[ Started: 2022-10-20 20:37:58 CEST ]
[ OmnipathR v3.5.24 for BioC-3.16 from https://github.com/saezlab/OmnipathR@master ]

[1] "Libraries: "                     "/home/omnipath/local/R/4.2-3.16"
[3] "/home/omnipath/local/R/4.2"      "/usr/lib/R/library"             
'getOption("repos")' replaces Bioconductor standard repositories, see
'?repositories' for details

replacement repositories:
    CRAN: https://cloud.r-project.org

Bioconductor version 3.16 (BiocManager 1.30.18), R 4.2.1 (2022-06-23)
Old packages: 'polyclip'
trying URL 'https://cloud.r-project.org/src/contrib/polyclip_1.10-4.tar.gz'
Content type 'application/x-gzip' length 80061 bytes (78 KB)
==================================================
downloaded 78 KB

* installing *source* package ‘polyclip’ ...
** package ‘polyclip’ successfully unpacked and MD5 sums checked
** using staged installation
compiling under C++11
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 we are using the GNU C++ compiler... yes
checking whether g++ -std=gnu++11 accepts -g... yes
Using PKG_CONFIG: pkg-config
Compiling against bundled copy of clipper library.
     In the clipper library, signed 64-bit integers (cInt)
     will be declared as 'signed long long'
     In the clipper library, unsigned 64-bit integers (cUInt)
     will be declared as 'unsigned long long'
configure: creating ./config.status
config.status: creating src/Makevars
** libs
gcc -I"/usr/share/R/include" -DNDEBUG -DPOLYCLIP_LONG64="signed long long" -DPOLYCLIP_ULONG64="unsigned long long"     -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c init.c -o init.o
g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -DPOLYCLIP_LONG64="signed long long" -DPOLYCLIP_ULONG64="unsigned long long"    -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c interface.cpp -o interface.o
g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -DPOLYCLIP_LONG64="signed long long" -DPOLYCLIP_ULONG64="unsigned long long"    -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c clipper.cpp -o clipper.o
g++ -std=gnu++11 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o polyclip.so init.o interface.o clipper.o -L/usr/lib/R/lib -lR
installing to /home/omnipath/local/R/4.2-3.16/00LOCK-polyclip/00new/polyclip/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 (polyclip)

The downloaded source packages are in
	‘/tmp/RtmpuJwDwR/downloaded_packages’

Skipping 19 packages ahead of CRAN: polyclip, BiocGenerics, graph, zlibbioc, GenomeInfoDbData, GenomeInfoDb, XVector, Biostrings, KEGGREST, S4Vectors, IRanges, Biobase, graphlayouts, Rgraphviz, supraHex, BiocFileCache, AnnotationDbi, biomaRt, BiocStyle
[ Finished: 2022-10-20 20:38:13 CEST ]