[ Started: 2024-05-15 15:22:01 CEST ] [ CARNIVAL v2.7.2 for BioC-3.18 from https://github.com/saezlab/CARNIVAL@master (2b8887a 2023-12-06 13:18:32) ] [1] "Libraries: " "/home/omnipath/local/R/4.3-3.18" [3] "/home/omnipath/local/R/4.3" "/usr/lib/R/library" Bioconductor version '3.18' is out-of-date; the current release version '3.19' is available with R version '4.4'; see https://bioconductor.org/install 'getOption("repos")' replaces Bioconductor standard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 3.18 (BiocManager 1.30.23), R 4.3.3 (2024-02-29) Old packages: 'fastmap', 'ragg', 'systemfonts', 'wppi', 'xfun' trying URL 'https://cloud.r-project.org/src/contrib/fastmap_1.2.0.tar.gz' Content type 'application/x-gzip' length 46710 bytes (45 KB) ================================================== downloaded 45 KB trying URL 'https://cloud.r-project.org/src/contrib/ragg_1.3.2.tar.gz' Content type 'application/x-gzip' length 430366 bytes (420 KB) ================================================== downloaded 420 KB trying URL 'https://cloud.r-project.org/src/contrib/systemfonts_1.1.0.tar.gz' Content type 'application/x-gzip' length 85584 bytes (83 KB) ================================================== downloaded 83 KB trying URL 'https://bioconductor.org/packages/3.18/bioc/src/contrib/wppi_1.10.0.tar.gz' Content type 'application/x-gzip' length 662114 bytes (646 KB) ================================================== downloaded 646 KB trying URL 'https://cloud.r-project.org/src/contrib/xfun_0.44.tar.gz' Content type 'application/x-gzip' length 158081 bytes (154 KB) ================================================== downloaded 154 KB * installing *source* package ‘fastmap’ ... ** package ‘fastmap’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -Ilib/ -DR_NO_REMAP -fpic -g -O2 -ffile-prefix-map=/build/r-base-14Q6vq/r-base-4.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c fastmap.cpp -o fastmap.o gcc -I"/usr/share/R/include" -DNDEBUG -Ilib/ -fpic -g -O2 -ffile-prefix-map=/build/r-base-14Q6vq/r-base-4.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c init.c -o init.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 fastmap.so fastmap.o init.o -L/usr/lib/R/lib -lR installing to /home/omnipath/local/R/4.3-3.18/00LOCK-fastmap/00new/fastmap/libs ** R ** 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 (fastmap) * 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"/usr/share/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/4.3-3.18/cpp11/include' -fpic -g -O2 -ffile-prefix-map=/build/r-base-14Q6vq/r-base-4.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c caches.cpp -o caches.o g++ -std=gnu++17 -I"/usr/share/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/4.3-3.18/cpp11/include' -fpic -g -O2 -ffile-prefix-map=/build/r-base-14Q6vq/r-base-4.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c cpp11.cpp -o cpp11.o g++ -std=gnu++17 -I"/usr/share/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/4.3-3.18/cpp11/include' -fpic -g -O2 -ffile-prefix-map=/build/r-base-14Q6vq/r-base-4.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c dev_metrics.cpp -o dev_metrics.o g++ -std=gnu++17 -I"/usr/share/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/4.3-3.18/cpp11/include' -fpic -g -O2 -ffile-prefix-map=/build/r-base-14Q6vq/r-base-4.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c font_matching.cpp -o font_matching.o g++ -std=gnu++17 -I"/usr/share/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/4.3-3.18/cpp11/include' -fpic -g -O2 -ffile-prefix-map=/build/r-base-14Q6vq/r-base-4.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c font_registry.cpp -o font_registry.o g++ -std=gnu++17 -I"/usr/share/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/4.3-3.18/cpp11/include' -fpic -g -O2 -ffile-prefix-map=/build/r-base-14Q6vq/r-base-4.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c ft_cache.cpp -o ft_cache.o g++ -std=gnu++17 -I"/usr/share/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/4.3-3.18/cpp11/include' -fpic -g -O2 -ffile-prefix-map=/build/r-base-14Q6vq/r-base-4.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c string_shape.cpp -o string_shape.o g++ -std=gnu++17 -I"/usr/share/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/4.3-3.18/cpp11/include' -fpic -g -O2 -ffile-prefix-map=/build/r-base-14Q6vq/r-base-4.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c font_metrics.cpp -o font_metrics.o g++ -std=gnu++17 -I"/usr/share/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/4.3-3.18/cpp11/include' -fpic -g -O2 -ffile-prefix-map=/build/r-base-14Q6vq/r-base-4.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c font_fallback.cpp -o font_fallback.o g++ -std=gnu++17 -I"/usr/share/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/4.3-3.18/cpp11/include' -fpic -g -O2 -ffile-prefix-map=/build/r-base-14Q6vq/r-base-4.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c string_metrics.cpp -o string_metrics.o g++ -std=gnu++17 -I"/usr/share/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/4.3-3.18/cpp11/include' -fpic -g -O2 -ffile-prefix-map=/build/r-base-14Q6vq/r-base-4.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c emoji.cpp -o emoji.o g++ -std=gnu++17 -I"/usr/share/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/4.3-3.18/cpp11/include' -fpic -g -O2 -ffile-prefix-map=/build/r-base-14Q6vq/r-base-4.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c cache_store.cpp -o cache_store.o g++ -std=gnu++17 -I"/usr/share/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/4.3-3.18/cpp11/include' -fpic -g -O2 -ffile-prefix-map=/build/r-base-14Q6vq/r-base-4.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c init.cpp -o init.o g++ -std=gnu++17 -I"/usr/share/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/4.3-3.18/cpp11/include' -fpic -g -O2 -ffile-prefix-map=/build/r-base-14Q6vq/r-base-4.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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 -flto=auto -Wl,-z,relro -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 -L/usr/lib/R/lib -lR installing to /home/omnipath/local/R/4.3-3.18/00LOCK-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 ‘wppi’ ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading [2024-05-15 15:22:33] [INFO] [OmnipathR] Setting up new cache directory `/home/omnipath/.cache/OmnipathR`. [2024-05-15 15:22:33] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-05-15 15:22:33] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-15 15:22:33] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2024-05-15 15:22:33] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2024-05-15 15:22:33] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`. [2024-05-15 15:22:33] [TRACE] [OmnipathR] Contains 1 files. [2024-05-15 15:22:33] [TRACE] [OmnipathR] Cache is locked: FALSE. [2024-05-15 15:22:33] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-05-15 15:22:33] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-15 15:22:33] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2024-05-15 15:22:33] [TRACE] [OmnipathR] Pandoc version: `2.9.2.1`. [2024-05-15 15:22:33] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.3-3.18/OmnipathR/db/db_def.json` (encoding: UTF-8). [2024-05-15 15:22:33] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-15 15:22:33] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.3-3.18/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2024-05-15 15:22:33] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-15 15:22:33] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.3-3.18/OmnipathR/internal/urls.json` (encoding: UTF-8). [2024-05-15 15:22:33] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-15 15:22:33] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.3-3.18/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2024-05-15 15:22:33] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-15 15:22:33] [TRACE] [OmnipathR] Cache locked: FALSE Note: wrong number of arguments to '/' ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location [2024-05-15 15:22:35] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-05-15 15:22:35] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-15 15:22:35] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2024-05-15 15:22:35] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2024-05-15 15:22:35] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`. [2024-05-15 15:22:35] [TRACE] [OmnipathR] Contains 1 files. [2024-05-15 15:22:35] [TRACE] [OmnipathR] Cache is locked: FALSE. [2024-05-15 15:22:35] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-05-15 15:22:35] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-15 15:22:35] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2024-05-15 15:22:35] [TRACE] [OmnipathR] Pandoc version: `2.9.2.1`. [2024-05-15 15:22:35] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.3-3.18/OmnipathR/db/db_def.json` (encoding: UTF-8). [2024-05-15 15:22:35] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-15 15:22:35] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.3-3.18/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2024-05-15 15:22:35] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-15 15:22:35] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.3-3.18/OmnipathR/internal/urls.json` (encoding: UTF-8). [2024-05-15 15:22:35] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-15 15:22:35] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.3-3.18/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2024-05-15 15:22:35] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-15 15:22:35] [TRACE] [OmnipathR] Cache locked: FALSE ** testing if installed package can be loaded from final location [2024-05-15 15:22:37] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-05-15 15:22:37] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-15 15:22:37] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2024-05-15 15:22:37] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2024-05-15 15:22:37] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`. [2024-05-15 15:22:37] [TRACE] [OmnipathR] Contains 1 files. [2024-05-15 15:22:37] [TRACE] [OmnipathR] Cache is locked: FALSE. [2024-05-15 15:22:37] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-05-15 15:22:37] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-15 15:22:37] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2024-05-15 15:22:37] [TRACE] [OmnipathR] Pandoc version: `2.9.2.1`. [2024-05-15 15:22:37] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.3-3.18/OmnipathR/db/db_def.json` (encoding: UTF-8). [2024-05-15 15:22:37] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-15 15:22:37] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.3-3.18/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2024-05-15 15:22:37] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-15 15:22:37] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.3-3.18/OmnipathR/internal/urls.json` (encoding: UTF-8). [2024-05-15 15:22:37] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-15 15:22:37] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.3-3.18/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2024-05-15 15:22:37] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-15 15:22:37] [TRACE] [OmnipathR] Cache locked: FALSE ** testing if installed package keeps a record of temporary installation path * DONE (wppi) * installing *source* package ‘xfun’ ... ** package ‘xfun’ successfully unpacked and MD5 sums checked ** 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 -fpic -g -O2 -ffile-prefix-map=/build/r-base-14Q6vq/r-base-4.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c base64.c -o base64.o gcc -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -ffile-prefix-map=/build/r-base-14Q6vq/r-base-4.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c init.c -o init.o gcc -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -o xfun.so base64.o init.o -L/usr/lib/R/lib -lR installing to /home/omnipath/local/R/4.3-3.18/00LOCK-xfun/00new/xfun/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 (xfun) * 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 ** libs using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ g++ -std=gnu++17 -I"/usr/share/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/4.3-3.18/systemfonts/include' -I'/home/omnipath/local/R/4.3-3.18/textshaping/include' -fpic -g -O2 -ffile-prefix-map=/build/r-base-14Q6vq/r-base-4.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c capture_dev.cpp -o capture_dev.o g++ -std=gnu++17 -I"/usr/share/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/4.3-3.18/systemfonts/include' -I'/home/omnipath/local/R/4.3-3.18/textshaping/include' -fpic -g -O2 -ffile-prefix-map=/build/r-base-14Q6vq/r-base-4.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c init.cpp -o init.o g++ -std=gnu++17 -I"/usr/share/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/4.3-3.18/systemfonts/include' -I'/home/omnipath/local/R/4.3-3.18/textshaping/include' -fpic -g -O2 -ffile-prefix-map=/build/r-base-14Q6vq/r-base-4.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c jpeg_dev.cpp -o jpeg_dev.o g++ -std=gnu++17 -I"/usr/share/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/4.3-3.18/systemfonts/include' -I'/home/omnipath/local/R/4.3-3.18/textshaping/include' -fpic -g -O2 -ffile-prefix-map=/build/r-base-14Q6vq/r-base-4.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c png_dev.cpp -o png_dev.o g++ -std=gnu++17 -I"/usr/share/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/4.3-3.18/systemfonts/include' -I'/home/omnipath/local/R/4.3-3.18/textshaping/include' -fpic -g -O2 -ffile-prefix-map=/build/r-base-14Q6vq/r-base-4.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c ppm_dev.cpp -o ppm_dev.o g++ -std=gnu++17 -I"/usr/share/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/4.3-3.18/systemfonts/include' -I'/home/omnipath/local/R/4.3-3.18/textshaping/include' -fpic -g -O2 -ffile-prefix-map=/build/r-base-14Q6vq/r-base-4.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c tiff_dev.cpp -o tiff_dev.o g++ -std=gnu++17 -I"/usr/share/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/4.3-3.18/systemfonts/include' -I'/home/omnipath/local/R/4.3-3.18/textshaping/include' -fpic -g -O2 -ffile-prefix-map=/build/r-base-14Q6vq/r-base-4.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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/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/4.3-3.18/systemfonts/include' -I'/home/omnipath/local/R/4.3-3.18/textshaping/include' -fpic -g -O2 -ffile-prefix-map=/build/r-base-14Q6vq/r-base-4.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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/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/4.3-3.18/systemfonts/include' -I'/home/omnipath/local/R/4.3-3.18/textshaping/include' -fpic -g -O2 -ffile-prefix-map=/build/r-base-14Q6vq/r-base-4.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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/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/4.3-3.18/systemfonts/include' -I'/home/omnipath/local/R/4.3-3.18/textshaping/include' -fpic -g -O2 -ffile-prefix-map=/build/r-base-14Q6vq/r-base-4.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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/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/4.3-3.18/systemfonts/include' -I'/home/omnipath/local/R/4.3-3.18/textshaping/include' -fpic -g -O2 -ffile-prefix-map=/build/r-base-14Q6vq/r-base-4.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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/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/4.3-3.18/systemfonts/include' -I'/home/omnipath/local/R/4.3-3.18/textshaping/include' -fpic -g -O2 -ffile-prefix-map=/build/r-base-14Q6vq/r-base-4.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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 -flto=auto -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 -L/usr/local/lib -lfreetype -lpng16 -lz -ltiff -ljpeg -L/usr/lib/R/lib -lR installing to /home/omnipath/local/R/4.3-3.18/00LOCK-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/RtmpGuwnqY/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 1.30.23), R 4.3.3 (2024-02-29) Warning message: package(s) not installed when version(s) same as or greater than current; use `force = TRUE` to re-install: 'BiocCheck' Skipping 3 packages ahead of CRAN: xfun, fastmap, BiocStyle [ Finished: 2024-05-15 15:24:55 CEST ]