[ Started: 2023-05-05 00:23:48 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" Warning: unable to access index for repository https://cran.uni-muenster.de/src/contrib: cannot open URL 'https://cran.uni-muenster.de/src/contrib/PACKAGES' Warning: unable to access index for repository https://cran.uni-muenster.de/src/contrib: cannot open URL 'https://cran.uni-muenster.de/src/contrib/PACKAGES' Bioconductor version '3.16' is out-of-date; the current release version '3.17' is available with R version '4.3'; see https://bioconductor.org/install 'getOption("repos")' replaces Bioconductor standard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 1.30.20), R 4.2.3 (2023-03-15) Old packages: 'cachem', 'class', 'graphlayouts', 'KernSmooth', 'later', 'MASS', 'nnet', 'pkgmaker', 'profvis', 'sass', 'scattermore', 'testthat', 'viridis', 'viridisLite', 'waldo' trying URL 'https://cloud.r-project.org/src/contrib/cachem_1.0.8.tar.gz' Content type 'application/x-gzip' length 26510 bytes (25 KB) ================================================== downloaded 25 KB trying URL 'https://cloud.r-project.org/src/contrib/class_7.3-22.tar.gz' Content type 'application/x-gzip' length 20812 bytes (20 KB) ================================================== downloaded 20 KB trying URL 'https://cloud.r-project.org/src/contrib/graphlayouts_1.0.0.tar.gz' Content type 'application/x-gzip' length 4195831 bytes (4.0 MB) ================================================== downloaded 4.0 MB trying URL 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================================================== downloaded 2.9 MB trying URL 'https://cloud.r-project.org/src/contrib/viridisLite_0.4.2.tar.gz' Content type 'application/x-gzip' length 1267121 bytes (1.2 MB) ================================================== downloaded 1.2 MB trying URL 'https://cloud.r-project.org/src/contrib/waldo_0.5.0.tar.gz' Content type 'application/x-gzip' length 39335 bytes (38 KB) ================================================== downloaded 38 KB * installing *source* package ‘cachem’ ... ** package ‘cachem’ successfully unpacked and MD5 sums checked ** using staged installation ** libs 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 cache.c -o cache.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 gcc -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -o cachem.so cache.o init.o -L/usr/lib/R/lib -lR installing to /home/omnipath/local/R/4.2-3.16/00LOCK-cachem/00new/cachem/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 (cachem) * 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 ‘KernSmooth’ ... ** package ‘KernSmooth’ 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 blkest.f -o blkest.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 cp.f -o cp.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 dgedi.f -o dgedi.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 dgefa.f -o dgefa.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 dgesl.f -o dgesl.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 linbin.f -o linbin.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 linbin2D.f -o linbin2D.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 locpoly.f -o locpoly.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 rlbin.f -o rlbin.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 sdiag.f -o sdiag.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 sstdiag.f -o sstdiag.o gcc -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -o KernSmooth.so blkest.o cp.o dgedi.o dgefa.o dgesl.o init.o linbin.o linbin2D.o locpoly.o rlbin.o sdiag.o sstdiag.o -lblas -lgfortran -lm -lquadmath -lgfortran -lm -lquadmath -L/usr/lib/R/lib -lR installing to /home/omnipath/local/R/4.2-3.16/00LOCK-KernSmooth/00new/KernSmooth/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 (KernSmooth) * installing *source* package ‘later’ ... ** package ‘later’ successfully unpacked and MD5 sums checked ** using staged installation Running configure script -latomic linker flag not needed. ** libs g++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG -pthread -DSTRICT_R_HEADERS -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++14 -I"/usr/share/R/include" -DNDEBUG -pthread -DSTRICT_R_HEADERS -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 callback_registry.cpp -o callback_registry.o g++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG -pthread -DSTRICT_R_HEADERS -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 debug.cpp -o debug.o gcc -I"/usr/share/R/include" -DNDEBUG -pthread -DSTRICT_R_HEADERS -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 init.c -o init.o g++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG -pthread -DSTRICT_R_HEADERS -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 later.cpp -o later.o g++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG -pthread -DSTRICT_R_HEADERS -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 later_posix.cpp -o later_posix.o g++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG -pthread -DSTRICT_R_HEADERS -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 later_win32.cpp -o later_win32.o g++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG -pthread -DSTRICT_R_HEADERS -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 timer_posix.cpp -o timer_posix.o g++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG -pthread -DSTRICT_R_HEADERS -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 timestamp_unix.cpp -o timestamp_unix.o g++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG -pthread -DSTRICT_R_HEADERS -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 timestamp_win32.cpp -o timestamp_win32.o gcc -I"/usr/share/R/include" -DNDEBUG -pthread -DSTRICT_R_HEADERS -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 tinycthread.c -o tinycthread.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 later.so RcppExports.o callback_registry.o debug.o init.o later.o later_posix.o later_win32.o timer_posix.o timestamp_unix.o timestamp_win32.o tinycthread.o -pthread -L/usr/lib/R/lib -lR installing to /home/omnipath/local/R/4.2-3.16/00LOCK-later/00new/later/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 (later) * installing *source* package ‘MASS’ ... ** package ‘MASS’ successfully unpacked and MD5 sums checked ** using staged installation ** libs 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 MASS.c -o MASS.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 lqs.c -o lqs.o gcc -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -o MASS.so MASS.o lqs.o -L/usr/lib/R/lib -lR installing to /home/omnipath/local/R/4.2-3.16/00LOCK-MASS/00new/MASS/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 (MASS) * installing *source* package ‘nnet’ ... ** package ‘nnet’ successfully unpacked and MD5 sums checked ** using staged installation ** libs 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 nnet.c -o nnet.o gcc -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -o nnet.so nnet.o -L/usr/lib/R/lib -lR installing to /home/omnipath/local/R/4.2-3.16/00LOCK-nnet/00new/nnet/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 (nnet) * installing *source* package ‘pkgmaker’ ... ** package ‘pkgmaker’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading Setting package specific options: package:pkgmaker:logger (1 default option(s)) Creating meta registry in package 'pkgmaker' ... OK Creating registry 'extra_handler' in package 'pkgmaker' ... OK Creating registry 'extra_action' in package 'pkgmaker' ... OK Registering extra handler 'install.packages' [function] ... OK ** 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 (pkgmaker) * installing *source* package ‘profvis’ ... ** package ‘profvis’ successfully unpacked and MD5 sums checked ** using staged installation ** libs 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 pause.c -o pause.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 profvis-init.c -o profvis-init.o gcc -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -o profvis.so pause.o profvis-init.o -L/usr/lib/R/lib -lR installing to /home/omnipath/local/R/4.2-3.16/00LOCK-profvis/00new/profvis/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 (profvis) * installing *source* package ‘sass’ ... ** package ‘sass’ successfully unpacked and MD5 sums checked ** using staged installation ** libs /usr/share/R/share/make/shlib.mk:18: warning: overriding recipe for target 'shlib-clean' Makevars:12: warning: ignoring old recipe for target 'shlib-clean' gcc -I"/usr/share/R/include" -DNDEBUG -I./libsass/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 compile.c -o compile.o g++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG -I./libsass/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 init.cpp -o init.o MAKEFLAGS= CC="gcc" CFLAGS="-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 " CXX="g++ -std=gnu++14" AR="ar" LDFLAGS="-Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro" make -C libsass make[1]: Entering directory '/tmp/RtmpScVzpN/R.INSTALLbc6b938da477c/sass/src/libsass' gcc -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 -O2 -I ./include -fPIC -c -o src/cencode.o src/cencode.c g++ -std=gnu++14 -Wall -O2 -std=c++11 -I ./include -fPIC -c -o src/ast.o src/ast.cpp g++ -std=gnu++14 -Wall -O2 -std=c++11 -I ./include -fPIC -c -o src/ast_values.o src/ast_values.cpp g++ -std=gnu++14 -Wall -O2 -std=c++11 -I ./include -fPIC -c -o src/ast_supports.o src/ast_supports.cpp g++ -std=gnu++14 -Wall -O2 -std=c++11 -I ./include -fPIC -c -o src/ast_sel_cmp.o src/ast_sel_cmp.cpp g++ -std=gnu++14 -Wall -O2 -std=c++11 -I ./include -fPIC -c -o src/ast_sel_unify.o src/ast_sel_unify.cpp g++ -std=gnu++14 -Wall -O2 -std=c++11 -I ./include -fPIC -c -o src/ast_sel_super.o src/ast_sel_super.cpp g++ -std=gnu++14 -Wall -O2 -std=c++11 -I ./include -fPIC -c -o src/ast_sel_weave.o src/ast_sel_weave.cpp g++ -std=gnu++14 -Wall -O2 -std=c++11 -I ./include -fPIC -c -o src/ast_selectors.o src/ast_selectors.cpp g++ -std=gnu++14 -Wall -O2 -std=c++11 -I ./include -fPIC -c -o src/context.o src/context.cpp g++ -std=gnu++14 -Wall -O2 -std=c++11 -I ./include -fPIC -c -o src/constants.o src/constants.cpp g++ -std=gnu++14 -Wall -O2 -std=c++11 -I ./include -fPIC -c -o src/fn_utils.o src/fn_utils.cpp g++ -std=gnu++14 -Wall -O2 -std=c++11 -I ./include -fPIC -c -o src/fn_miscs.o src/fn_miscs.cpp g++ -std=gnu++14 -Wall -O2 -std=c++11 -I ./include -fPIC -c -o src/fn_maps.o src/fn_maps.cpp g++ -std=gnu++14 -Wall -O2 -std=c++11 -I ./include -fPIC -c -o src/fn_lists.o src/fn_lists.cpp g++ -std=gnu++14 -Wall -O2 -std=c++11 -I ./include -fPIC -c -o src/fn_colors.o src/fn_colors.cpp g++ -std=gnu++14 -Wall -O2 -std=c++11 -I ./include -fPIC -c -o src/fn_numbers.o src/fn_numbers.cpp g++ -std=gnu++14 -Wall -O2 -std=c++11 -I ./include -fPIC -c -o src/fn_strings.o src/fn_strings.cpp g++ -std=gnu++14 -Wall -O2 -std=c++11 -I ./include -fPIC -c -o src/fn_selectors.o src/fn_selectors.cpp g++ -std=gnu++14 -Wall -O2 -std=c++11 -I ./include -fPIC -c -o src/color_maps.o src/color_maps.cpp g++ -std=gnu++14 -Wall -O2 -std=c++11 -I ./include -fPIC -c -o src/environment.o src/environment.cpp g++ -std=gnu++14 -Wall -O2 -std=c++11 -I ./include -fPIC -c -o src/ast_fwd_decl.o src/ast_fwd_decl.cpp g++ -std=gnu++14 -Wall -O2 -std=c++11 -I ./include -fPIC -c -o src/bind.o src/bind.cpp g++ -std=gnu++14 -Wall -O2 -std=c++11 -I ./include -fPIC -c -o src/file.o src/file.cpp g++ -std=gnu++14 -Wall -O2 -std=c++11 -I ./include -fPIC -c -o src/util.o src/util.cpp g++ -std=gnu++14 -Wall -O2 -std=c++11 -I ./include -fPIC -c -o src/util_string.o src/util_string.cpp g++ -std=gnu++14 -Wall -O2 -std=c++11 -I ./include -fPIC -c -o src/json.o src/json.cpp g++ -std=gnu++14 -Wall -O2 -std=c++11 -I ./include -fPIC -c -o src/units.o src/units.cpp g++ -std=gnu++14 -Wall -O2 -std=c++11 -I ./include -fPIC -c -o src/values.o src/values.cpp g++ -std=gnu++14 -Wall -O2 -std=c++11 -I ./include -fPIC -c -o src/plugins.o src/plugins.cpp g++ -std=gnu++14 -Wall -O2 -std=c++11 -I ./include -fPIC -c -o src/source.o src/source.cpp g++ -std=gnu++14 -Wall -O2 -std=c++11 -I ./include -fPIC -c -o src/position.o src/position.cpp g++ -std=gnu++14 -Wall -O2 -std=c++11 -I ./include -fPIC -c -o src/lexer.o src/lexer.cpp g++ -std=gnu++14 -Wall -O2 -std=c++11 -I ./include -fPIC -c -o src/parser.o src/parser.cpp g++ -std=gnu++14 -Wall -O2 -std=c++11 -I ./include -fPIC -c -o src/parser_selectors.o src/parser_selectors.cpp g++ -std=gnu++14 -Wall -O2 -std=c++11 -I ./include -fPIC -c -o src/prelexer.o src/prelexer.cpp g++ -std=gnu++14 -Wall -O2 -std=c++11 -I ./include -fPIC -c -o src/eval.o src/eval.cpp g++ -std=gnu++14 -Wall -O2 -std=c++11 -I ./include -fPIC -c -o src/eval_selectors.o src/eval_selectors.cpp g++ -std=gnu++14 -Wall -O2 -std=c++11 -I ./include -fPIC -c -o src/expand.o src/expand.cpp g++ -std=gnu++14 -Wall -O2 -std=c++11 -I ./include -fPIC -c -o src/listize.o src/listize.cpp g++ -std=gnu++14 -Wall -O2 -std=c++11 -I ./include -fPIC -c -o src/cssize.o src/cssize.cpp g++ -std=gnu++14 -Wall -O2 -std=c++11 -I ./include -fPIC -c -o src/extender.o src/extender.cpp g++ -std=gnu++14 -Wall -O2 -std=c++11 -I ./include -fPIC -c -o src/extension.o src/extension.cpp g++ -std=gnu++14 -Wall -O2 -std=c++11 -I ./include -fPIC -c -o src/stylesheet.o src/stylesheet.cpp g++ -std=gnu++14 -Wall -O2 -std=c++11 -I ./include -fPIC -c -o src/output.o src/output.cpp g++ -std=gnu++14 -Wall -O2 -std=c++11 -I ./include -fPIC -c -o src/inspect.o src/inspect.cpp g++ -std=gnu++14 -Wall -O2 -std=c++11 -I ./include -fPIC -c -o src/emitter.o src/emitter.cpp g++ -std=gnu++14 -Wall -O2 -std=c++11 -I ./include -fPIC -c -o src/check_nesting.o src/check_nesting.cpp g++ -std=gnu++14 -Wall -O2 -std=c++11 -I ./include -fPIC -c -o src/remove_placeholders.o src/remove_placeholders.cpp g++ -std=gnu++14 -Wall -O2 -std=c++11 -I ./include -fPIC -c -o src/sass.o src/sass.cpp g++ -std=gnu++14 -Wall -O2 -std=c++11 -I ./include -fPIC -c -o src/sass_values.o src/sass_values.cpp g++ -std=gnu++14 -Wall -O2 -std=c++11 -I ./include -fPIC -c -o src/sass_context.o src/sass_context.cpp g++ -std=gnu++14 -Wall -O2 -std=c++11 -I ./include -fPIC -c -o src/sass_functions.o src/sass_functions.cpp g++ -std=gnu++14 -Wall -O2 -std=c++11 -I ./include -fPIC -c -o src/sass2scss.o src/sass2scss.cpp g++ -std=gnu++14 -Wall -O2 -std=c++11 -I ./include -fPIC -c -o src/backtrace.o src/backtrace.cpp g++ -std=gnu++14 -Wall -O2 -std=c++11 -I ./include -fPIC -c -o src/operators.o src/operators.cpp g++ -std=gnu++14 -Wall -O2 -std=c++11 -I ./include -fPIC -c -o src/ast2c.o src/ast2c.cpp g++ -std=gnu++14 -Wall -O2 -std=c++11 -I ./include -fPIC -c -o src/c2ast.o src/c2ast.cpp g++ -std=gnu++14 -Wall -O2 -std=c++11 -I ./include -fPIC -c -o src/to_value.o src/to_value.cpp g++ -std=gnu++14 -Wall -O2 -std=c++11 -I ./include -fPIC -c -o src/source_map.o src/source_map.cpp g++ -std=gnu++14 -Wall -O2 -std=c++11 -I ./include -fPIC -c -o src/error_handling.o src/error_handling.cpp g++ -std=gnu++14 -Wall -O2 -std=c++11 -I ./include -fPIC -c -o src/memory/allocator.o src/memory/allocator.cpp g++ -std=gnu++14 -Wall -O2 -std=c++11 -I ./include -fPIC -c -o src/memory/shared_ptr.o src/memory/shared_ptr.cpp g++ -std=gnu++14 -Wall -O2 -std=c++11 -I ./include -fPIC -c -o src/utf8_string.o src/utf8_string.cpp g++ -std=gnu++14 -Wall -O2 -std=c++11 -I ./include -fPIC -c -o src/base64vlq.o src/base64vlq.cpp mkdir lib ar rcvs lib/libsass.a src/cencode.o src/ast.o src/ast_values.o src/ast_supports.o src/ast_sel_cmp.o src/ast_sel_unify.o src/ast_sel_super.o src/ast_sel_weave.o src/ast_selectors.o src/context.o src/constants.o src/fn_utils.o src/fn_miscs.o src/fn_maps.o src/fn_lists.o src/fn_colors.o src/fn_numbers.o src/fn_strings.o src/fn_selectors.o src/color_maps.o src/environment.o src/ast_fwd_decl.o src/bind.o src/file.o src/util.o src/util_string.o src/json.o src/units.o src/values.o src/plugins.o src/source.o src/position.o src/lexer.o src/parser.o src/parser_selectors.o src/prelexer.o src/eval.o src/eval_selectors.o src/expand.o src/listize.o src/cssize.o src/extender.o src/extension.o src/stylesheet.o src/output.o src/inspect.o src/emitter.o src/check_nesting.o src/remove_placeholders.o src/sass.o src/sass_values.o src/sass_context.o src/sass_functions.o src/sass2scss.o src/backtrace.o src/operators.o src/ast2c.o src/c2ast.o src/to_value.o src/source_map.o src/error_handling.o src/memory/allocator.o src/memory/shared_ptr.o src/utf8_string.o src/base64vlq.o a - src/cencode.o a - src/ast.o a - src/ast_values.o a - src/ast_supports.o a - src/ast_sel_cmp.o a - src/ast_sel_unify.o a - src/ast_sel_super.o a - src/ast_sel_weave.o a - src/ast_selectors.o a - src/context.o a - src/constants.o a - src/fn_utils.o a - src/fn_miscs.o a - src/fn_maps.o a - src/fn_lists.o a - src/fn_colors.o a - src/fn_numbers.o a - src/fn_strings.o a - src/fn_selectors.o a - src/color_maps.o a - src/environment.o a - src/ast_fwd_decl.o a - src/bind.o a - src/file.o a - src/util.o a - src/util_string.o a - src/json.o a - src/units.o a - src/values.o a - src/plugins.o a - src/source.o a - src/position.o a - src/lexer.o a - src/parser.o a - src/parser_selectors.o a - src/prelexer.o a - src/eval.o a - src/eval_selectors.o a - src/expand.o a - src/listize.o a - src/cssize.o a - src/extender.o a - src/extension.o a - src/stylesheet.o a - src/output.o a - src/inspect.o a - src/emitter.o a - src/check_nesting.o a - src/remove_placeholders.o a - src/sass.o a - src/sass_values.o a - src/sass_context.o a - src/sass_functions.o a - src/sass2scss.o a - src/backtrace.o a - src/operators.o a - src/ast2c.o a - src/c2ast.o a - src/to_value.o a - src/source_map.o a - src/error_handling.o a - src/memory/allocator.o a - src/memory/shared_ptr.o a - src/utf8_string.o a - src/base64vlq.o make[1]: Leaving directory '/tmp/RtmpScVzpN/R.INSTALLbc6b938da477c/sass/src/libsass' g++ -std=gnu++14 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -o sass.so compile.o init.o ./libsass/lib/libsass.a -L/usr/lib/R/lib -lR installing to /home/omnipath/local/R/4.2-3.16/00LOCK-sass/00new/sass/libs ** R ** 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 (sass) * 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) * installing *source* package ‘viridisLite’ ... ** package ‘viridisLite’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** inst ** 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 ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (viridisLite) * installing *source* package ‘waldo’ ... ** package ‘waldo’ successfully unpacked and MD5 sums checked ** using staged installation ** 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 ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (waldo) * installing *source* package ‘class’ ... ** package ‘class’ successfully unpacked and MD5 sums checked ** using staged installation ** libs 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 class.c -o class.o gcc -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -o class.so class.o -L/usr/lib/R/lib -lR installing to /home/omnipath/local/R/4.2-3.16/00LOCK-class/00new/class/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 (class) * installing *source* package ‘testthat’ ... ** package ‘testthat’ successfully unpacked and MD5 sums checked ** using staged installation ** libs gcc -I"/usr/share/R/include" -DNDEBUG -I../inst/include -DCOMPILING_TESTTHAT -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 gcc -I"/usr/share/R/include" -DNDEBUG -I../inst/include -DCOMPILING_TESTTHAT -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 reassign.c -o reassign.o g++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG -I../inst/include -DCOMPILING_TESTTHAT -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 test-catch.cpp -o test-catch.o g++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG -I../inst/include -DCOMPILING_TESTTHAT -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 test-example.cpp -o test-example.o g++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG -I../inst/include -DCOMPILING_TESTTHAT -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 test-runner.cpp -o test-runner.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 testthat.so init.o reassign.o test-catch.o test-example.o test-runner.o -L/usr/lib/R/lib -lR installing to /home/omnipath/local/R/4.2-3.16/00LOCK-testthat/00new/testthat/libs ** R ** 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 (testthat) * installing *source* package ‘viridis’ ... ** package ‘viridis’ successfully unpacked and MD5 sums checked ** using staged installation ** 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 ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (viridis) The downloaded source packages are in ‘/tmp/Rtmpl2HeO6/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' Skipping 17 packages not available: BiocManager, yaml, rmarkdown, knitr, bookdown, sessioninfo, testthat, covr, RefManageR, rjson, tidyr, tibble, dplyr, igraph, lpSolve, stringr, readr [ Finished: 2023-05-05 00:36:25 CEST ]