG_LIBS=-lfontconfig -lfreetype ** libs using C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’ rm -f systemfonts.so caches.o cpp11.o dev_metrics.o font_matching.o font_local.o font_registry.o ft_cache.o string_shape.o font_metrics.o font_outlines.o font_fallback.o string_metrics.o emoji.o cache_store.o init.o unix/FontManagerLinux.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I/usr/include/freetype2 -I/usr/include/libpng16 -I'/home/omnipath/local/R/4.4-3.19/cpp11/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 caches.cpp -o caches.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I/usr/include/freetype2 -I/usr/include/libpng16 -I'/home/omnipath/local/R/4.4-3.19/cpp11/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 cpp11.cpp -o cpp11.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I/usr/include/freetype2 -I/usr/include/libpng16 -I'/home/omnipath/local/R/4.4-3.19/cpp11/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 dev_metrics.cpp -o dev_metrics.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I/usr/include/freetype2 -I/usr/include/libpng16 -I'/home/omnipath/local/R/4.4-3.19/cpp11/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 font_matching.cpp -o font_matching.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I/usr/include/freetype2 -I/usr/include/libpng16 -I'/home/omnipath/local/R/4.4-3.19/cpp11/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 font_local.cpp -o font_local.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I/usr/include/freetype2 -I/usr/include/libpng16 -I'/home/omnipath/local/R/4.4-3.19/cpp11/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 font_registry.cpp -o font_registry.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I/usr/include/freetype2 -I/usr/include/libpng16 -I'/home/omnipath/local/R/4.4-3.19/cpp11/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 ft_cache.cpp -o ft_cache.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I/usr/include/freetype2 -I/usr/include/libpng16 -I'/home/omnipath/local/R/4.4-3.19/cpp11/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 string_shape.cpp -o string_shape.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I/usr/include/freetype2 -I/usr/include/libpng16 -I'/home/omnipath/local/R/4.4-3.19/cpp11/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 font_metrics.cpp -o font_metrics.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I/usr/include/freetype2 -I/usr/include/libpng16 -I'/home/omnipath/local/R/4.4-3.19/cpp11/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 font_outlines.cpp -o font_outlines.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I/usr/include/freetype2 -I/usr/include/libpng16 -I'/home/omnipath/local/R/4.4-3.19/cpp11/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 font_fallback.cpp -o font_fallback.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I/usr/include/freetype2 -I/usr/include/libpng16 -I'/home/omnipath/local/R/4.4-3.19/cpp11/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 string_metrics.cpp -o string_metrics.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I/usr/include/freetype2 -I/usr/include/libpng16 -I'/home/omnipath/local/R/4.4-3.19/cpp11/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 emoji.cpp -o emoji.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I/usr/include/freetype2 -I/usr/include/libpng16 -I'/home/omnipath/local/R/4.4-3.19/cpp11/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 cache_store.cpp -o cache_store.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I/usr/include/freetype2 -I/usr/include/libpng16 -I'/home/omnipath/local/R/4.4-3.19/cpp11/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/usr/include/freetype2 -I/usr/include/libpng16 -I'/home/omnipath/local/R/4.4-3.19/cpp11/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 unix/FontManagerLinux.cpp -o unix/FontManagerLinux.o g++ -std=gnu++17 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -o systemfonts.so caches.o cpp11.o dev_metrics.o font_matching.o font_local.o font_registry.o ft_cache.o string_shape.o font_metrics.o font_outlines.o font_fallback.o string_metrics.o emoji.o cache_store.o init.o unix/FontManagerLinux.o -lfontconfig -lfreetype -L/usr/lib/R/lib -lR installing to /home/omnipath/local/R/4.4-3.19/00LOCK-systemfonts/00new/systemfonts/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 (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/include/harfbuzz -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/fribidi Using PKG_LIBS=-lharfbuzz -lfreetype -lfribidi ** libs using C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’ 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"/usr/share/R/include" -DNDEBUG -DNDEBUG -I/usr/include/harfbuzz -I/usr/include/freetype2 -I/usr/include/libpng16 -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/4.4-3.19/cpp11/include' -I'/home/omnipath/local/R/4.4-3.19/systemfonts/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 cpp11.cpp -o cpp11.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -DNDEBUG -I/usr/include/harfbuzz -I/usr/include/freetype2 -I/usr/include/libpng16 -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/4.4-3.19/cpp11/include' -I'/home/omnipath/local/R/4.4-3.19/systemfonts/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 face_feature.cpp -o face_feature.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -DNDEBUG -I/usr/include/harfbuzz -I/usr/include/freetype2 -I/usr/include/libpng16 -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/4.4-3.19/cpp11/include' -I'/home/omnipath/local/R/4.4-3.19/systemfonts/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 hb_shaper.cpp -o hb_shaper.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -DNDEBUG -I/usr/include/harfbuzz -I/usr/include/freetype2 -I/usr/include/libpng16 -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/4.4-3.19/cpp11/include' -I'/home/omnipath/local/R/4.4-3.19/systemfonts/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 -DNDEBUG -I/usr/include/harfbuzz -I/usr/include/freetype2 -I/usr/include/libpng16 -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/4.4-3.19/cpp11/include' -I'/home/omnipath/local/R/4.4-3.19/systemfonts/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 string_bidi.cpp -o string_bidi.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -DNDEBUG -I/usr/include/harfbuzz -I/usr/include/freetype2 -I/usr/include/libpng16 -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/4.4-3.19/cpp11/include' -I'/home/omnipath/local/R/4.4-3.19/systemfonts/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 string_metrics.cpp -o string_metrics.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -DNDEBUG -I/usr/include/harfbuzz -I/usr/include/freetype2 -I/usr/include/libpng16 -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/4.4-3.19/cpp11/include' -I'/home/omnipath/local/R/4.4-3.19/systemfonts/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 string_shape.cpp -o string_shape.o g++ -std=gnu++17 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -o textshaping.so cpp11.o face_feature.o hb_shaper.o init.o string_bidi.o string_metrics.o string_shape.o -lharfbuzz -lfreetype -lfribidi -L/usr/lib/R/lib -lR installing to /home/omnipath/local/R/4.4-3.19/00LOCK-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/RtmpDEAEP7/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 3.19 (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: 2025-01-20 12:22:05 CET ]