[ Started: 2024-02-13 11:51:14 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/rvest_1.0.4.tar.gz' Content type 'application/x-gzip' length 115876 bytes (113 KB) ================================================== downloaded 113 KB * installing *source* package ‘rvest’ ... ** package ‘rvest’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** demo ** 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 (rvest) The downloaded source packages are in ‘/tmp/RtmpIaZ8nQ/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: 'edgeR', 'SparseArray' trying URL 'https://bioconductor.org/packages/3.18/bioc/src/contrib/edgeR_4.0.15.tar.gz' Content type 'application/x-gzip' length 3571596 bytes (3.4 MB) ================================================== downloaded 3.4 MB trying URL 'https://bioconductor.org/packages/3.18/bioc/src/contrib/SparseArray_1.2.4.tar.gz' Content type 'application/x-gzip' length 367778 bytes (359 KB) ================================================== downloaded 359 KB * installing *source* package ‘edgeR’ ... ** 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 -I'/home/omnipath/local/R/4.3-3.18/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 R_add_prior_count.cpp -o R_add_prior_count.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.3-3.18/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 R_ave_log_cpm.cpp -o R_ave_log_cpm.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.3-3.18/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 R_calculate_cpm.cpp -o R_calculate_cpm.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.3-3.18/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 R_check_poisson_bound.cpp -o R_check_poisson_bound.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.3-3.18/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 R_compute_apl.cpp -o R_compute_apl.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.3-3.18/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 R_compute_nbdev.cpp -o R_compute_nbdev.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.3-3.18/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 R_exact_test_by_deviance.cpp -o R_exact_test_by_deviance.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.3-3.18/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 R_fit_levenberg.cpp -o R_fit_levenberg.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.3-3.18/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 R_fit_one_group.cpp -o R_fit_one_group.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.3-3.18/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 R_get_one_way_fitted.cpp -o R_get_one_way_fitted.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.3-3.18/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 R_initialize_levenberg.cpp -o R_initialize_levenberg.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.3-3.18/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 R_loess_by_col.cpp -o R_loess_by_col.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.3-3.18/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 R_maximize_interpolant.cpp -o R_maximize_interpolant.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.3-3.18/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 R_process_hairpin_reads.c -o R_process_hairpin_reads.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.3-3.18/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 R_ql_glm.c -o R_ql_glm.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.3-3.18/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 R_simple_good_turing.cpp -o R_simple_good_turing.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.3-3.18/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 add_prior.cpp -o add_prior.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.3-3.18/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 adj_coxreid.cpp -o adj_coxreid.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.3-3.18/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 fmm_spline.c -o fmm_spline.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.3-3.18/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 glm_levenberg.cpp -o glm_levenberg.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.3-3.18/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 glm_one_group.cpp -o glm_one_group.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.3-3.18/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.cpp -o init.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.3-3.18/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 interpolator.cpp -o interpolator.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.3-3.18/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 nbdev.c -o nbdev.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.3-3.18/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 objects.cpp -o objects.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.3-3.18/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 ql_glm.c -o ql_glm.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.3-3.18/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 ql_weights.c -o ql_weights.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.3-3.18/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 qr_hat.c -o qr_hat.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 edgeR.so R_add_prior_count.o R_ave_log_cpm.o R_calculate_cpm.o R_check_poisson_bound.o R_compute_apl.o R_compute_nbdev.o R_exact_test_by_deviance.o R_fit_levenberg.o R_fit_one_group.o R_get_one_way_fitted.o R_initialize_levenberg.o R_loess_by_col.o R_maximize_interpolant.o R_process_hairpin_reads.o R_ql_glm.o R_simple_good_turing.o add_prior.o adj_coxreid.o fmm_spline.o glm_levenberg.o glm_one_group.o init.o interpolator.o nbdev.o objects.o ql_glm.o ql_weights.o qr_hat.o -llapack -lblas -lgfortran -lm -lquadmath -L/usr/lib/R/lib -lR installing to /home/omnipath/local/R/4.3-3.18/00LOCK-edgeR/00new/edgeR/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 (edgeR) * installing *source* package ‘SparseArray’ ... ** using staged installation ** libs using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.3-3.18/S4Vectors/include' -I'/home/omnipath/local/R/4.3-3.18/IRanges/include' -I'/home/omnipath/local/R/4.3-3.18/XVector/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 ExtendableJaggedArray.c -o ExtendableJaggedArray.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.3-3.18/S4Vectors/include' -I'/home/omnipath/local/R/4.3-3.18/IRanges/include' -I'/home/omnipath/local/R/4.3-3.18/XVector/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 IRanges_stubs.c -o IRanges_stubs.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.3-3.18/S4Vectors/include' -I'/home/omnipath/local/R/4.3-3.18/IRanges/include' -I'/home/omnipath/local/R/4.3-3.18/XVector/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 R_init_SparseArray.c -o R_init_SparseArray.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.3-3.18/S4Vectors/include' -I'/home/omnipath/local/R/4.3-3.18/IRanges/include' -I'/home/omnipath/local/R/4.3-3.18/XVector/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 Rvector_summarization.c -o Rvector_summarization.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.3-3.18/S4Vectors/include' -I'/home/omnipath/local/R/4.3-3.18/IRanges/include' -I'/home/omnipath/local/R/4.3-3.18/XVector/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 Rvector_utils.c -o Rvector_utils.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.3-3.18/S4Vectors/include' -I'/home/omnipath/local/R/4.3-3.18/IRanges/include' -I'/home/omnipath/local/R/4.3-3.18/XVector/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 S4Vectors_stubs.c -o S4Vectors_stubs.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.3-3.18/S4Vectors/include' -I'/home/omnipath/local/R/4.3-3.18/IRanges/include' -I'/home/omnipath/local/R/4.3-3.18/XVector/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 SBT_utils.c -o SBT_utils.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.3-3.18/S4Vectors/include' -I'/home/omnipath/local/R/4.3-3.18/IRanges/include' -I'/home/omnipath/local/R/4.3-3.18/XVector/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 SVT_SparseArray_class.c -o SVT_SparseArray_class.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.3-3.18/S4Vectors/include' -I'/home/omnipath/local/R/4.3-3.18/IRanges/include' -I'/home/omnipath/local/R/4.3-3.18/XVector/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 SparseArray_Complex_methods.c -o SparseArray_Complex_methods.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.3-3.18/S4Vectors/include' -I'/home/omnipath/local/R/4.3-3.18/IRanges/include' -I'/home/omnipath/local/R/4.3-3.18/XVector/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 SparseArray_Math_methods.c -o SparseArray_Math_methods.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.3-3.18/S4Vectors/include' -I'/home/omnipath/local/R/4.3-3.18/IRanges/include' -I'/home/omnipath/local/R/4.3-3.18/XVector/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 SparseArray_Ops_methods.c -o SparseArray_Ops_methods.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.3-3.18/S4Vectors/include' -I'/home/omnipath/local/R/4.3-3.18/IRanges/include' -I'/home/omnipath/local/R/4.3-3.18/XVector/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 SparseArray_abind.c -o SparseArray_abind.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.3-3.18/S4Vectors/include' -I'/home/omnipath/local/R/4.3-3.18/IRanges/include' -I'/home/omnipath/local/R/4.3-3.18/XVector/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 SparseArray_aperm.c -o SparseArray_aperm.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.3-3.18/S4Vectors/include' -I'/home/omnipath/local/R/4.3-3.18/IRanges/include' -I'/home/omnipath/local/R/4.3-3.18/XVector/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 SparseArray_class.c -o SparseArray_class.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.3-3.18/S4Vectors/include' -I'/home/omnipath/local/R/4.3-3.18/IRanges/include' -I'/home/omnipath/local/R/4.3-3.18/XVector/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 SparseArray_dim_tuning.c -o SparseArray_dim_tuning.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.3-3.18/S4Vectors/include' -I'/home/omnipath/local/R/4.3-3.18/IRanges/include' -I'/home/omnipath/local/R/4.3-3.18/XVector/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 SparseArray_subassignment.c -o SparseArray_subassignment.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.3-3.18/S4Vectors/include' -I'/home/omnipath/local/R/4.3-3.18/IRanges/include' -I'/home/omnipath/local/R/4.3-3.18/XVector/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 SparseArray_subsetting.c -o SparseArray_subsetting.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.3-3.18/S4Vectors/include' -I'/home/omnipath/local/R/4.3-3.18/IRanges/include' -I'/home/omnipath/local/R/4.3-3.18/XVector/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 SparseArray_summarization.c -o SparseArray_summarization.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.3-3.18/S4Vectors/include' -I'/home/omnipath/local/R/4.3-3.18/IRanges/include' -I'/home/omnipath/local/R/4.3-3.18/XVector/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 SparseMatrix_mult.c -o SparseMatrix_mult.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.3-3.18/S4Vectors/include' -I'/home/omnipath/local/R/4.3-3.18/IRanges/include' -I'/home/omnipath/local/R/4.3-3.18/XVector/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 XVector_stubs.c -o XVector_stubs.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.3-3.18/S4Vectors/include' -I'/home/omnipath/local/R/4.3-3.18/IRanges/include' -I'/home/omnipath/local/R/4.3-3.18/XVector/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 coerceVector2.c -o coerceVector2.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.3-3.18/S4Vectors/include' -I'/home/omnipath/local/R/4.3-3.18/IRanges/include' -I'/home/omnipath/local/R/4.3-3.18/XVector/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 leaf_vector_Arith.c -o leaf_vector_Arith.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.3-3.18/S4Vectors/include' -I'/home/omnipath/local/R/4.3-3.18/IRanges/include' -I'/home/omnipath/local/R/4.3-3.18/XVector/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 leaf_vector_Compare.c -o leaf_vector_Compare.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.3-3.18/S4Vectors/include' -I'/home/omnipath/local/R/4.3-3.18/IRanges/include' -I'/home/omnipath/local/R/4.3-3.18/XVector/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 leaf_vector_Logic.c -o leaf_vector_Logic.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.3-3.18/S4Vectors/include' -I'/home/omnipath/local/R/4.3-3.18/IRanges/include' -I'/home/omnipath/local/R/4.3-3.18/XVector/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 leaf_vector_dotprod.c -o leaf_vector_dotprod.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.3-3.18/S4Vectors/include' -I'/home/omnipath/local/R/4.3-3.18/IRanges/include' -I'/home/omnipath/local/R/4.3-3.18/XVector/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 leaf_vector_summarization.c -o leaf_vector_summarization.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.3-3.18/S4Vectors/include' -I'/home/omnipath/local/R/4.3-3.18/IRanges/include' -I'/home/omnipath/local/R/4.3-3.18/XVector/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 leaf_vector_utils.c -o leaf_vector_utils.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.3-3.18/S4Vectors/include' -I'/home/omnipath/local/R/4.3-3.18/IRanges/include' -I'/home/omnipath/local/R/4.3-3.18/XVector/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 matrixStats_methods.c -o matrixStats_methods.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.3-3.18/S4Vectors/include' -I'/home/omnipath/local/R/4.3-3.18/IRanges/include' -I'/home/omnipath/local/R/4.3-3.18/XVector/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 randomSparseArray.c -o randomSparseArray.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.3-3.18/S4Vectors/include' -I'/home/omnipath/local/R/4.3-3.18/IRanges/include' -I'/home/omnipath/local/R/4.3-3.18/XVector/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 readSparseCSV.c -o readSparseCSV.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.3-3.18/S4Vectors/include' -I'/home/omnipath/local/R/4.3-3.18/IRanges/include' -I'/home/omnipath/local/R/4.3-3.18/XVector/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 rowsum_methods.c -o rowsum_methods.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.3-3.18/S4Vectors/include' -I'/home/omnipath/local/R/4.3-3.18/IRanges/include' -I'/home/omnipath/local/R/4.3-3.18/XVector/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 sparseMatrix_utils.c -o sparseMatrix_utils.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.3-3.18/S4Vectors/include' -I'/home/omnipath/local/R/4.3-3.18/IRanges/include' -I'/home/omnipath/local/R/4.3-3.18/XVector/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 test.c -o test.o gcc -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -o SparseArray.so ExtendableJaggedArray.o IRanges_stubs.o R_init_SparseArray.o Rvector_summarization.o Rvector_utils.o S4Vectors_stubs.o SBT_utils.o SVT_SparseArray_class.o SparseArray_Complex_methods.o SparseArray_Math_methods.o SparseArray_Ops_methods.o SparseArray_abind.o SparseArray_aperm.o SparseArray_class.o SparseArray_dim_tuning.o SparseArray_subassignment.o SparseArray_subsetting.o SparseArray_summarization.o SparseMatrix_mult.o XVector_stubs.o coerceVector2.o leaf_vector_Arith.o leaf_vector_Compare.o leaf_vector_Logic.o leaf_vector_dotprod.o leaf_vector_summarization.o leaf_vector_utils.o matrixStats_methods.o randomSparseArray.o readSparseCSV.o rowsum_methods.o sparseMatrix_utils.o test.o -L/usr/lib/R/lib -lR installing to /home/omnipath/local/R/4.3-3.18/00LOCK-SparseArray/00new/SparseArray/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 (SparseArray) The downloaded source packages are in ‘/tmp/RtmpIaZ8nQ/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: 2024-02-13 11:53:01 CET ]