[ Started: 2023-09-20 00:16:11 CEST ]
[ CARNIVAL v2.7.2 for BioC-3.16 from https://github.com/saezlab/CARNIVAL@master ]

[1] "Libraries: "                     "/home/omnipath/local/R/4.2-3.16"
[3] "/home/omnipath/local/R/4.2"      "/usr/lib/R/library"             
trying URL 'https://cran.uni-muenster.de/src/contrib/RcppHNSW_0.5.0.tar.gz'
Content type 'application/x-gzip' length 34538 bytes (33 KB)
==================================================
downloaded 33 KB

* installing *source* package ‘RcppHNSW’ ...
** package ‘RcppHNSW’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
g++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG -I../inst/include/ -I'/home/omnipath/local/R/4.2-3.16/Rcpp/include'   -DNO_MANUAL_VECTORIZATION -DSTRICT_R_HEADERS -fpic  -g -O2 -ffile-prefix-map=/build/r-base-LhKvHL/r-base-4.2.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG -I../inst/include/ -I'/home/omnipath/local/R/4.2-3.16/Rcpp/include'   -DNO_MANUAL_VECTORIZATION -DSTRICT_R_HEADERS -fpic  -g -O2 -ffile-prefix-map=/build/r-base-LhKvHL/r-base-4.2.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c hnsw.cpp -o hnsw.o
g++ -std=gnu++14 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -o RcppHNSW.so RcppExports.o hnsw.o -L/usr/lib/R/lib -lR
installing to /home/omnipath/local/R/4.2-3.16/00LOCK-RcppHNSW/00new/RcppHNSW/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 (RcppHNSW)

The downloaded source packages are in
	‘/tmp/RtmpDSGUUf/downloaded_packages’
Bioconductor version '3.16' is out-of-date; the current release version '3.17'
  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 3.16 (BiocManager 1.30.22), R 4.2.3 (2023-03-15)
Old packages: 'graphlayouts', 'sctransform'
trying URL 'https://cloud.r-project.org/src/contrib/graphlayouts_1.0.1.tar.gz'
Content type 'application/x-gzip' length 3807746 bytes (3.6 MB)
==================================================
downloaded 3.6 MB

trying URL 'https://cloud.r-project.org/src/contrib/sctransform_0.4.0.tar.gz'
Content type 'application/x-gzip' length 186672 bytes (182 KB)
==================================================
downloaded 182 KB

* installing *source* package ‘graphlayouts’ ...
** package ‘graphlayouts’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
g++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I'/home/omnipath/local/R/4.2-3.16/Rcpp/include' -I'/home/omnipath/local/R/4.2-3.16/RcppArmadillo/include'    -fpic  -g -O2 -ffile-prefix-map=/build/r-base-LhKvHL/r-base-4.2.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I'/home/omnipath/local/R/4.2-3.16/Rcpp/include' -I'/home/omnipath/local/R/4.2-3.16/RcppArmadillo/include'    -fpic  -g -O2 -ffile-prefix-map=/build/r-base-LhKvHL/r-base-4.2.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c constrained_stress.cpp -o constrained_stress.o
g++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I'/home/omnipath/local/R/4.2-3.16/Rcpp/include' -I'/home/omnipath/local/R/4.2-3.16/RcppArmadillo/include'    -fpic  -g -O2 -ffile-prefix-map=/build/r-base-LhKvHL/r-base-4.2.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c constrained_stress3D.cpp -o constrained_stress3D.o
g++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I'/home/omnipath/local/R/4.2-3.16/Rcpp/include' -I'/home/omnipath/local/R/4.2-3.16/RcppArmadillo/include'    -fpic  -g -O2 -ffile-prefix-map=/build/r-base-LhKvHL/r-base-4.2.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c reweight.cpp -o reweight.o
g++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I'/home/omnipath/local/R/4.2-3.16/Rcpp/include' -I'/home/omnipath/local/R/4.2-3.16/RcppArmadillo/include'    -fpic  -g -O2 -ffile-prefix-map=/build/r-base-LhKvHL/r-base-4.2.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c sparseStress.cpp -o sparseStress.o
g++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I'/home/omnipath/local/R/4.2-3.16/Rcpp/include' -I'/home/omnipath/local/R/4.2-3.16/RcppArmadillo/include'    -fpic  -g -O2 -ffile-prefix-map=/build/r-base-LhKvHL/r-base-4.2.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c stress.cpp -o stress.o
g++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I'/home/omnipath/local/R/4.2-3.16/Rcpp/include' -I'/home/omnipath/local/R/4.2-3.16/RcppArmadillo/include'    -fpic  -g -O2 -ffile-prefix-map=/build/r-base-LhKvHL/r-base-4.2.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c stress3D.cpp -o stress3D.o
g++ -std=gnu++14 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -o graphlayouts.so RcppExports.o constrained_stress.o constrained_stress3D.o reweight.o sparseStress.o stress.o stress3D.o -L/usr/lib/R/lib -lR
installing to /home/omnipath/local/R/4.2-3.16/00LOCK-graphlayouts/00new/graphlayouts/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** 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 (graphlayouts)
* installing *source* package ‘sctransform’ ...
** package ‘sctransform’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.2-3.16/RcppArmadillo/include' -I'/home/omnipath/local/R/4.2-3.16/Rcpp/include'    -fpic  -g -O2 -ffile-prefix-map=/build/r-base-LhKvHL/r-base-4.2.3=. -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'/home/omnipath/local/R/4.2-3.16/RcppArmadillo/include' -I'/home/omnipath/local/R/4.2-3.16/Rcpp/include'    -fpic  -g -O2 -ffile-prefix-map=/build/r-base-LhKvHL/r-base-4.2.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c utils.cpp -o utils.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 sctransform.so RcppExports.o utils.o -llapack -lblas -lgfortran -lm -lquadmath -L/usr/lib/R/lib -lR
installing to /home/omnipath/local/R/4.2-3.16/00LOCK-sctransform/00new/sctransform/libs
** R
** data
*** moving datasets to lazyload DB
** 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 (sctransform)

The downloaded source packages are in
	‘/tmp/RtmpDSGUUf/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 3.16 (BiocManager 1.30.22), R 4.2.3 (2023-03-15)
Warning message:
package(s) not installed when version(s) same as or greater than current; use
  `force = TRUE` to re-install: 'BiocCheck' 

[ Finished: 2023-09-20 00:17:44 CEST ]