[ Started: 2024-01-13 11:51:13 CET ] [ CARNIVAL v2.7.2 for BioC-3.18 from https://github.com/saezlab/CARNIVAL@master ] [1] "Libraries: " "/home/omnipath/local/R/4.3-3.18" [3] "/home/omnipath/local/R/4.3" "/usr/lib/R/library" trying URL 'https://cran.uni-muenster.de/src/contrib/DBI_1.2.1.tar.gz' Content type 'application/x-gzip' length 1116529 bytes (1.1 MB) ================================================== downloaded 1.1 MB trying URL 'https://cran.uni-muenster.de/src/contrib/FNN_1.1.4.tar.gz' Content type 'application/x-gzip' length 79913 bytes (78 KB) ================================================== downloaded 78 KB * installing *source* package ‘DBI’ ... ** package ‘DBI’ 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 ** 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 (DBI) * installing *source* package ‘FNN’ ... ** package ‘FNN’ 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’ g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -Iinclude -DUSING_R -DUSING_RPRINT -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 ANN.cpp -o ANN.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -Iinclude -DUSING_R -DUSING_RPRINT -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 KNN_ANN.cpp -o KNN_ANN.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -Iinclude -DUSING_R -DUSING_RPRINT -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 KNN_correlation_distance.cpp -o KNN_correlation_distance.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -Iinclude -DUSING_R -DUSING_RPRINT -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 KNN_cover_test.cpp -o KNN_cover_test.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -Iinclude -DUSING_R -DUSING_RPRINT -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 KNN_cover_tree.cpp -o KNN_cover_tree.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -Iinclude -DUSING_R -DUSING_RPRINT -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 KNN_mutual_information.cpp -o KNN_mutual_information.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -Iinclude -DUSING_R -DUSING_RPRINT -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 bd_fix_rad_search.cpp -o bd_fix_rad_search.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -Iinclude -DUSING_R -DUSING_RPRINT -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 bd_pr_search.cpp -o bd_pr_search.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -Iinclude -DUSING_R -DUSING_RPRINT -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 bd_search.cpp -o bd_search.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -Iinclude -DUSING_R -DUSING_RPRINT -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 bd_tree.cpp -o bd_tree.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -Iinclude -DUSING_R -DUSING_RPRINT -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 brute.cpp -o brute.o gcc -I"/usr/share/R/include" -DNDEBUG -Iinclude -DUSING_R -DUSING_RPRINT -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_FNN.c -o init_FNN.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -Iinclude -DUSING_R -DUSING_RPRINT -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 kd_dump.cpp -o kd_dump.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -Iinclude -DUSING_R -DUSING_RPRINT -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 kd_fix_rad_search.cpp -o kd_fix_rad_search.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -Iinclude -DUSING_R -DUSING_RPRINT -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 kd_pr_search.cpp -o kd_pr_search.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -Iinclude -DUSING_R -DUSING_RPRINT -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 kd_search.cpp -o kd_search.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -Iinclude -DUSING_R -DUSING_RPRINT -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 kd_split.cpp -o kd_split.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -Iinclude -DUSING_R -DUSING_RPRINT -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 kd_tree.cpp -o kd_tree.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -Iinclude -DUSING_R -DUSING_RPRINT -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 kd_util.cpp -o kd_util.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -Iinclude -DUSING_R -DUSING_RPRINT -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 label_point.cpp -o label_point.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -Iinclude -DUSING_R -DUSING_RPRINT -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 perf.cpp -o perf.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 FNN.so ANN.o KNN_ANN.o KNN_correlation_distance.o KNN_cover_test.o KNN_cover_tree.o KNN_mutual_information.o bd_fix_rad_search.o bd_pr_search.o bd_search.o bd_tree.o brute.o init_FNN.o kd_dump.o kd_fix_rad_search.o kd_pr_search.o kd_search.o kd_split.o kd_tree.o kd_util.o label_point.o perf.o -L/usr/lib/R/lib -lR rm -f *.o core installing to /home/omnipath/local/R/4.3-3.18/00LOCK-FNN/00new/FNN/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 (FNN) The downloaded source packages are in ‘/tmp/RtmpR706ao/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 3.18 (BiocManager 1.30.22), R 4.3.1 (2023-06-16) Old packages: 'densvis' trying URL 'https://bioconductor.org/packages/3.18/bioc/src/contrib/densvis_1.12.1.tar.gz' Content type 'application/x-gzip' length 1734181 bytes (1.7 MB) ================================================== downloaded 1.7 MB * installing *source* package ‘densvis’ ... ** using non-staged installation via StagedInstall field ** libs using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.3-3.18/Rcpp/include' -fopenmp -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'/home/omnipath/local/R/4.3-3.18/Rcpp/include' -fopenmp -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 densne.cpp -o densne.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.3-3.18/Rcpp/include' -fopenmp -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 densvis.cpp -o densvis.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.3-3.18/Rcpp/include' -fopenmp -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 sptree.cpp -o sptree.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 densvis.so RcppExports.o densne.o densvis.o sptree.o -llapack -lblas -lgfortran -lm -lquadmath -fopenmp -L/usr/lib/R/lib -lR installing to /home/omnipath/local/R/4.3-3.18/densvis/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 * DONE (densvis) The downloaded source packages are in ‘/tmp/RtmpR706ao/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 3.18 (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: 2024-01-13 11:51:54 CET ]