[ Started: 2024-03-17 11:53:07 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/processx_3.8.4.tar.gz'
Content type 'application/x-gzip' length 163983 bytes (160 KB)
==================================================
downloaded 160 KB

* installing *source* package ‘processx’ ...
** package ‘processx’ 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 -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  -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -Wall tools/px.c -o tools/px
gcc -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  -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -I../inst/include -Wall tools/sock.c -o tools/sock
gcc -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  -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro supervisor/supervisor.c \
      supervisor/utils.c -o supervisor/supervisor
gcc -I"/usr/share/R/include" -DNDEBUG       -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 base64.c -o base64.o
gcc -I"/usr/share/R/include" -DNDEBUG       -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 client.c -o client.o
gcc -I"/usr/share/R/include" -DNDEBUG       -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 errors.c -o errors.o
gcc -shared -L"/usr/lib/R/lib" -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -o client.so base64.o client.o errors.o  \
	 -L"/usr/lib/R/lib" -lR
if [ -n "" ]; then \
    echo Removing libR.so dependency from client.so; \
    patchelf --remove-needed libR.so client.so; \
fi
gcc -I"/usr/share/R/include" -DNDEBUG       -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.c -o init.o
gcc -I"/usr/share/R/include" -DNDEBUG       -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 poll.c -o poll.o
gcc -I"/usr/share/R/include" -DNDEBUG       -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 processx-connection.c -o processx-connection.o
gcc -I"/usr/share/R/include" -DNDEBUG       -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 processx-vector.c -o processx-vector.o
gcc -I"/usr/share/R/include" -DNDEBUG       -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 create-time.c -o create-time.o
gcc -I"/usr/share/R/include" -DNDEBUG       -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 unix/childlist.c -o unix/childlist.o
gcc -I"/usr/share/R/include" -DNDEBUG       -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 unix/connection.c -o unix/connection.o
gcc -I"/usr/share/R/include" -DNDEBUG       -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 unix/processx.c -o unix/processx.o
gcc -I"/usr/share/R/include" -DNDEBUG       -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 unix/sigchld.c -o unix/sigchld.o
gcc -I"/usr/share/R/include" -DNDEBUG       -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 unix/utils.c -o unix/utils.o
gcc -I"/usr/share/R/include" -DNDEBUG       -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 unix/named_pipe.c -o unix/named_pipe.o
gcc -I"/usr/share/R/include" -DNDEBUG       -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 cleancall.c -o cleancall.o
gcc -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -o processx.so init.o poll.o errors.o processx-connection.o processx-vector.o create-time.o base64.o unix/childlist.o unix/connection.o unix/processx.o unix/sigchld.o unix/utils.o unix/named_pipe.o cleancall.o -L/usr/lib/R/lib -lR
installing via 'install.libs.R' to /home/omnipath/local/R/4.3-3.17/00LOCK-processx/00new/processx
** R
** inst
** 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 (processx)

The downloaded source packages are in
	‘/tmp/RtmpTW7Zt2/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: 2024-03-17 11:53:24 CET ]