[ Started: 2024-05-15 15:18:12 CEST ]
[ CARNIVAL v2.7.2 for BioC-3.19 from https://github.com/saezlab/CARNIVAL@master (2b8887a 2023-12-06 13:18:32) ]

[1] "Libraries: "                     "/home/omnipath/local/R/4.4-3.19"
[3] "/home/omnipath/local/R/4.4"      "/opt/R-alpha/lib/R/library"     
Warning message:
package ‘remotes’ was built under R version 4.5.0 
Bioconductor version 3.19 (BiocManager 1.30.23), R 4.4.0 alpha (2024-04-04
  r86334)
Old packages: 'fastmap', 'ragg', 'systemfonts', 'wppi', 'xfun'
trying URL 'https://cloud.r-project.org/src/contrib/fastmap_1.2.0.tar.gz'
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downloaded 45 KB

trying URL 'https://cloud.r-project.org/src/contrib/ragg_1.3.2.tar.gz'
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downloaded 420 KB

trying URL 'https://cloud.r-project.org/src/contrib/systemfonts_1.1.0.tar.gz'
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trying URL 'https://bioconductor.org/packages/3.19/bioc/src/contrib/wppi_1.12.0.tar.gz'
Content type 'application/x-gzip' length 661086 bytes (645 KB)
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downloaded 645 KB

trying URL 'https://cloud.r-project.org/src/contrib/xfun_0.44.tar.gz'
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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"/opt/R-alpha/lib/R/include" -DNDEBUG -Ilib/  -I/usr/local/include   -DR_NO_REMAP -fpic  -g -O2   -c fastmap.cpp -o fastmap.o
gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -Ilib/  -I/usr/local/include    -fpic  -g -O2  -c init.c -o init.o
g++ -std=gnu++17 -shared -L/usr/local/lib -o fastmap.so fastmap.o init.o
installing to /home/omnipath/local/R/4.4-3.19/00LOCK-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"/opt/R-alpha/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/4.4-3.19/cpp11/include' -I/usr/local/include    -fpic  -g -O2   -c caches.cpp -o caches.o
g++ -std=gnu++17 -I"/opt/R-alpha/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/4.4-3.19/cpp11/include' -I/usr/local/include    -fpic  -g -O2   -c cpp11.cpp -o cpp11.o
g++ -std=gnu++17 -I"/opt/R-alpha/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/4.4-3.19/cpp11/include' -I/usr/local/include    -fpic  -g -O2   -c dev_metrics.cpp -o dev_metrics.o
g++ -std=gnu++17 -I"/opt/R-alpha/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/4.4-3.19/cpp11/include' -I/usr/local/include    -fpic  -g -O2   -c font_matching.cpp -o font_matching.o
g++ -std=gnu++17 -I"/opt/R-alpha/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/4.4-3.19/cpp11/include' -I/usr/local/include    -fpic  -g -O2   -c font_registry.cpp -o font_registry.o
g++ -std=gnu++17 -I"/opt/R-alpha/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/4.4-3.19/cpp11/include' -I/usr/local/include    -fpic  -g -O2   -c ft_cache.cpp -o ft_cache.o
g++ -std=gnu++17 -I"/opt/R-alpha/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/4.4-3.19/cpp11/include' -I/usr/local/include    -fpic  -g -O2   -c string_shape.cpp -o string_shape.o
g++ -std=gnu++17 -I"/opt/R-alpha/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/4.4-3.19/cpp11/include' -I/usr/local/include    -fpic  -g -O2   -c font_metrics.cpp -o font_metrics.o
g++ -std=gnu++17 -I"/opt/R-alpha/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/4.4-3.19/cpp11/include' -I/usr/local/include    -fpic  -g -O2   -c font_fallback.cpp -o font_fallback.o
g++ -std=gnu++17 -I"/opt/R-alpha/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/4.4-3.19/cpp11/include' -I/usr/local/include    -fpic  -g -O2   -c string_metrics.cpp -o string_metrics.o
g++ -std=gnu++17 -I"/opt/R-alpha/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/4.4-3.19/cpp11/include' -I/usr/local/include    -fpic  -g -O2   -c emoji.cpp -o emoji.o
g++ -std=gnu++17 -I"/opt/R-alpha/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/4.4-3.19/cpp11/include' -I/usr/local/include    -fpic  -g -O2   -c cache_store.cpp -o cache_store.o
g++ -std=gnu++17 -I"/opt/R-alpha/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/4.4-3.19/cpp11/include' -I/usr/local/include    -fpic  -g -O2   -c init.cpp -o init.o
g++ -std=gnu++17 -I"/opt/R-alpha/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/4.4-3.19/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/4.4-3.19/00LOCK-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 ‘wppi’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
[2024-05-15 15:18:43] [INFO]    [OmnipathR] Setting up new cache directory `/home/omnipath/.cache/OmnipathR`.
[2024-05-15 15:18:43] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-15 15:18:43] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-15 15:18:43] [INFO]    [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`.
[2024-05-15 15:18:43] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-05-15 15:18:43] [TRACE]   [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`.
[2024-05-15 15:18:43] [TRACE]   [OmnipathR] Contains 1 files.
[2024-05-15 15:18:43] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-05-15 15:18:43] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-15 15:18:43] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-15 15:18:43] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`.
[2024-05-15 15:18:43] [TRACE]   [OmnipathR] Pandoc version: `2.9.2.1`.
[2024-05-15 15:18:43] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.19/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-05-15 15:18:43] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-15 15:18:43] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.19/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-05-15 15:18:43] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-15 15:18:44] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.19/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-05-15 15:18:44] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-15 15:18:44] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.19/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-05-15 15:18:44] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-15 15:18:44] [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 15:18:46] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-15 15:18:46] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-15 15:18:46] [INFO]    [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`.
[2024-05-15 15:18:46] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-05-15 15:18:46] [TRACE]   [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`.
[2024-05-15 15:18:46] [TRACE]   [OmnipathR] Contains 1 files.
[2024-05-15 15:18:46] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-05-15 15:18:46] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-15 15:18:46] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-15 15:18:46] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`.
[2024-05-15 15:18:46] [TRACE]   [OmnipathR] Pandoc version: `2.9.2.1`.
[2024-05-15 15:18:46] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.19/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-05-15 15:18:46] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-15 15:18:46] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.19/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-05-15 15:18:46] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-15 15:18:46] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.19/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-05-15 15:18:46] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-15 15:18:46] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.19/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-05-15 15:18:46] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-15 15:18:46] [TRACE]   [OmnipathR] Cache locked: FALSE
** testing if installed package can be loaded from final location
[2024-05-15 15:18:47] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-15 15:18:47] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-15 15:18:47] [INFO]    [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`.
[2024-05-15 15:18:47] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-05-15 15:18:47] [TRACE]   [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`.
[2024-05-15 15:18:47] [TRACE]   [OmnipathR] Contains 1 files.
[2024-05-15 15:18:47] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-05-15 15:18:47] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-15 15:18:47] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-15 15:18:47] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`.
[2024-05-15 15:18:47] [TRACE]   [OmnipathR] Pandoc version: `2.9.2.1`.
[2024-05-15 15:18:47] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.19/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-05-15 15:18:47] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-15 15:18:47] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.19/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-05-15 15:18:47] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-15 15:18:48] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.19/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-05-15 15:18:48] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-15 15:18:48] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.19/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-05-15 15:18:48] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-15 15:18:48] [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"/opt/R-alpha/lib/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -c base64.c -o base64.o
gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -c init.c -o init.o
gcc -shared -L/usr/local/lib -o xfun.so base64.o init.o
installing to /home/omnipath/local/R/4.4-3.19/00LOCK-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"/opt/R-alpha/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/4.4-3.19/systemfonts/include' -I'/home/omnipath/local/R/4.4-3.19/textshaping/include' -I/usr/local/include    -fpic  -g -O2   -c capture_dev.cpp -o capture_dev.o
g++ -std=gnu++17 -I"/opt/R-alpha/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/4.4-3.19/systemfonts/include' -I'/home/omnipath/local/R/4.4-3.19/textshaping/include' -I/usr/local/include    -fpic  -g -O2   -c init.cpp -o init.o
g++ -std=gnu++17 -I"/opt/R-alpha/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/4.4-3.19/systemfonts/include' -I'/home/omnipath/local/R/4.4-3.19/textshaping/include' -I/usr/local/include    -fpic  -g -O2   -c jpeg_dev.cpp -o jpeg_dev.o
g++ -std=gnu++17 -I"/opt/R-alpha/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/4.4-3.19/systemfonts/include' -I'/home/omnipath/local/R/4.4-3.19/textshaping/include' -I/usr/local/include    -fpic  -g -O2   -c png_dev.cpp -o png_dev.o
g++ -std=gnu++17 -I"/opt/R-alpha/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/4.4-3.19/systemfonts/include' -I'/home/omnipath/local/R/4.4-3.19/textshaping/include' -I/usr/local/include    -fpic  -g -O2   -c ppm_dev.cpp -o ppm_dev.o
g++ -std=gnu++17 -I"/opt/R-alpha/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/4.4-3.19/systemfonts/include' -I'/home/omnipath/local/R/4.4-3.19/textshaping/include' -I/usr/local/include    -fpic  -g -O2   -c tiff_dev.cpp -o tiff_dev.o
g++ -std=gnu++17 -I"/opt/R-alpha/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/4.4-3.19/systemfonts/include' -I'/home/omnipath/local/R/4.4-3.19/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-alpha/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/4.4-3.19/systemfonts/include' -I'/home/omnipath/local/R/4.4-3.19/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-alpha/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/4.4-3.19/systemfonts/include' -I'/home/omnipath/local/R/4.4-3.19/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-alpha/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/4.4-3.19/systemfonts/include' -I'/home/omnipath/local/R/4.4-3.19/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-alpha/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/4.4-3.19/systemfonts/include' -I'/home/omnipath/local/R/4.4-3.19/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-alpha/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/4.4-3.19/systemfonts/include' -I'/home/omnipath/local/R/4.4-3.19/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
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/RtmpHqRFQ4/downloaded_packages’
Bioconductor version 3.19 (BiocManager 1.30.23), R 4.4.0 alpha (2024-04-04
  r86334)
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 15:21:00 CEST ]