[ Started: 2024-01-24 11:53:51 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/RcppAnnoy_0.0.22.tar.gz'
Content type 'application/x-gzip' length 156284 bytes (152 KB)
==================================================
downloaded 152 KB

* installing *source* package ‘RcppAnnoy’ ...
** package ‘RcppAnnoy’ 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’
using C++17
g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I../inst/include/  -I'/home/omnipath/local/R/4.3-3.17/Rcpp/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 RcppExports.cpp -o RcppExports.o
g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I../inst/include/  -I'/home/omnipath/local/R/4.3-3.17/Rcpp/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 annoy.cpp -o annoy.o
g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I../inst/include/  -I'/home/omnipath/local/R/4.3-3.17/Rcpp/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 arch.cpp -o arch.o
gcc -I"/usr/share/R/include" -DNDEBUG -I../inst/include/  -I'/home/omnipath/local/R/4.3-3.17/Rcpp/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 init.c -o init.o
g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I../inst/include/  -I'/home/omnipath/local/R/4.3-3.17/Rcpp/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 version.cpp -o version.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 RcppAnnoy.so RcppExports.o annoy.o arch.o init.o version.o -L/usr/lib/R/lib -lR
installing to /home/omnipath/local/R/4.3-3.17/00LOCK-RcppAnnoy/00new/RcppAnnoy/libs
** R
** demo
** 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 (RcppAnnoy)

The downloaded source packages are in
	‘/tmp/RtmpJR0p1i/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)
Old packages: 'R.oo'
trying URL 'https://cloud.r-project.org/src/contrib/R.oo_1.26.0.tar.gz'
Content type 'application/x-gzip' length 383646 bytes (374 KB)
==================================================
downloaded 374 KB

* installing *source* package ‘R.oo’ ...
** package ‘R.oo’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
Warning in setGenericS3.default(name, export = exportGeneric, envir = envir,  :
  Renamed the preexisting function getMethods to getMethods.default, which was defined in environment R.oo.
Warning in setGenericS3.default(name, export = exportGeneric, envir = envir,  :
  Renamed the preexisting function getClasses to getClasses.default, which was defined in environment R.oo.
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (R.oo)

The downloaded source packages are in
	‘/tmp/RtmpJR0p1i/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 3.17 (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: 2024-01-24 11:54:32 CET ]