[ Started: 2023-05-18 00:41:38 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"/home/omnipath/local/R/4.2-3.16" [3] "/home/omnipath/local/R/4.2" "/usr/lib/R/library" Bioconductor version '3.16' is out-of-date; the current release version '3.17' is available with R version '4.3'; see https://bioconductor.org/install 'getOption("repos")' replaces Bioconductor standard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 1.30.20), R 4.2.3 (2023-03-15) Old packages: 'deldir', 'scattermore' trying URL 'https://cloud.r-project.org/src/contrib/deldir_1.0-9.tar.gz' Content type 'application/x-gzip' length 127119 bytes (124 KB) ================================================== downloaded 124 KB trying URL 'https://cloud.r-project.org/src/contrib/scattermore_1.1.tar.gz' Content type 'application/x-gzip' length 261031 bytes (254 KB) ================================================== downloaded 254 KB * installing *source* package ‘deldir’ ... ** package ‘deldir’ successfully unpacked and MD5 sums checked ** using staged installation ** libs gfortran -fno-optimize-sibling-calls -fpic -g -O2 -ffile-prefix-map=/build/r-base-LhKvHL/r-base-4.2.3=. -fstack-protector-strong -c acchk.f -o acchk.o gfortran -fno-optimize-sibling-calls -fpic -g -O2 -ffile-prefix-map=/build/r-base-LhKvHL/r-base-4.2.3=. -fstack-protector-strong -c addpt.f -o addpt.o gfortran -fno-optimize-sibling-calls -fpic -g -O2 -ffile-prefix-map=/build/r-base-LhKvHL/r-base-4.2.3=. -fstack-protector-strong -c adjchk.f -o adjchk.o gfortran -fno-optimize-sibling-calls -fpic -g -O2 -ffile-prefix-map=/build/r-base-LhKvHL/r-base-4.2.3=. -fstack-protector-strong -c binsrt.f -o binsrt.o gfortran -fno-optimize-sibling-calls -fpic -g -O2 -ffile-prefix-map=/build/r-base-LhKvHL/r-base-4.2.3=. -fstack-protector-strong -c circen.f -o circen.o gfortran -fno-optimize-sibling-calls -fpic -g -O2 -ffile-prefix-map=/build/r-base-LhKvHL/r-base-4.2.3=. -fstack-protector-strong -c cross.f -o cross.o gfortran -fno-optimize-sibling-calls -fpic -g -O2 -ffile-prefix-map=/build/r-base-LhKvHL/r-base-4.2.3=. -fstack-protector-strong -c crossutil.f -o crossutil.o gfortran -fno-optimize-sibling-calls -fpic -g -O2 -ffile-prefix-map=/build/r-base-LhKvHL/r-base-4.2.3=. -fstack-protector-strong -c delet.f -o delet.o gfortran -fno-optimize-sibling-calls -fpic -g -O2 -ffile-prefix-map=/build/r-base-LhKvHL/r-base-4.2.3=. -fstack-protector-strong -c delet1.f -o delet1.o gfortran -fno-optimize-sibling-calls -fpic -g -O2 -ffile-prefix-map=/build/r-base-LhKvHL/r-base-4.2.3=. -fstack-protector-strong -c delout.f -o delout.o gfortran -fno-optimize-sibling-calls -fpic -g -O2 -ffile-prefix-map=/build/r-base-LhKvHL/r-base-4.2.3=. -fstack-protector-strong -c delseg.f -o delseg.o gfortran -fno-optimize-sibling-calls -fpic -g -O2 -ffile-prefix-map=/build/r-base-LhKvHL/r-base-4.2.3=. -fstack-protector-strong -c dirout.f -o dirout.o gfortran -fno-optimize-sibling-calls -fpic -g -O2 -ffile-prefix-map=/build/r-base-LhKvHL/r-base-4.2.3=. -fstack-protector-strong -c dirseg.f -o dirseg.o gfortran -fno-optimize-sibling-calls -fpic -g -O2 -ffile-prefix-map=/build/r-base-LhKvHL/r-base-4.2.3=. -fstack-protector-strong -c dldins.f -o dldins.o gcc -I"/usr/share/R/include" -DNDEBUG -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 init.c -o init.o gfortran -fno-optimize-sibling-calls -fpic -g -O2 -ffile-prefix-map=/build/r-base-LhKvHL/r-base-4.2.3=. -fstack-protector-strong -c initad.f -o initad.o gfortran -fno-optimize-sibling-calls -fpic -g -O2 -ffile-prefix-map=/build/r-base-LhKvHL/r-base-4.2.3=. -fstack-protector-strong -c insrt.f -o insrt.o gfortran -fno-optimize-sibling-calls -fpic -g -O2 -ffile-prefix-map=/build/r-base-LhKvHL/r-base-4.2.3=. -fstack-protector-strong -c insrt1.f -o insrt1.o gfortran -fno-optimize-sibling-calls -fpic -g -O2 -ffile-prefix-map=/build/r-base-LhKvHL/r-base-4.2.3=. -fstack-protector-strong -c intri.f -o intri.o gfortran -fno-optimize-sibling-calls -fpic -g -O2 -ffile-prefix-map=/build/r-base-LhKvHL/r-base-4.2.3=. -fstack-protector-strong -c locn.f -o locn.o gfortran -fno-optimize-sibling-calls -fpic -g -O2 -ffile-prefix-map=/build/r-base-LhKvHL/r-base-4.2.3=. -fstack-protector-strong -c master.f -o master.o gfortran -fno-optimize-sibling-calls -fpic -g -O2 -ffile-prefix-map=/build/r-base-LhKvHL/r-base-4.2.3=. -fstack-protector-strong -c mnnd.f -o mnnd.o gfortran -fno-optimize-sibling-calls -fpic -g -O2 -ffile-prefix-map=/build/r-base-LhKvHL/r-base-4.2.3=. -fstack-protector-strong -c pred.f -o pred.o gfortran -fno-optimize-sibling-calls -fpic -g -O2 -ffile-prefix-map=/build/r-base-LhKvHL/r-base-4.2.3=. -fstack-protector-strong -c qtest.f -o qtest.o gfortran -fno-optimize-sibling-calls -fpic -g -O2 -ffile-prefix-map=/build/r-base-LhKvHL/r-base-4.2.3=. -fstack-protector-strong -c qtest1.f -o qtest1.o gfortran -fno-optimize-sibling-calls -fpic -g -O2 -ffile-prefix-map=/build/r-base-LhKvHL/r-base-4.2.3=. -fstack-protector-strong -c stoke.f -o stoke.o gfortran -fno-optimize-sibling-calls -fpic -g -O2 -ffile-prefix-map=/build/r-base-LhKvHL/r-base-4.2.3=. -fstack-protector-strong -c succ.f -o succ.o gfortran -fno-optimize-sibling-calls -fpic -g -O2 -ffile-prefix-map=/build/r-base-LhKvHL/r-base-4.2.3=. -fstack-protector-strong -c swap.f -o swap.o gfortran -fno-optimize-sibling-calls -fpic -g -O2 -ffile-prefix-map=/build/r-base-LhKvHL/r-base-4.2.3=. -fstack-protector-strong -c testeq.f -o testeq.o gfortran -fno-optimize-sibling-calls -fpic -g -O2 -ffile-prefix-map=/build/r-base-LhKvHL/r-base-4.2.3=. -fstack-protector-strong -c triar.f -o triar.o gfortran -fno-optimize-sibling-calls -fpic -g -O2 -ffile-prefix-map=/build/r-base-LhKvHL/r-base-4.2.3=. -fstack-protector-strong -c trifnd.f -o trifnd.o gcc -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -o deldir.so acchk.o addpt.o adjchk.o binsrt.o circen.o cross.o crossutil.o delet.o delet1.o delout.o delseg.o dirout.o dirseg.o dldins.o init.o initad.o insrt.o insrt1.o intri.o locn.o master.o mnnd.o pred.o qtest.o qtest1.o stoke.o succ.o swap.o testeq.o triar.o trifnd.o -lgfortran -lm -lquadmath -L/usr/lib/R/lib -lR installing to /home/omnipath/local/R/4.2-3.16/00LOCK-deldir/00new/deldir/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 (deldir) * installing *source* package ‘scattermore’ ... ** package ‘scattermore’ successfully unpacked and MD5 sums checked ** using staged installation ** libs g++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG -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 histogram_to_rgbwt.cpp -o histogram_to_rgbwt.o g++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG -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 kernel_histogram.cpp -o kernel_histogram.o g++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG -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 kernel_rgbwt.cpp -o kernel_rgbwt.o g++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG -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 scatter_histogram.cpp -o scatter_histogram.o g++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG -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 scatter_indexed_rgbwt.cpp -o scatter_indexed_rgbwt.o g++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG -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 scatter_lines_histogram.cpp -o scatter_lines_histogram.o g++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG -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 scatter_lines_rgbwt.cpp -o scatter_lines_rgbwt.o g++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG -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 scatter_multicolor_rgbwt.cpp -o scatter_multicolor_rgbwt.o g++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG -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 scatter_singlecolor_rgbwt.cpp -o scatter_singlecolor_rgbwt.o gcc -I"/usr/share/R/include" -DNDEBUG -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 scattermore.c -o scattermore.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 scattermore.so histogram_to_rgbwt.o kernel_histogram.o kernel_rgbwt.o scatter_histogram.o scatter_indexed_rgbwt.o scatter_lines_histogram.o scatter_lines_rgbwt.o scatter_multicolor_rgbwt.o scatter_singlecolor_rgbwt.o scattermore.o -L/usr/lib/R/lib -lR installing to /home/omnipath/local/R/4.2-3.16/00LOCK-scattermore/00new/scattermore/libs ** R ** 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 (scattermore) The downloaded source packages are in ‘/tmp/Rtmp6gDosz/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 1.30.20), 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: 2023-05-18 00:41:56 CEST ]