[ Started: 2023-12-18 13:30:23 CET ]
[ OmnipathR v3.11.1 for BioC-3.18 from https://github.com/saezlab/OmnipathR@master ]

[1] "Libraries: "                     "/home/omnipath/local/R/4.3-3.18"
[3] "/home/omnipath/local/R/4.3"      "/usr/lib/R/library"             
'getOption("repos")' replaces Bioconductor standard repositories, see
'help("repositories", package = "BiocManager")' for details.
Replacement repositories:
    CRAN: https://cloud.r-project.org
Bioconductor version 3.18 (BiocManager 1.30.22), R 4.3.1 (2023-06-16)
Old packages: 'tidygraph'
trying URL 'https://cloud.r-project.org/src/contrib/tidygraph_1.3.0.tar.gz'
Content type 'application/x-gzip' length 133378 bytes (130 KB)
==================================================
downloaded 130 KB

* installing *source* package ‘tidygraph’ ...
** package ‘tidygraph’ successfully unpacked and MD5 sums checked
** using staged installation
** 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'/home/omnipath/local/R/4.3-3.18/cpp11/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 cpp11.cpp -o cpp11.o
g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.3-3.18/cpp11/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 get_paths.cpp -o get_paths.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 tidygraph.so cpp11.o get_paths.o -L/usr/lib/R/lib -lR
installing to /home/omnipath/local/R/4.3-3.18/00LOCK-tidygraph/00new/tidygraph/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 (tidygraph)

The downloaded source packages are in
	‘/tmp/RtmpW325JX/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 3.18 (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' 

Skipping 1 packages ahead of CRAN: tidygraph
[ Finished: 2023-12-18 13:30:37 CET ]