[ Started: 2025-03-16 00:50:01 CET ]
[ cosmosR v1.9.1 for BioC-3.21 from https://github.com/saezlab/cosmosR@master (ef9d5aa 2025-03-09 13:20:11) ]

[1] "Libraries: "                     "/home/omnipath/local/R/4.5-3.21"
[3] "/home/omnipath/local/R/4.5"      "/opt/R-devel/lib/R/library"     
Bioconductor version 3.21 (BiocManager 1.30.25), R Under development (unstable)
  (2025-02-12 r87715)
Old packages: 'spatstat.utils', 'tzdb'
trying URL 'https://cloud.r-project.org/src/contrib/spatstat.utils_3.1-3.tar.gz'
trying URL 'https://cloud.r-project.org/src/contrib/tzdb_0.5.0.tar.gz'
* installing *source* package ‘spatstat.utils’ ...
** this is package ‘spatstat.utils’ version ‘3.1-3’
** package ‘spatstat.utils’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -c circxseg.c -o circxseg.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -c distseg.c -o distseg.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -c fastinterv.c -o fastinterv.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -c init.c -o init.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -c inxyp.c -o inxyp.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -c matchindices.c -o matchindices.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -c matchpoints.c -o matchpoints.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -c ply.c -o ply.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -c primefax.c -o primefax.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -c revcum.c -o revcum.o
gcc -shared -L/usr/local/lib -o spatstat.utils.so circxseg.o distseg.o fastinterv.o init.o inxyp.o matchindices.o matchpoints.o ply.o primefax.o revcum.o
installing to /home/omnipath/local/R/4.5-3.21/00LOCK-spatstat.utils/00new/spatstat.utils/libs
** R
** inst
** 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 (spatstat.utils)
* installing *source* package ‘tzdb’ ...
** this is package ‘tzdb’ version ‘0.5.0’
** package ‘tzdb’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.5-3.21/cpp11/include' -I/usr/local/include   -I../inst/include -DINSTALL=dummy -DAUTO_DOWNLOAD=0 -DHAS_REMOTE_API=0 -DUSE_OS_TZDB=0 -DONLY_C_LOCALE=1 -fpic  -g -O2   -c api.cpp -o api.o
g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.5-3.21/cpp11/include' -I/usr/local/include   -I../inst/include -DINSTALL=dummy -DAUTO_DOWNLOAD=0 -DHAS_REMOTE_API=0 -DUSE_OS_TZDB=0 -DONLY_C_LOCALE=1 -fpic  -g -O2   -c cpp11.cpp -o cpp11.o
g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.5-3.21/cpp11/include' -I/usr/local/include   -I../inst/include -DINSTALL=dummy -DAUTO_DOWNLOAD=0 -DHAS_REMOTE_API=0 -DUSE_OS_TZDB=0 -DONLY_C_LOCALE=1 -fpic  -g -O2   -c names.cpp -o names.o
g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.5-3.21/cpp11/include' -I/usr/local/include   -I../inst/include -DINSTALL=dummy -DAUTO_DOWNLOAD=0 -DHAS_REMOTE_API=0 -DUSE_OS_TZDB=0 -DONLY_C_LOCALE=1 -fpic  -g -O2   -c path.cpp -o path.o
g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.5-3.21/cpp11/include' -I/usr/local/include   -I../inst/include -DINSTALL=dummy -DAUTO_DOWNLOAD=0 -DHAS_REMOTE_API=0 -DUSE_OS_TZDB=0 -DONLY_C_LOCALE=1 -fpic  -g -O2   -c tz.cpp -o tz.o
g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.5-3.21/cpp11/include' -I/usr/local/include   -I../inst/include -DINSTALL=dummy -DAUTO_DOWNLOAD=0 -DHAS_REMOTE_API=0 -DUSE_OS_TZDB=0 -DONLY_C_LOCALE=1 -fpic  -g -O2   -c version.cpp -o version.o
g++ -std=gnu++17 -shared -L/usr/local/lib -o tzdb.so api.o cpp11.o names.o path.o tz.o version.o
installing to /home/omnipath/local/R/4.5-3.21/00LOCK-tzdb/00new/tzdb/libs
** R
** inst
** 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 (tzdb)

The downloaded source packages are in
	‘/tmp/RtmpjJYWnc/downloaded_packages’
Bioconductor version 3.21 (BiocManager 1.30.25), R Under development (unstable)
  (2025-02-12 r87715)
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: tzdb
[ Finished: 2025-03-16 00:50:24 CET ]