[ Started: 2024-03-14 11:55:58 CET ]
[ 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"      "/usr/lib/R/library"             
trying URL 'https://cran.uni-muenster.de/src/contrib/ragg_1.3.0.tar.gz'
Content type 'application/x-gzip' length 430242 bytes (420 KB)
==================================================
downloaded 420 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/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/4.3-3.17/systemfonts/include' -I'/home/omnipath/local/R/4.3-3.17/textshaping/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 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/4.3-3.17/systemfonts/include' -I'/home/omnipath/local/R/4.3-3.17/textshaping/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 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/4.3-3.17/systemfonts/include' -I'/home/omnipath/local/R/4.3-3.17/textshaping/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 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/4.3-3.17/systemfonts/include' -I'/home/omnipath/local/R/4.3-3.17/textshaping/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 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/4.3-3.17/systemfonts/include' -I'/home/omnipath/local/R/4.3-3.17/textshaping/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 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/4.3-3.17/systemfonts/include' -I'/home/omnipath/local/R/4.3-3.17/textshaping/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 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/4.3-3.17/systemfonts/include' -I'/home/omnipath/local/R/4.3-3.17/textshaping/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 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/4.3-3.17/systemfonts/include' -I'/home/omnipath/local/R/4.3-3.17/textshaping/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 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/4.3-3.17/systemfonts/include' -I'/home/omnipath/local/R/4.3-3.17/textshaping/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 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/4.3-3.17/systemfonts/include' -I'/home/omnipath/local/R/4.3-3.17/textshaping/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 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/4.3-3.17/systemfonts/include' -I'/home/omnipath/local/R/4.3-3.17/textshaping/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 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/4.3-3.17/systemfonts/include' -I'/home/omnipath/local/R/4.3-3.17/textshaping/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 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/4.3-3.17/00LOCK-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/RtmpRRp6lA/downloaded_packages’
Bioconductor version '3.17' is out-of-date; the current release version '3.18'
  is available with R version '4.3'; 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 3.17 (BiocManager 1.30.22), R 4.3.1 (2023-06-16)
'getOption("repos")' replaces Bioconductor standard repositories, see
'help("repositories", package = "BiocManager")' for details.
Replacement repositories:
    CRAN: https://cloud.r-project.org
Bioconductor version 3.17 (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: 2024-03-14 11:58:18 CET ]