[ Started: 2024-09-12 15:35:20 CEST ]
[ 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"             
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/4.4-3.19/systemfonts/include' -I'/home/omnipath/local/R/4.4-3.19/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/4.4-3.19/systemfonts/include' -I'/home/omnipath/local/R/4.4-3.19/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/4.4-3.19/systemfonts/include' -I'/home/omnipath/local/R/4.4-3.19/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/4.4-3.19/systemfonts/include' -I'/home/omnipath/local/R/4.4-3.19/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/4.4-3.19/systemfonts/include' -I'/home/omnipath/local/R/4.4-3.19/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/4.4-3.19/systemfonts/include' -I'/home/omnipath/local/R/4.4-3.19/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/4.4-3.19/systemfonts/include' -I'/home/omnipath/local/R/4.4-3.19/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/4.4-3.19/systemfonts/include' -I'/home/omnipath/local/R/4.4-3.19/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/4.4-3.19/systemfonts/include' -I'/home/omnipath/local/R/4.4-3.19/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/4.4-3.19/systemfonts/include' -I'/home/omnipath/local/R/4.4-3.19/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/4.4-3.19/systemfonts/include' -I'/home/omnipath/local/R/4.4-3.19/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/4.4-3.19/systemfonts/include' -I'/home/omnipath/local/R/4.4-3.19/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/4.4-3.19/00LOCK-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/RtmpvUxfzm/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)
Old packages: 'RcppArmadillo'
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 ‘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/4.4-3.19/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/4.4-3.19/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/4.4-3.19/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/4.4-3.19/00LOCK-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/RtmpvUxfzm/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: 2024-09-12 15:38:18 CEST ]