[ Started: 2026-10-02 14:57:05 CEST ] [ MetaProViz v4.1.1 for BioC-3.24 from https://github.com/saezlab/MetaProViz@devel (a3ac947 2026-10-02 14:43:51) | R version 4.6.1 (2026-06-24) -- "Happy Hop" | docker | OVERRIDES from GitHub: saezlab/OmnipathR@devel ] 'getOption("repos")' replaces Bioconductor standard repositories, see 'help("repositories", package = "BiocManager")' for details. Replacement repositories: CRAN: https://p3m.dev/cran/__linux__/noble/latest Bioconductor version 3.24 (BiocManager 1.30.27), R 4.6.1 (2026-06-24) Installing package(s) 'BiocCheck' also installing the dependencies ‘stringr’, ‘bit’, ‘blob’, ‘tidyr’, ‘tidyselect’, ‘generics’, ‘bit64’, ‘BH’, ‘bitops’, ‘dbplyr’, ‘dplyr’, ‘RSQLite’, ‘DBI’, ‘filelock’, ‘Biobase’, ‘RBGL’, ‘XML’, ‘RCurl’, ‘RUnit’, ‘BiocGenerics’, ‘httr’, ‘selectr’, ‘BiocBaseUtils’, ‘BiocFileCache’, ‘biocViews’, ‘graph’, ‘rvest’, ‘stringdist’ trying URL 'https://bioconductor.org/packages/3.24/container-binaries/bioconductor_docker_devel-amd64/src/contrib/stringr_1.6.0_R_x86_64-pc-linux-gnu.tar.gz' trying URL 'https://bioconductor.org/packages/3.24/container-binaries/bioconductor_docker_devel-amd64/src/contrib/bit_4.6.0_R_x86_64-pc-linux-gnu.tar.gz' trying URL 'https://bioconductor.org/packages/3.24/container-binaries/bioconductor_docker_devel-amd64/src/contrib/blob_1.3.0_R_x86_64-pc-linux-gnu.tar.gz' trying URL 'https://bioconductor.org/packages/3.24/container-binaries/bioconductor_docker_devel-amd64/src/contrib/tidyr_1.3.2_R_x86_64-pc-linux-gnu.tar.gz' trying URL 'https://bioconductor.org/packages/3.24/container-binaries/bioconductor_docker_devel-amd64/src/contrib/tidyselect_1.2.1_R_x86_64-pc-linux-gnu.tar.gz' trying URL 'https://bioconductor.org/packages/3.24/container-binaries/bioconductor_docker_devel-amd64/src/contrib/generics_0.1.4_R_x86_64-pc-linux-gnu.tar.gz' trying URL 'https://p3m.dev/cran/__linux__/noble/latest/src/contrib/bit64_4.8.6.tar.gz' trying URL 'https://bioconductor.org/packages/3.24/container-binaries/bioconductor_docker_devel-amd64/src/contrib/BH_1.90.0-1_R_x86_64-pc-linux-gnu.tar.gz' trying URL 'https://p3m.dev/cran/__linux__/noble/latest/src/contrib/bitops_1.1-0.tar.gz' trying URL 'https://bioconductor.org/packages/3.24/container-binaries/bioconductor_docker_devel-amd64/src/contrib/dbplyr_2.6.0_R_x86_64-pc-linux-gnu.tar.gz' trying URL 'https://bioconductor.org/packages/3.24/container-binaries/bioconductor_docker_devel-amd64/src/contrib/dplyr_1.2.1_R_x86_64-pc-linux-gnu.tar.gz' trying URL 'https://bioconductor.org/packages/3.24/container-binaries/bioconductor_docker_devel-amd64/src/contrib/RSQLite_3.53.3_R_x86_64-pc-linux-gnu.tar.gz' trying URL 'https://bioconductor.org/packages/3.24/container-binaries/bioconductor_docker_devel-amd64/src/contrib/DBI_1.3.0_R_x86_64-pc-linux-gnu.tar.gz' trying URL 'https://bioconductor.org/packages/3.24/container-binaries/bioconductor_docker_devel-amd64/src/contrib/filelock_1.0.3_R_x86_64-pc-linux-gnu.tar.gz' trying URL 'https://bioconductor.org/packages/3.24/bioc/src/contrib/Biobase_2.73.2.tar.gz' trying URL 'https://bioconductor.org/packages/3.24/container-binaries/bioconductor_docker_devel-amd64/src/contrib/RBGL_1.89.0_R_x86_64-pc-linux-gnu.tar.gz' trying URL 'https://p3m.dev/cran/__linux__/noble/latest/src/contrib/XML_3.99-0.25.tar.gz' trying URL 'https://p3m.dev/cran/__linux__/noble/latest/src/contrib/RCurl_1.98-1.20.tar.gz' trying URL 'https://bioconductor.org/packages/3.24/container-binaries/bioconductor_docker_devel-amd64/src/contrib/RUnit_0.4.33.1_R_x86_64-pc-linux-gnu.tar.gz' trying URL 'https://bioconductor.org/packages/3.24/bioc/src/contrib/BiocGenerics_0.59.12.tar.gz' trying URL 'https://p3m.dev/cran/__linux__/noble/latest/src/contrib/httr_1.4.9.tar.gz' trying URL 'https://p3m.dev/cran/__linux__/noble/latest/src/contrib/selectr_0.8-0.tar.gz' trying URL 'https://bioconductor.org/packages/3.24/container-binaries/bioconductor_docker_devel-amd64/src/contrib/BiocBaseUtils_1.15.1_R_x86_64-pc-linux-gnu.tar.gz' trying URL 'https://bioconductor.org/packages/3.24/container-binaries/bioconductor_docker_devel-amd64/src/contrib/BiocFileCache_3.3.0_R_x86_64-pc-linux-gnu.tar.gz' trying URL 'https://bioconductor.org/packages/3.24/container-binaries/bioconductor_docker_devel-amd64/src/contrib/biocViews_1.81.1_R_x86_64-pc-linux-gnu.tar.gz' trying URL 'https://bioconductor.org/packages/3.24/container-binaries/bioconductor_docker_devel-amd64/src/contrib/graph_1.91.0_R_x86_64-pc-linux-gnu.tar.gz' trying URL 'https://bioconductor.org/packages/3.24/container-binaries/bioconductor_docker_devel-amd64/src/contrib/rvest_1.0.5_R_x86_64-pc-linux-gnu.tar.gz' trying URL 'https://bioconductor.org/packages/3.24/container-binaries/bioconductor_docker_devel-amd64/src/contrib/stringdist_0.9.17_R_x86_64-pc-linux-gnu.tar.gz' trying URL 'https://bioconductor.org/packages/3.24/bioc/src/contrib/BiocCheck_1.49.31.tar.gz' * installing *binary* package ‘stringr’ ... * package ‘stringr’ successfully unpacked and SHA256 sums checked * DONE (stringr) * installing *binary* package ‘bit’ ... * package ‘bit’ successfully unpacked and SHA256 sums checked * DONE (bit) * installing *binary* package ‘blob’ ... * package ‘blob’ successfully unpacked and SHA256 sums checked * DONE (blob) * installing *binary* package ‘tidyselect’ ... * package ‘tidyselect’ successfully unpacked and SHA256 sums checked * DONE (tidyselect) * installing *binary* package ‘generics’ ... * package ‘generics’ successfully unpacked and SHA256 sums checked * DONE (generics) * installing *binary* package ‘BH’ ... * package ‘BH’ successfully unpacked and SHA256 sums checked * DONE (BH) * installing *binary* package ‘bitops’ ... * package ‘bitops’ successfully unpacked and SHA256 sums checked * DONE (bitops) * installing *binary* package ‘DBI’ ... * package ‘DBI’ successfully unpacked and SHA256 sums checked * DONE (DBI) * installing *binary* package ‘filelock’ ... * package ‘filelock’ successfully unpacked and SHA256 sums checked * DONE (filelock) * installing *binary* package ‘XML’ ... * package ‘XML’ successfully unpacked and SHA256 sums checked * DONE (XML) * installing *binary* package ‘RUnit’ ... * package ‘RUnit’ successfully unpacked and SHA256 sums checked * DONE (RUnit) * installing *binary* package ‘httr’ ... * package ‘httr’ successfully unpacked and SHA256 sums checked * DONE (httr) * installing *binary* package ‘selectr’ ... * package ‘selectr’ successfully unpacked and SHA256 sums checked * DONE (selectr) * installing *binary* package ‘BiocBaseUtils’ ... * package ‘BiocBaseUtils’ successfully unpacked and SHA256 sums checked * DONE (BiocBaseUtils) * installing *binary* package ‘stringdist’ ... * package ‘stringdist’ successfully unpacked and SHA256 sums checked * DONE (stringdist) * installing *binary* package ‘bit64’ ... * package ‘bit64’ successfully unpacked and SHA256 sums checked * DONE (bit64) * installing *binary* package ‘dplyr’ ... * package ‘dplyr’ successfully unpacked and SHA256 sums checked * DONE (dplyr) * installing *binary* package ‘RCurl’ ... * package ‘RCurl’ successfully unpacked and SHA256 sums checked * DONE (RCurl) * installing *source* package ‘BiocGenerics’ ... ** this is package ‘BiocGenerics’ version ‘0.59.12’ ** package ‘BiocGenerics’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading Creating a new generic function for ‘aperm’ in package ‘BiocGenerics’ Creating a new generic function for ‘append’ in package ‘BiocGenerics’ Creating a new generic function for ‘as.data.frame’ in package ‘BiocGenerics’ Creating a new generic function for ‘cbind’ in package ‘BiocGenerics’ Creating a new generic function for ‘rbind’ in package ‘BiocGenerics’ Creating a new generic function for ‘do.call’ in package ‘BiocGenerics’ Creating a new generic function for ‘duplicated’ in package ‘BiocGenerics’ Creating a new generic function for ‘anyDuplicated’ in package ‘BiocGenerics’ Creating a new generic function for ‘eval’ in package ‘BiocGenerics’ Creating a new generic function for ‘pmax’ in package ‘BiocGenerics’ Creating a new generic function for ‘pmin’ in package ‘BiocGenerics’ Creating a new generic function for ‘pmax.int’ in package ‘BiocGenerics’ Creating a new generic function for ‘pmin.int’ in package ‘BiocGenerics’ Creating a new generic function for ‘Reduce’ in package ‘BiocGenerics’ Creating a new generic function for ‘Filter’ in package ‘BiocGenerics’ Creating a new generic function for ‘Find’ in package ‘BiocGenerics’ Creating a new generic function for ‘Map’ in package ‘BiocGenerics’ Creating a new generic function for ‘Position’ in package ‘BiocGenerics’ Creating a new generic function for ‘get’ in package ‘BiocGenerics’ Creating a new generic function for ‘mget’ in package ‘BiocGenerics’ Creating a new generic function for ‘grep’ in package ‘BiocGenerics’ Creating a new generic function for ‘grepl’ in package ‘BiocGenerics’ Creating a new generic function for ‘is.unsorted’ in package ‘BiocGenerics’ Creating a new generic function for ‘lapply’ in package ‘BiocGenerics’ Creating a new generic function for ‘sapply’ in package ‘BiocGenerics’ Creating a new generic function for ‘mapply’ in package ‘BiocGenerics’ Creating a new generic function for ‘match’ in package ‘BiocGenerics’ Creating a new generic function for ‘order’ in package ‘BiocGenerics’ Creating a new generic function for ‘paste’ in package ‘BiocGenerics’ Creating a new generic function for ‘rank’ in package ‘BiocGenerics’ Creating a new generic function for ‘rownames’ in package ‘BiocGenerics’ Creating a new generic function for ‘colnames’ in package ‘BiocGenerics’ Creating a new generic function for ‘saveRDS’ in package ‘BiocGenerics’ Creating a new generic function for ‘scale’ in package ‘BiocGenerics’ Creating a new generic function for ‘sequence’ in package ‘BiocGenerics’ Creating a new generic function for ‘table’ in package ‘BiocGenerics’ Creating a new generic function for ‘tapply’ in package ‘BiocGenerics’ Creating a new generic function for ‘transform’ in package ‘BiocGenerics’ Creating a new generic function for ‘unique’ in package ‘BiocGenerics’ Creating a new generic function for ‘unsplit’ in package ‘BiocGenerics’ Creating a new generic function for ‘which.min’ in package ‘BiocGenerics’ Creating a new generic function for ‘which.max’ in package ‘BiocGenerics’ Creating a new generic function for ‘data’ in package ‘BiocGenerics’ Creating a new generic function for ‘IQR’ in package ‘BiocGenerics’ Creating a new generic function for ‘mad’ in package ‘BiocGenerics’ Creating a new generic function for ‘var’ in package ‘BiocGenerics’ Creating a new generic function for ‘sd’ in package ‘BiocGenerics’ Creating a new generic function for ‘xtabs’ in package ‘BiocGenerics’ Creating a new generic function for ‘basename’ in package ‘BiocGenerics’ Creating a new generic function for ‘dirname’ in package ‘BiocGenerics’ ** 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 (BiocGenerics) * installing *binary* package ‘rvest’ ... * package ‘rvest’ successfully unpacked and SHA256 sums checked * DONE (rvest) * installing *binary* package ‘tidyr’ ... * package ‘tidyr’ successfully unpacked and SHA256 sums checked * DONE (tidyr) * installing *binary* package ‘RSQLite’ ... * package ‘RSQLite’ successfully unpacked and SHA256 sums checked * DONE (RSQLite) * installing *source* package ‘Biobase’ ... ** this is package ‘Biobase’ version ‘2.73.2’ ** package ‘Biobase’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0’ gcc -std=gnu2x -I"/usr/local/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c Rinit.c -o Rinit.o gcc -std=gnu2x -I"/usr/local/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c envir.c -o envir.o gcc -std=gnu2x -I"/usr/local/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c matchpt.c -o matchpt.o gcc -std=gnu2x -I"/usr/local/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c rowMedians.c -o rowMedians.o gcc -std=gnu2x -I"/usr/local/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c sublist_extract.c -o sublist_extract.o gcc -std=gnu2x -shared -L/usr/local/lib/R/lib -L/usr/local/lib -o Biobase.so Rinit.o envir.o matchpt.o rowMedians.o sublist_extract.o -L/usr/local/lib/R/lib -lR installing to /usr/local/lib/R/site-library/00LOCK-Biobase/00new/Biobase/libs ** R ** data ** 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 (Biobase) * installing *binary* package ‘graph’ ... * package ‘graph’ successfully unpacked and SHA256 sums checked * DONE (graph) * installing *binary* package ‘dbplyr’ ... * package ‘dbplyr’ successfully unpacked and SHA256 sums checked * DONE (dbplyr) * installing *binary* package ‘RBGL’ ... * package ‘RBGL’ successfully unpacked and SHA256 sums checked * DONE (RBGL) * installing *binary* package ‘BiocFileCache’ ... * package ‘BiocFileCache’ successfully unpacked and SHA256 sums checked * DONE (BiocFileCache) * installing *binary* package ‘biocViews’ ... * package ‘biocViews’ successfully unpacked and SHA256 sums checked * DONE (biocViews) * installing *source* package ‘BiocCheck’ ... ** this is package ‘BiocCheck’ version ‘1.49.31’ ** package ‘BiocCheck’ successfully unpacked and MD5 sums checked ** using staged installation ** 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 ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (BiocCheck) The downloaded source packages are in ‘/tmp/RtmptTQfk1/downloaded_packages’ 'getOption("repos")' replaces Bioconductor standard repositories, see 'help("repositories", package = "BiocManager")' for details. Replacement repositories: CRAN: https://p3m.dev/cran/__linux__/noble/latest Bioconductor version 3.24 (BiocManager 1.30.27), R 4.6.1 (2026-06-24) Installing package(s) 'broom', 'ComplexUpset', 'cosmosR', 'EnhancedVolcano', 'factoextra', 'ggbeeswarm', 'ggfortify', 'ggplot2', 'ggpubr', 'ggrepel', 'gridExtra', 'gtools', 'hash', 'igraph', 'ggraph', 'inflection', 'limma', 'logger', 'OmnipathR', 'patchwork', 'pheatmap', 'Polychrome', 'qvalue', 'readr', 'rstatix', 'S4Vectors', 'SummarizedExperiment', 'writexl', 'BiocStyle', 'ggupset', 'ggVennDiagram', 'kableExtra', 'magick', 'svglite', 'ggbreak' also installing the dependencies ‘fracdiff’, ‘lmtest’, ‘timeDate’, ‘urca’, ‘zoo’, ‘lazyeval’, ‘Deriv’, ‘forecast’, ‘modelr’, ‘rbibutils’, ‘crosstalk’, ‘estimability’, ‘mvtnorm’, ‘numDeriv’, ‘showtextdb’, ‘rematch’, ‘doBy’, ‘SparseM’, ‘MatrixModels’, ‘Rdpack’, ‘minqa’, ‘nloptr’, ‘reformulas’, ‘RcppEigen’, ‘XVector’, ‘labeling’, ‘DT’, ‘ellipse’, ‘emmeans’, ‘flashClust’, ‘irlba’, ‘leaps’, ‘multcompView’, ‘showtext’, ‘sysfonts’, ‘tweenr’, ‘polyclip’, ‘RcppArmadillo’, ‘timechange’, ‘cellranger’, ‘R.oo’, ‘R.methodsS3’, ‘plyr’, ‘carData’, ‘abind’, ‘Formula’, ‘pbkrtest’, ‘quantreg’, ‘lme4’, ‘matrixStats’, ‘SparseArray’, ‘admisc’, ‘gridGraphics’, ‘backports’, ‘scales’, ‘colorspace’, ‘dendextend’, ‘FactoMineR’, ‘beeswarm’, ‘vipor’, ‘gtable’, ‘isoband’, ‘S7’, ‘ggsci’, ‘cowplot’, ‘ggsignif’, ‘polynom’, ‘ggforce’, ‘viridis’, ‘tidygraph’, ‘graphlayouts’, ‘statmod’, ‘checkmate’, ‘lubridate’, ‘progress’, ‘readxl’, ‘R.utils’, ‘farver’, ‘RColorBrewer’, ‘scatterplot3d’, ‘reshape2’, ‘hms’, ‘vroom’, ‘tzdb’, ‘corrplot’, ‘car’, ‘MatrixGenerics’, ‘GenomicRanges’, ‘IRanges’, ‘Seqinfo’, ‘S4Arrays’, ‘DelayedArray’, ‘bookdown’, ‘aplot’, ‘venn’, ‘yulab.utils’, ‘forcats’, ‘viridisLite’, ‘ggfun’, ‘ggplotify’ trying URL 'https://bioconductor.org/packages/3.24/container-binaries/bioconductor_docker_devel-amd64/src/contrib/fracdiff_1.5-4_R_x86_64-pc-linux-gnu.tar.gz' trying URL 'https://bioconductor.org/packages/3.24/container-binaries/bioconductor_docker_devel-amd64/src/contrib/lmtest_0.9-40_R_x86_64-pc-linux-gnu.tar.gz' trying URL 'https://bioconductor.org/packages/3.24/container-binaries/bioconductor_docker_devel-amd64/src/contrib/timeDate_4052.112_R_x86_64-pc-linux-gnu.tar.gz' trying URL 'https://bioconductor.org/packages/3.24/container-binaries/bioconductor_docker_devel-amd64/src/contrib/urca_1.3-4_R_x86_64-pc-linux-gnu.tar.gz' trying URL 'https://p3m.dev/cran/__linux__/noble/latest/src/contrib/zoo_1.9-1.tar.gz' trying URL 'https://bioconductor.org/packages/3.24/container-binaries/bioconductor_docker_devel-amd64/src/contrib/lazyeval_0.2.3_R_x86_64-pc-linux-gnu.tar.gz' trying URL 'https://p3m.dev/cran/__linux__/noble/latest/src/contrib/Deriv_4.3.5.tar.gz' trying URL 'https://bioconductor.org/packages/3.24/container-binaries/bioconductor_docker_devel-amd64/src/contrib/forecast_9.0.2_R_x86_64-pc-linux-gnu.tar.gz' trying URL 'https://bioconductor.org/packages/3.24/container-binaries/bioconductor_docker_devel-amd64/src/contrib/modelr_0.1.11_R_x86_64-pc-linux-gnu.tar.gz' trying URL 'https://bioconductor.org/packages/3.24/container-binaries/bioconductor_docker_devel-amd64/src/contrib/rbibutils_2.4.1_R_x86_64-pc-linux-gnu.tar.gz' trying URL 'https://bioconductor.org/packages/3.24/container-binaries/bioconductor_docker_devel-amd64/src/contrib/crosstalk_1.2.2_R_x86_64-pc-linux-gnu.tar.gz' trying URL 'https://bioconductor.org/packages/3.24/container-binaries/bioconductor_docker_devel-amd64/src/contrib/estimability_2.0.0_R_x86_64-pc-linux-gnu.tar.gz' trying URL 'https://bioconductor.org/packages/3.24/container-binaries/bioconductor_docker_devel-amd64/src/contrib/mvtnorm_1.4-2_R_x86_64-pc-linux-gnu.tar.gz' trying URL 'https://bioconductor.org/packages/3.24/container-binaries/bioconductor_docker_devel-amd64/src/contrib/numDeriv_2016.8-1.1_R_x86_64-pc-linux-gnu.tar.gz' trying URL 'https://bioconductor.org/packages/3.24/container-binaries/bioconductor_docker_devel-amd64/src/contrib/showtextdb_3.0_R_x86_64-pc-linux-gnu.tar.gz' trying URL 'https://bioconductor.org/packages/3.24/container-binaries/bioconductor_docker_devel-amd64/src/contrib/rematch_2.0.0_R_x86_64-pc-linux-gnu.tar.gz' trying URL 'https://bioconductor.org/packages/3.24/container-binaries/bioconductor_docker_devel-amd64/src/contrib/doBy_4.7.2_R_x86_64-pc-linux-gnu.tar.gz' trying URL 'https://bioconductor.org/packages/3.24/container-binaries/bioconductor_docker_devel-amd64/src/contrib/SparseM_1.84-2_R_x86_64-pc-linux-gnu.tar.gz' trying URL 'https://bioconductor.org/packages/3.24/container-binaries/bioconductor_docker_devel-amd64/src/contrib/MatrixModels_0.5-4_R_x86_64-pc-linux-gnu.tar.gz' trying URL 'https://bioconductor.org/packages/3.24/container-binaries/bioconductor_docker_devel-amd64/src/contrib/Rdpack_2.6.6_R_x86_64-pc-linux-gnu.tar.gz' trying URL 'https://bioconductor.org/packages/3.24/container-binaries/bioconductor_docker_devel-amd64/src/contrib/minqa_1.2.8_R_x86_64-pc-linux-gnu.tar.gz' trying URL 'https://bioconductor.org/packages/3.24/container-binaries/bioconductor_docker_devel-amd64/src/contrib/nloptr_2.2.1_R_x86_64-pc-linux-gnu.tar.gz' trying URL 'https://bioconductor.org/packages/3.24/container-binaries/bioconductor_docker_devel-amd64/src/contrib/reformulas_0.4.4_R_x86_64-pc-linux-gnu.tar.gz' trying URL 'https://bioconductor.org/packages/3.24/container-binaries/bioconductor_docker_devel-amd64/src/contrib/RcppEigen_0.3.4.0.2_R_x86_64-pc-linux-gnu.tar.gz' trying URL 'https://bioconductor.org/packages/3.24/container-binaries/bioconductor_docker_devel-amd64/src/contrib/XVector_0.53.0_R_x86_64-pc-linux-gnu.tar.gz' trying URL 'https://bioconductor.org/packages/3.24/container-binaries/bioconductor_docker_devel-amd64/src/contrib/labeling_0.4.3_R_x86_64-pc-linux-gnu.tar.gz' trying URL 'https://bioconductor.org/packages/3.24/container-binaries/bioconductor_docker_devel-amd64/src/contrib/DT_0.34.0_R_x86_64-pc-linux-gnu.tar.gz' trying URL 'https://bioconductor.org/packages/3.24/container-binaries/bioconductor_docker_devel-amd64/src/contrib/ellipse_0.5.0_R_x86_64-pc-linux-gnu.tar.gz' trying URL 'https://bioconductor.org/packages/3.24/container-binaries/bioconductor_docker_devel-amd64/src/contrib/emmeans_2.0.4_R_x86_64-pc-linux-gnu.tar.gz' trying URL 'https://bioconductor.org/packages/3.24/container-binaries/bioconductor_docker_devel-amd64/src/contrib/flashClust_1.1-4_R_x86_64-pc-linux-gnu.tar.gz' trying URL 'https://bioconductor.org/packages/3.24/container-binaries/bioconductor_docker_devel-amd64/src/contrib/irlba_2.3.7_R_x86_64-pc-linux-gnu.tar.gz' trying URL 'https://bioconductor.org/packages/3.24/container-binaries/bioconductor_docker_devel-amd64/src/contrib/leaps_3.2_R_x86_64-pc-linux-gnu.tar.gz' trying URL 'https://p3m.dev/cran/__linux__/noble/latest/src/contrib/multcompView_0.1-12.tar.gz' trying URL 'https://bioconductor.org/packages/3.24/container-binaries/bioconductor_docker_devel-amd64/src/contrib/showtext_0.9-8_R_x86_64-pc-linux-gnu.tar.gz' trying URL 'https://bioconductor.org/packages/3.24/container-binaries/bioconductor_docker_devel-amd64/src/contrib/sysfonts_0.8.9_R_x86_64-pc-linux-gnu.tar.gz' trying URL 'https://bioconductor.org/packages/3.24/container-binaries/bioconductor_docker_devel-amd64/src/contrib/tweenr_2.0.3_R_x86_64-pc-linux-gnu.tar.gz' trying URL 'https://bioconductor.org/packages/3.24/container-binaries/bioconductor_docker_devel-amd64/src/contrib/polyclip_1.10-7_R_x86_64-pc-linux-gnu.tar.gz' trying URL 'https://p3m.dev/cran/__linux__/noble/latest/src/contrib/RcppArmadillo_15.6.0-1.tar.gz' trying URL 'https://bioconductor.org/packages/3.24/container-binaries/bioconductor_docker_devel-amd64/src/contrib/timechange_0.4.0_R_x86_64-pc-linux-gnu.tar.gz' trying URL 'https://bioconductor.org/packages/3.24/container-binaries/bioconductor_docker_devel-amd64/src/contrib/cellranger_1.1.0_R_x86_64-pc-linux-gnu.tar.gz' trying URL 'https://bioconductor.org/packages/3.24/container-binaries/bioconductor_docker_devel-amd64/src/contrib/R.oo_1.27.1_R_x86_64-pc-linux-gnu.tar.gz' trying URL 'https://bioconductor.org/packages/3.24/container-binaries/bioconductor_docker_devel-amd64/src/contrib/R.methodsS3_1.8.2_R_x86_64-pc-linux-gnu.tar.gz' trying URL 'https://bioconductor.org/packages/3.24/container-binaries/bioconductor_docker_devel-amd64/src/contrib/plyr_1.8.9_R_x86_64-pc-linux-gnu.tar.gz' trying URL 'https://bioconductor.org/packages/3.24/container-binaries/bioconductor_docker_devel-amd64/src/contrib/carData_3.0-6_R_x86_64-pc-linux-gnu.tar.gz' trying URL 'https://bioconductor.org/packages/3.24/container-binaries/bioconductor_docker_devel-amd64/src/contrib/abind_1.4-8_R_x86_64-pc-linux-gnu.tar.gz' trying URL 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'https://p3m.dev/cran/__linux__/noble/latest/src/contrib/writexl_2.0.1.tar.gz' trying URL 'https://bioconductor.org/packages/3.24/container-binaries/bioconductor_docker_devel-amd64/src/contrib/BiocStyle_2.41.0_R_x86_64-pc-linux-gnu.tar.gz' trying URL 'https://bioconductor.org/packages/3.24/container-binaries/bioconductor_docker_devel-amd64/src/contrib/ggupset_0.4.1_R_x86_64-pc-linux-gnu.tar.gz' trying URL 'https://bioconductor.org/packages/3.24/container-binaries/bioconductor_docker_devel-amd64/src/contrib/ggVennDiagram_1.5.7_R_x86_64-pc-linux-gnu.tar.gz' trying URL 'https://bioconductor.org/packages/3.24/container-binaries/bioconductor_docker_devel-amd64/src/contrib/kableExtra_1.4.1_R_x86_64-pc-linux-gnu.tar.gz' trying URL 'https://bioconductor.org/packages/3.24/container-binaries/bioconductor_docker_devel-amd64/src/contrib/magick_2.9.1_R_x86_64-pc-linux-gnu.tar.gz' trying URL 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unpacked and SHA256 sums checked * DONE (RColorBrewer) * installing *binary* package ‘scatterplot3d’ ... * package ‘scatterplot3d’ successfully unpacked and SHA256 sums checked * DONE (scatterplot3d) * installing *binary* package ‘hms’ ... * package ‘hms’ successfully unpacked and SHA256 sums checked * DONE (hms) * installing *binary* package ‘tzdb’ ... * package ‘tzdb’ successfully unpacked and SHA256 sums checked * DONE (tzdb) * installing *binary* package ‘corrplot’ ... * package ‘corrplot’ successfully unpacked and SHA256 sums checked * DONE (corrplot) * installing *binary* package ‘bookdown’ ... * package ‘bookdown’ successfully unpacked and SHA256 sums checked * DONE (bookdown) * installing *binary* package ‘yulab.utils’ ... * package ‘yulab.utils’ successfully unpacked and SHA256 sums checked * DONE (yulab.utils) * installing *binary* package ‘forcats’ ... * package ‘forcats’ successfully unpacked and SHA256 sums checked * DONE (forcats) * installing *binary* package ‘viridisLite’ ... * package ‘viridisLite’ successfully unpacked and SHA256 sums checked * DONE (viridisLite) * installing *binary* package ‘gtools’ ... * package ‘gtools’ successfully unpacked and SHA256 sums checked * DONE (gtools) * installing *binary* package ‘hash’ ... * package ‘hash’ successfully unpacked and SHA256 sums checked * DONE (hash) * installing *binary* package ‘igraph’ ... * package ‘igraph’ successfully unpacked and SHA256 sums checked * DONE (igraph) * installing *binary* package ‘inflection’ ... * package ‘inflection’ successfully unpacked and SHA256 sums checked * DONE (inflection) * installing *binary* package ‘logger’ ... * package ‘logger’ successfully unpacked and SHA256 sums checked * DONE (logger) * installing *source* package ‘S4Vectors’ ... ** this is package ‘S4Vectors’ version ‘0.51.10’ ** package ‘S4Vectors’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0’ gcc -std=gnu2x -I"/usr/local/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c AEbufs.c -o AEbufs.o gcc -std=gnu2x -I"/usr/local/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c DFrame_class.c -o DFrame_class.o gcc -std=gnu2x -I"/usr/local/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c Hits_class.c -o Hits_class.o In file included from /usr/include/string.h:548, from /usr/local/lib/R/include/R_ext/RS.h:34, from /usr/local/lib/R/include/Rdefines.h:38, from ../inst/include/S4Vectors_defines.h:18, from S4Vectors.h:1, from Hits_class.c:4: In function ‘memcpy’, inlined from ‘tsort_hits’ at Hits_class.c:113:3: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:29:10: warning: ‘__builtin_memcpy’ specified bound between 18446744065119617024 and 18446744073709551612 exceeds maximum object size 9223372036854775807 [-Wstringop-overflow=] 29 | return __builtin___memcpy_chk (__dest, __src, __len, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 30 | __glibc_objsize0 (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -std=gnu2x -I"/usr/local/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c LLint_class.c -o LLint_class.o gcc -std=gnu2x -I"/usr/local/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c List_class.c -o List_class.o gcc -std=gnu2x -I"/usr/local/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c R_init_S4Vectors.c -o R_init_S4Vectors.o gcc -std=gnu2x -I"/usr/local/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c Rle_class.c -o Rle_class.o gcc -std=gnu2x -I"/usr/local/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c Rle_utils.c -o Rle_utils.o gcc -std=gnu2x -I"/usr/local/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c SEXP_utils.c -o SEXP_utils.o gcc -std=gnu2x -I"/usr/local/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c SimpleList_class.c -o SimpleList_class.o gcc -std=gnu2x -I"/usr/local/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c character_utils.c -o character_utils.o gcc -std=gnu2x -I"/usr/local/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c hash_utils.c -o hash_utils.o gcc -std=gnu2x -I"/usr/local/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c integer_utils.c -o integer_utils.o gcc -std=gnu2x -I"/usr/local/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c logical_utils.c -o logical_utils.o gcc -std=gnu2x -I"/usr/local/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c map_ranges_to_runs.c -o map_ranges_to_runs.o gcc -std=gnu2x -I"/usr/local/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c raw_utils.c -o raw_utils.o gcc -std=gnu2x -I"/usr/local/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c safe_arithm.c -o safe_arithm.o gcc -std=gnu2x -I"/usr/local/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c sort_utils.c -o sort_utils.o gcc -std=gnu2x -I"/usr/local/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c subsetting_utils.c -o subsetting_utils.o gcc -std=gnu2x -I"/usr/local/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c vector_utils.c -o vector_utils.o gcc -std=gnu2x -shared -L/usr/local/lib/R/lib -L/usr/local/lib -o S4Vectors.so AEbufs.o DFrame_class.o Hits_class.o LLint_class.o List_class.o R_init_S4Vectors.o Rle_class.o Rle_utils.o SEXP_utils.o SimpleList_class.o character_utils.o hash_utils.o integer_utils.o logical_utils.o map_ranges_to_runs.o raw_utils.o safe_arithm.o sort_utils.o subsetting_utils.o vector_utils.o -L/usr/local/lib/R/lib -lR installing to /usr/local/lib/R/site-library/00LOCK-S4Vectors/00new/S4Vectors/libs ** R ** inst ** byte-compile and prepare package for lazy loading in method for ‘normalizeSingleBracketReplacementValue’ with signature ‘"List"’: no definition for class “List” Creating a new generic function for ‘unname’ in package ‘S4Vectors’ Creating a new generic function for ‘expand.grid’ in package ‘S4Vectors’ Creating a new generic function for ‘findMatches’ in package ‘S4Vectors’ in method for ‘coerce’ with signature ‘"Hits","DFrame"’: no definition for class “DFrame” Creating a generic function for ‘as.factor’ from package ‘base’ in package ‘S4Vectors’ Creating a generic function for ‘tabulate’ from package ‘base’ in package ‘S4Vectors’ Creating a generic function for ‘cov’ from package ‘stats’ in package ‘S4Vectors’ Creating a generic function for ‘cor’ from package ‘stats’ in package ‘S4Vectors’ Creating a generic function for ‘smoothEnds’ from package ‘stats’ in package ‘S4Vectors’ Creating a generic function for ‘runmed’ from package ‘stats’ in package ‘S4Vectors’ Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’ Creating a generic function for ‘substr’ from package ‘base’ in package ‘S4Vectors’ Creating a generic function for ‘substring’ from package ‘base’ in package ‘S4Vectors’ Creating a generic function for ‘chartr’ from package ‘base’ in package ‘S4Vectors’ Creating a generic function for ‘tolower’ from package ‘base’ in package ‘S4Vectors’ Creating a generic function for ‘toupper’ from package ‘base’ in package ‘S4Vectors’ Creating a generic function for ‘sub’ from package ‘base’ in package ‘S4Vectors’ Creating a generic function for ‘gsub’ from package ‘base’ in package ‘S4Vectors’ Creating a generic function for ‘nlevels’ from package ‘base’ in package ‘S4Vectors’ in method for ‘coerce’ with signature ‘"data.table","DFrame"’: no definition for class “data.table” Creating a generic function for ‘complete.cases’ from package ‘stats’ in package ‘S4Vectors’ ** 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 (S4Vectors) * installing *binary* package ‘writexl’ ... * package ‘writexl’ successfully unpacked and SHA256 sums checked * DONE (writexl) * installing *binary* package ‘magick’ ... * package ‘magick’ successfully unpacked and SHA256 sums checked * DONE (magick) * installing *binary* package ‘svglite’ ... * package ‘svglite’ successfully unpacked and SHA256 sums checked * DONE (svglite) * installing *binary* package ‘lmtest’ ... * package ‘lmtest’ successfully unpacked and SHA256 sums checked * DONE (lmtest) * installing *binary* package ‘crosstalk’ ... * package ‘crosstalk’ successfully unpacked and SHA256 sums checked * DONE (crosstalk) * installing *binary* package ‘showtextdb’ ... * package ‘showtextdb’ successfully unpacked and SHA256 sums checked * DONE (showtextdb) * installing *binary* package ‘Rdpack’ ... * package ‘Rdpack’ successfully unpacked and SHA256 sums checked * DONE (Rdpack) * installing *binary* package ‘emmeans’ ... * package ‘emmeans’ successfully unpacked and SHA256 sums checked * DONE (emmeans) * installing *binary* package ‘tweenr’ ... * package ‘tweenr’ successfully unpacked and SHA256 sums checked * DONE (tweenr) * installing *binary* package ‘cellranger’ ... * package ‘cellranger’ successfully unpacked and SHA256 sums checked * DONE (cellranger) * installing *binary* package ‘R.oo’ ... * package ‘R.oo’ successfully unpacked and SHA256 sums checked * DONE (R.oo) * installing *binary* package ‘quantreg’ ... * package ‘quantreg’ successfully unpacked and SHA256 sums checked * DONE (quantreg) * installing *binary* package ‘scales’ ... * package ‘scales’ successfully unpacked and SHA256 sums checked * DONE (scales) * installing *binary* package ‘tidygraph’ ... * package ‘tidygraph’ successfully unpacked and SHA256 sums checked * DONE (tidygraph) * installing *binary* package ‘graphlayouts’ ... * package ‘graphlayouts’ successfully unpacked and SHA256 sums checked * DONE (graphlayouts) * installing *binary* package ‘checkmate’ ... * package ‘checkmate’ successfully unpacked and SHA256 sums checked * DONE (checkmate) * installing *binary* package ‘lubridate’ ... * package ‘lubridate’ successfully unpacked and SHA256 sums checked * DONE (lubridate) * installing *binary* package ‘progress’ ... * package ‘progress’ successfully unpacked and SHA256 sums checked * DONE (progress) * installing *binary* package ‘reshape2’ ... * package ‘reshape2’ successfully unpacked and SHA256 sums checked * DONE (reshape2) * installing *binary* package ‘MatrixGenerics’ ... * package ‘MatrixGenerics’ successfully unpacked and SHA256 sums checked * DONE (MatrixGenerics) * installing *source* package ‘IRanges’ ... ** this is package ‘IRanges’ version ‘2.47.5’ ** package ‘IRanges’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0’ gcc -std=gnu2x -I"/usr/local/lib/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/S4Vectors/include' -I/usr/local/include -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c CompressedAtomicList_utils.c -o CompressedAtomicList_utils.o gcc -std=gnu2x -I"/usr/local/lib/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/S4Vectors/include' -I/usr/local/include -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c CompressedIRangesList_class.c -o CompressedIRangesList_class.o gcc -std=gnu2x -I"/usr/local/lib/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/S4Vectors/include' -I/usr/local/include -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c CompressedList_class.c -o CompressedList_class.o gcc -std=gnu2x -I"/usr/local/lib/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/S4Vectors/include' -I/usr/local/include -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c Grouping_class.c -o Grouping_class.o gcc -std=gnu2x -I"/usr/local/lib/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/S4Vectors/include' -I/usr/local/include -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c IPosRanges_comparison.c -o IPosRanges_comparison.o gcc -std=gnu2x -I"/usr/local/lib/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/S4Vectors/include' -I/usr/local/include -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c IRanges_class.c -o IRanges_class.o gcc -std=gnu2x -I"/usr/local/lib/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/S4Vectors/include' -I/usr/local/include -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c IRanges_constructor.c -o IRanges_constructor.o gcc -std=gnu2x -I"/usr/local/lib/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/S4Vectors/include' -I/usr/local/include -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c NCList.c -o NCList.o gcc -std=gnu2x -I"/usr/local/lib/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/S4Vectors/include' -I/usr/local/include -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c R_init_IRanges.c -o R_init_IRanges.o gcc -std=gnu2x -I"/usr/local/lib/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/S4Vectors/include' -I/usr/local/include -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c Ranges_class.c -o Ranges_class.o gcc -std=gnu2x -I"/usr/local/lib/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/S4Vectors/include' -I/usr/local/include -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c RleViews_summarization.c -o RleViews_summarization.o gcc -std=gnu2x -I"/usr/local/lib/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/S4Vectors/include' -I/usr/local/include -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c S4Vectors_stubs.c -o S4Vectors_stubs.o gcc -std=gnu2x -I"/usr/local/lib/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/S4Vectors/include' -I/usr/local/include -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c SimpleIRangesList_class.c -o SimpleIRangesList_class.o gcc -std=gnu2x -I"/usr/local/lib/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/S4Vectors/include' -I/usr/local/include -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c coverage_methods.c -o coverage_methods.o gcc -std=gnu2x -I"/usr/local/lib/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/S4Vectors/include' -I/usr/local/include -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c extractListFragments.c -o extractListFragments.o gcc -std=gnu2x -I"/usr/local/lib/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/S4Vectors/include' -I/usr/local/include -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c inter_range_methods.c -o inter_range_methods.o gcc -std=gnu2x -I"/usr/local/lib/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/S4Vectors/include' -I/usr/local/include -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c thread_control.c -o thread_control.o gcc -std=gnu2x -shared -L/usr/local/lib/R/lib -L/usr/local/lib -o IRanges.so CompressedAtomicList_utils.o CompressedIRangesList_class.o CompressedList_class.o Grouping_class.o IPosRanges_comparison.o IRanges_class.o IRanges_constructor.o NCList.o R_init_IRanges.o Ranges_class.o RleViews_summarization.o S4Vectors_stubs.o SimpleIRangesList_class.o coverage_methods.o extractListFragments.o inter_range_methods.o thread_control.o -fopenmp -L/usr/local/lib/R/lib -lR installing to /usr/local/lib/R/site-library/00LOCK-IRanges/00new/IRanges/libs ** R ** inst ** byte-compile and prepare package for lazy loading Creating a generic function for ‘drop’ from package ‘base’ in package ‘IRanges’ Creating a generic function for ‘runmed’ from package ‘stats’ in package ‘IRanges’ Creating a generic function for ‘chartr’ from package ‘base’ in package ‘IRanges’ Creating a generic function for ‘toupper’ from package ‘base’ in package ‘IRanges’ Creating a generic function for ‘tolower’ from package ‘base’ in package ‘IRanges’ Creating a generic function for ‘sub’ from package ‘base’ in package ‘IRanges’ Creating a generic function for ‘gsub’ from package ‘base’ in package ‘IRanges’ Creating a generic function for ‘startsWith’ from package ‘base’ in package ‘IRanges’ Creating a generic function for ‘endsWith’ from package ‘base’ in package ‘IRanges’ Creating a generic function for ‘smoothEnds’ from package ‘stats’ in package ‘IRanges’ ** 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 (IRanges) * installing *binary* package ‘venn’ ... * package ‘venn’ successfully unpacked and SHA256 sums checked * DONE (venn) * installing *binary* package ‘broom’ ... * package ‘broom’ successfully unpacked and SHA256 sums checked * DONE (broom) * installing *binary* package ‘gridExtra’ ... * package ‘gridExtra’ successfully unpacked and SHA256 sums checked * DONE (gridExtra) * installing *source* package ‘limma’ ... ** this is package ‘limma’ version ‘3.99.0’ ** package ‘limma’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0’ gcc -std=gnu2x -I"/usr/local/lib/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c R_exports.c -o R_exports.o gcc -std=gnu2x -I"/usr/local/lib/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c awreml.c -o awreml.o gcc -std=gnu2x -I"/usr/local/lib/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c dupcor.c -o dupcor.o gcc -std=gnu2x -I"/usr/local/lib/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c gls.c -o gls.o gcc -std=gnu2x -I"/usr/local/lib/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c init.c -o init.o gcc -std=gnu2x -I"/usr/local/lib/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c lm.c -o lm.o gcc -std=gnu2x -I"/usr/local/lib/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c normexp.c -o normexp.o gcc -std=gnu2x -I"/usr/local/lib/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c poisson.c -o poisson.o gcc -std=gnu2x -I"/usr/local/lib/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c qr.c -o qr.o gcc -std=gnu2x -I"/usr/local/lib/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c threads.c -o threads.o gcc -std=gnu2x -I"/usr/local/lib/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c weighted_lowess.c -o weighted_lowess.o gcc -std=gnu2x -shared -L/usr/local/lib/R/lib -L/usr/local/lib -o limma.so R_exports.o awreml.o dupcor.o gls.o init.o lm.o normexp.o poisson.o qr.o threads.o weighted_lowess.o -fopenmp -llapack -lblas -lgfortran -lm -lquadmath -L/usr/local/lib/R/lib -lR installing to /usr/local/lib/R/site-library/00LOCK-limma/00new/limma/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 (limma) * installing *binary* package ‘Polychrome’ ... * package ‘Polychrome’ successfully unpacked and SHA256 sums checked * DONE (Polychrome) * installing *binary* package ‘BiocStyle’ ... * package ‘BiocStyle’ successfully unpacked and SHA256 sums checked * DONE (BiocStyle) * installing *binary* package ‘modelr’ ... * package ‘modelr’ successfully unpacked and SHA256 sums checked * DONE (modelr) * installing *binary* package ‘reformulas’ ... * package ‘reformulas’ successfully unpacked and SHA256 sums checked * DONE (reformulas) * installing *binary* package ‘XVector’ ... * package ‘XVector’ successfully unpacked and SHA256 sums checked * DONE (XVector) * installing *binary* package ‘DT’ ... * package ‘DT’ successfully unpacked and SHA256 sums checked * DONE (DT) * installing *binary* package ‘showtext’ ... * package ‘showtext’ successfully unpacked and SHA256 sums checked * DONE (showtext) * installing *binary* package ‘readxl’ ... * package ‘readxl’ successfully unpacked and SHA256 sums checked * DONE (readxl) * installing *binary* package ‘R.utils’ ... * package ‘R.utils’ successfully unpacked and SHA256 sums checked * DONE (R.utils) * installing *binary* package ‘vroom’ ... * package ‘vroom’ successfully unpacked and SHA256 sums checked * DONE (vroom) * installing *source* package ‘Seqinfo’ ... ** this is package ‘Seqinfo’ version ‘1.3.2’ ** package ‘Seqinfo’ successfully unpacked and MD5 sums checked ** using staged installation ** 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 ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (Seqinfo) * installing *source* package ‘S4Arrays’ ... ** this is package ‘S4Arrays’ version ‘1.13.2’ ** package ‘S4Arrays’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0’ gcc -std=gnu2x -I"/usr/local/lib/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/S4Vectors/include' -I/usr/local/include -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c R_init_S4Arrays.c -o R_init_S4Arrays.o gcc -std=gnu2x -I"/usr/local/lib/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/S4Vectors/include' -I/usr/local/include -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c S4Vectors_stubs.c -o S4Vectors_stubs.o gcc -std=gnu2x -I"/usr/local/lib/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/S4Vectors/include' -I/usr/local/include -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c abind.c -o abind.o gcc -std=gnu2x -I"/usr/local/lib/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/S4Vectors/include' -I/usr/local/include -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c array_selection.c -o array_selection.o gcc -std=gnu2x -I"/usr/local/lib/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/S4Vectors/include' -I/usr/local/include -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c dim_tuning_utils.c -o dim_tuning_utils.o gcc -std=gnu2x -I"/usr/local/lib/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/S4Vectors/include' -I/usr/local/include -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c rowsum.c -o rowsum.o gcc -std=gnu2x -shared -L/usr/local/lib/R/lib -L/usr/local/lib -o S4Arrays.so R_init_S4Arrays.o S4Vectors_stubs.o abind.o array_selection.o dim_tuning_utils.o rowsum.o -L/usr/local/lib/R/lib -lR installing to /usr/local/lib/R/site-library/00LOCK-S4Arrays/00new/S4Arrays/libs ** R ** inst ** byte-compile and prepare package for lazy loading Creating a new generic function for ‘rowsum’ in package ‘S4Arrays’ Creating a new generic function for ‘abind’ in package ‘S4Arrays’ ** 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 (S4Arrays) * installing *binary* package ‘ggplot2’ ... * package ‘ggplot2’ successfully unpacked and SHA256 sums checked * DONE (ggplot2) * installing *binary* package ‘pheatmap’ ... * package ‘pheatmap’ successfully unpacked and SHA256 sums checked * DONE (pheatmap) * installing *binary* package ‘kableExtra’ ... * package ‘kableExtra’ successfully unpacked and SHA256 sums checked * DONE (kableExtra) * installing *binary* package ‘forecast’ ... * package ‘forecast’ successfully unpacked and SHA256 sums checked * DONE (forecast) * installing *binary* package ‘lme4’ ... * package ‘lme4’ successfully unpacked and SHA256 sums checked * DONE (lme4) * installing *source* package ‘SparseArray’ ... ** this is package ‘SparseArray’ version ‘1.13.4’ ** package ‘SparseArray’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0’ gcc -std=gnu2x -I"/usr/local/lib/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/S4Vectors/include' -I'/usr/local/lib/R/site-library/IRanges/include' -I'/usr/local/lib/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c ExtendableJaggedArray.c -o ExtendableJaggedArray.o gcc -std=gnu2x -I"/usr/local/lib/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/S4Vectors/include' -I'/usr/local/lib/R/site-library/IRanges/include' -I'/usr/local/lib/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c IRanges_stubs.c -o IRanges_stubs.o gcc -std=gnu2x -I"/usr/local/lib/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/S4Vectors/include' -I'/usr/local/lib/R/site-library/IRanges/include' -I'/usr/local/lib/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c OPBufTree.c -o OPBufTree.o gcc -std=gnu2x -I"/usr/local/lib/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/S4Vectors/include' -I'/usr/local/lib/R/site-library/IRanges/include' -I'/usr/local/lib/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c R_init_SparseArray.c -o R_init_SparseArray.o gcc -std=gnu2x -I"/usr/local/lib/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/S4Vectors/include' -I'/usr/local/lib/R/site-library/IRanges/include' -I'/usr/local/lib/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c Rvector_summarization.c -o Rvector_summarization.o gcc -std=gnu2x -I"/usr/local/lib/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/S4Vectors/include' -I'/usr/local/lib/R/site-library/IRanges/include' -I'/usr/local/lib/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c Rvector_utils.c -o Rvector_utils.o gcc -std=gnu2x -I"/usr/local/lib/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/S4Vectors/include' -I'/usr/local/lib/R/site-library/IRanges/include' -I'/usr/local/lib/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c S4Vectors_stubs.c -o S4Vectors_stubs.o gcc -std=gnu2x -I"/usr/local/lib/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/S4Vectors/include' -I'/usr/local/lib/R/site-library/IRanges/include' -I'/usr/local/lib/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c SBT_utils.c -o SBT_utils.o gcc -std=gnu2x -I"/usr/local/lib/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/S4Vectors/include' -I'/usr/local/lib/R/site-library/IRanges/include' -I'/usr/local/lib/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c SVT_SparseArray_class.c -o SVT_SparseArray_class.o gcc -std=gnu2x -I"/usr/local/lib/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/S4Vectors/include' -I'/usr/local/lib/R/site-library/IRanges/include' -I'/usr/local/lib/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c SparseArray_Arith_methods.c -o SparseArray_Arith_methods.o gcc -std=gnu2x -I"/usr/local/lib/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/S4Vectors/include' -I'/usr/local/lib/R/site-library/IRanges/include' -I'/usr/local/lib/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c SparseArray_Compare_methods.c -o SparseArray_Compare_methods.o gcc -std=gnu2x -I"/usr/local/lib/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/S4Vectors/include' -I'/usr/local/lib/R/site-library/IRanges/include' -I'/usr/local/lib/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c SparseArray_Complex_methods.c -o SparseArray_Complex_methods.o gcc -std=gnu2x -I"/usr/local/lib/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/S4Vectors/include' -I'/usr/local/lib/R/site-library/IRanges/include' -I'/usr/local/lib/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c SparseArray_Logic_methods.c -o SparseArray_Logic_methods.o gcc -std=gnu2x -I"/usr/local/lib/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/S4Vectors/include' -I'/usr/local/lib/R/site-library/IRanges/include' -I'/usr/local/lib/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c SparseArray_Math_methods.c -o SparseArray_Math_methods.o gcc -std=gnu2x -I"/usr/local/lib/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/S4Vectors/include' -I'/usr/local/lib/R/site-library/IRanges/include' -I'/usr/local/lib/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c SparseArray_abind.c -o SparseArray_abind.o gcc -std=gnu2x -I"/usr/local/lib/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/S4Vectors/include' -I'/usr/local/lib/R/site-library/IRanges/include' -I'/usr/local/lib/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c SparseArray_aperm.c -o SparseArray_aperm.o gcc -std=gnu2x -I"/usr/local/lib/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/S4Vectors/include' -I'/usr/local/lib/R/site-library/IRanges/include' -I'/usr/local/lib/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c SparseArray_dim_tuning.c -o SparseArray_dim_tuning.o gcc -std=gnu2x -I"/usr/local/lib/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/S4Vectors/include' -I'/usr/local/lib/R/site-library/IRanges/include' -I'/usr/local/lib/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c SparseArray_matrixStats.c -o SparseArray_matrixStats.o gcc -std=gnu2x -I"/usr/local/lib/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/S4Vectors/include' -I'/usr/local/lib/R/site-library/IRanges/include' -I'/usr/local/lib/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c SparseArray_misc_methods.c -o SparseArray_misc_methods.o gcc -std=gnu2x -I"/usr/local/lib/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/S4Vectors/include' -I'/usr/local/lib/R/site-library/IRanges/include' -I'/usr/local/lib/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c SparseArray_subassignment.c -o SparseArray_subassignment.o gcc -std=gnu2x -I"/usr/local/lib/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/S4Vectors/include' -I'/usr/local/lib/R/site-library/IRanges/include' -I'/usr/local/lib/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c SparseArray_subsetting.c -o SparseArray_subsetting.o SparseArray_subsetting.c: In function ‘REC_subset_SVT_as_SVT’: SparseArray_subsetting.c:843:26: warning: comparison between pointer and integer 843 | if (offs != i2 || ans_elt != subSVT) | ^~ gcc -std=gnu2x -I"/usr/local/lib/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/S4Vectors/include' -I'/usr/local/lib/R/site-library/IRanges/include' -I'/usr/local/lib/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c SparseArray_summarization.c -o SparseArray_summarization.o gcc -std=gnu2x -I"/usr/local/lib/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/S4Vectors/include' -I'/usr/local/lib/R/site-library/IRanges/include' -I'/usr/local/lib/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c SparseMatrix_mult.c -o SparseMatrix_mult.o gcc -std=gnu2x -I"/usr/local/lib/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/S4Vectors/include' -I'/usr/local/lib/R/site-library/IRanges/include' -I'/usr/local/lib/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c SparseVec.c -o SparseVec.o gcc -std=gnu2x -I"/usr/local/lib/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/S4Vectors/include' -I'/usr/local/lib/R/site-library/IRanges/include' -I'/usr/local/lib/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c SparseVec_Arith.c -o SparseVec_Arith.o gcc -std=gnu2x -I"/usr/local/lib/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/S4Vectors/include' -I'/usr/local/lib/R/site-library/IRanges/include' -I'/usr/local/lib/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c SparseVec_Compare.c -o SparseVec_Compare.o gcc -std=gnu2x -I"/usr/local/lib/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/S4Vectors/include' -I'/usr/local/lib/R/site-library/IRanges/include' -I'/usr/local/lib/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c SparseVec_Logic.c -o SparseVec_Logic.o gcc -std=gnu2x -I"/usr/local/lib/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/S4Vectors/include' -I'/usr/local/lib/R/site-library/IRanges/include' -I'/usr/local/lib/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c SparseVec_Math.c -o SparseVec_Math.o gcc -std=gnu2x -I"/usr/local/lib/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/S4Vectors/include' -I'/usr/local/lib/R/site-library/IRanges/include' -I'/usr/local/lib/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c SparseVec_dotprod.c -o SparseVec_dotprod.o gcc -std=gnu2x -I"/usr/local/lib/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/S4Vectors/include' -I'/usr/local/lib/R/site-library/IRanges/include' -I'/usr/local/lib/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c SparseVec_subassignment.c -o SparseVec_subassignment.o gcc -std=gnu2x -I"/usr/local/lib/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/S4Vectors/include' -I'/usr/local/lib/R/site-library/IRanges/include' -I'/usr/local/lib/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c SparseVec_subsetting.c -o SparseVec_subsetting.o gcc -std=gnu2x -I"/usr/local/lib/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/S4Vectors/include' -I'/usr/local/lib/R/site-library/IRanges/include' -I'/usr/local/lib/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c XVector_stubs.c -o XVector_stubs.o gcc -std=gnu2x -I"/usr/local/lib/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/S4Vectors/include' -I'/usr/local/lib/R/site-library/IRanges/include' -I'/usr/local/lib/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c argcheck_utils.c -o argcheck_utils.o gcc -std=gnu2x -I"/usr/local/lib/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/S4Vectors/include' -I'/usr/local/lib/R/site-library/IRanges/include' -I'/usr/local/lib/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c coerceVector2.c -o coerceVector2.o gcc -std=gnu2x -I"/usr/local/lib/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/S4Vectors/include' -I'/usr/local/lib/R/site-library/IRanges/include' -I'/usr/local/lib/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c leaf_utils.c -o leaf_utils.o gcc -std=gnu2x -I"/usr/local/lib/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/S4Vectors/include' -I'/usr/local/lib/R/site-library/IRanges/include' -I'/usr/local/lib/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c misc_utils.c -o misc_utils.o gcc -std=gnu2x -I"/usr/local/lib/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/S4Vectors/include' -I'/usr/local/lib/R/site-library/IRanges/include' -I'/usr/local/lib/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c randomSparseArray.c -o randomSparseArray.o gcc -std=gnu2x -I"/usr/local/lib/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/S4Vectors/include' -I'/usr/local/lib/R/site-library/IRanges/include' -I'/usr/local/lib/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c readSparseCSV.c -o readSparseCSV.o gcc -std=gnu2x -I"/usr/local/lib/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/S4Vectors/include' -I'/usr/local/lib/R/site-library/IRanges/include' -I'/usr/local/lib/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c rowsum_methods.c -o rowsum_methods.o gcc -std=gnu2x -I"/usr/local/lib/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/S4Vectors/include' -I'/usr/local/lib/R/site-library/IRanges/include' -I'/usr/local/lib/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c sparseMatrix_utils.c -o sparseMatrix_utils.o gcc -std=gnu2x -I"/usr/local/lib/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/S4Vectors/include' -I'/usr/local/lib/R/site-library/IRanges/include' -I'/usr/local/lib/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c test.c -o test.o gcc -std=gnu2x -I"/usr/local/lib/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/S4Vectors/include' -I'/usr/local/lib/R/site-library/IRanges/include' -I'/usr/local/lib/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c thread_control.c -o thread_control.o gcc -std=gnu2x -shared -L/usr/local/lib/R/lib -L/usr/local/lib -o SparseArray.so ExtendableJaggedArray.o IRanges_stubs.o OPBufTree.o R_init_SparseArray.o Rvector_summarization.o Rvector_utils.o S4Vectors_stubs.o SBT_utils.o SVT_SparseArray_class.o SparseArray_Arith_methods.o SparseArray_Compare_methods.o SparseArray_Complex_methods.o SparseArray_Logic_methods.o SparseArray_Math_methods.o SparseArray_abind.o SparseArray_aperm.o SparseArray_dim_tuning.o SparseArray_matrixStats.o SparseArray_misc_methods.o SparseArray_subassignment.o SparseArray_subsetting.o SparseArray_summarization.o SparseMatrix_mult.o SparseVec.o SparseVec_Arith.o SparseVec_Compare.o SparseVec_Logic.o SparseVec_Math.o SparseVec_dotprod.o SparseVec_subassignment.o SparseVec_subsetting.o XVector_stubs.o argcheck_utils.o coerceVector2.o leaf_utils.o misc_utils.o randomSparseArray.o readSparseCSV.o rowsum_methods.o sparseMatrix_utils.o test.o thread_control.o -fopenmp -L/usr/local/lib/R/lib -lR installing to /usr/local/lib/R/site-library/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 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‘DelayedArray’ Creating a new generic function for ‘sweep’ in package ‘DelayedArray’ Creating a generic function for ‘dnorm’ from package ‘stats’ in package ‘DelayedArray’ Creating a generic function for ‘pnorm’ from package ‘stats’ in package ‘DelayedArray’ Creating a generic function for ‘qnorm’ from package ‘stats’ in package ‘DelayedArray’ Creating a generic function for ‘dbinom’ from package ‘stats’ in package ‘DelayedArray’ Creating a generic function for ‘pbinom’ from package ‘stats’ in package ‘DelayedArray’ Creating a generic function for ‘qbinom’ from package ‘stats’ in package ‘DelayedArray’ Creating a generic function for ‘dpois’ from package ‘stats’ in package ‘DelayedArray’ Creating a generic function for ‘ppois’ from package ‘stats’ in package ‘DelayedArray’ Creating a generic function for ‘qpois’ from package ‘stats’ in package ‘DelayedArray’ Creating a generic function for ‘dlogis’ from package ‘stats’ in package ‘DelayedArray’ Creating a generic function for ‘plogis’ from package ‘stats’ in package ‘DelayedArray’ Creating a generic function for ‘qlogis’ from package ‘stats’ in package ‘DelayedArray’ ** help *** installing help indices ** 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 (DelayedArray) * installing *binary* package ‘aplot’ ... * package ‘aplot’ successfully unpacked and SHA256 sums checked * DONE (aplot) * installing *binary* package ‘ComplexUpset’ ... * package ‘ComplexUpset’ successfully unpacked and SHA256 sums checked * DONE (ComplexUpset) * installing *binary* package ‘EnhancedVolcano’ ... * package ‘EnhancedVolcano’ successfully unpacked and SHA256 sums checked * DONE (EnhancedVolcano) * installing *binary* package ‘ggraph’ ... * package ‘ggraph’ successfully unpacked and SHA256 sums checked * DONE (ggraph) * installing *binary* package ‘OmnipathR’ ... * package ‘OmnipathR’ successfully unpacked and SHA256 sums checked * DONE (OmnipathR) * installing *binary* package ‘pbkrtest’ ... * package ‘pbkrtest’ successfully unpacked and SHA256 sums checked * DONE (pbkrtest) * installing *binary* package ‘SummarizedExperiment’ ... * package ‘SummarizedExperiment’ successfully unpacked and SHA256 sums checked * DONE (SummarizedExperiment) * installing *binary* package ‘ggVennDiagram’ ... * package ‘ggVennDiagram’ successfully unpacked and SHA256 sums checked * DONE (ggVennDiagram) * installing *binary* package ‘ggbreak’ ... * package ‘ggbreak’ successfully unpacked and SHA256 sums checked * DONE (ggbreak) * installing *binary* package ‘car’ ... * package ‘car’ successfully unpacked and SHA256 sums checked * DONE (car) * installing *binary* package ‘FactoMineR’ ... * package ‘FactoMineR’ successfully unpacked and SHA256 sums checked * DONE (FactoMineR) * installing *binary* package ‘rstatix’ ... * package ‘rstatix’ successfully unpacked and SHA256 sums checked * DONE (rstatix) * installing *binary* package ‘ggpubr’ ... * package ‘ggpubr’ successfully unpacked and SHA256 sums checked * DONE (ggpubr) * installing *binary* package ‘factoextra’ ... * package ‘factoextra’ successfully unpacked and SHA256 sums checked * DONE (factoextra) The downloaded source packages are in ‘/tmp/RtmptTQfk1/downloaded_packages’ Warning messages: 1: package(s) not installed when version(s) same as or greater than current; use `force = TRUE` to re-install: 'DBI' 'dplyr' 'grid' 'magrittr' 'methods' 'purrr' 'rappdirs' 'rlang' 'stringr' 'tibble' 'tidyr' 'tidyselect' 'knitr' 'pkgdown' 'rmarkdown' 'testthat' 2: package ‘cosmosR’ is not available for Bioconductor version '3.24' A version of this package for your version of R might be available elsewhere, see the ideas at https://cran.r-project.org/doc/manuals/r-patched/R-admin.html#Installing-packages Not in repos, trying GitHub: saezlab/cosmosR Downloading GitHub repo saezlab/cosmosR@HEAD Installing 20 packages: formatR, futile.options, lambda.r, snow, futile.logger, Biostrings, png, KEGGREST, AnnotationDbi, litedown, parallelly, BiocParallel, annotate, rjson, lpSolve, markdown, decoupleR, visNetwork, GSEABase, CARNIVAL Installing packages into ‘/usr/local/lib/R/site-library’ (as ‘lib’ is unspecified) trying URL 'https://p3m.dev/cran/__linux__/noble/latest/src/contrib/formatR_1.14.tar.gz' trying URL 'https://p3m.dev/cran/__linux__/noble/latest/src/contrib/futile.options_1.0.1.tar.gz' trying URL 'https://p3m.dev/cran/__linux__/noble/latest/src/contrib/lambda.r_1.2.4.tar.gz' trying URL 'https://p3m.dev/cran/__linux__/noble/latest/src/contrib/snow_0.4-4.tar.gz' trying URL 'https://p3m.dev/cran/__linux__/noble/latest/src/contrib/futile.logger_1.4.9.tar.gz' trying URL 'https://bioconductor.org/packages/3.23/bioc/src/contrib/Biostrings_2.80.2.tar.gz' trying URL 'https://p3m.dev/cran/__linux__/noble/latest/src/contrib/png_0.1-9.tar.gz' trying URL 'https://bioconductor.org/packages/3.23/bioc/src/contrib/KEGGREST_1.52.2.tar.gz' trying URL 'https://bioconductor.org/packages/3.23/bioc/src/contrib/AnnotationDbi_1.74.0.tar.gz' trying URL 'https://p3m.dev/cran/__linux__/noble/latest/src/contrib/litedown_0.11.tar.gz' trying URL 'https://p3m.dev/cran/__linux__/noble/latest/src/contrib/parallelly_1.48.0.tar.gz' trying URL 'https://bioconductor.org/packages/3.23/bioc/src/contrib/BiocParallel_1.46.0.tar.gz' trying URL 'https://bioconductor.org/packages/3.23/bioc/src/contrib/annotate_1.90.0.tar.gz' trying URL 'https://p3m.dev/cran/__linux__/noble/latest/src/contrib/rjson_0.2.23.tar.gz' trying URL 'https://p3m.dev/cran/__linux__/noble/latest/src/contrib/lpSolve_5.6.23.tar.gz' trying URL 'https://p3m.dev/cran/__linux__/noble/latest/src/contrib/markdown_2.0.tar.gz' trying URL 'https://bioconductor.org/packages/3.23/bioc/src/contrib/decoupleR_2.17.0.tar.gz' trying URL 'https://p3m.dev/cran/__linux__/noble/latest/src/contrib/visNetwork_2.1.4.tar.gz' trying URL 'https://bioconductor.org/packages/3.23/bioc/src/contrib/GSEABase_1.74.0.tar.gz' trying URL 'https://bioconductor.org/packages/3.23/bioc/src/contrib/CARNIVAL_2.22.0.tar.gz' * installing *binary* package ‘formatR’ ... * package ‘formatR’ successfully unpacked and SHA256 sums checked * DONE (formatR) * installing *binary* package ‘futile.options’ ... * package ‘futile.options’ successfully unpacked and SHA256 sums checked * DONE (futile.options) * installing *binary* package ‘snow’ ... * package ‘snow’ successfully unpacked and SHA256 sums checked * DONE (snow) * installing *source* package ‘Biostrings’ ... ** this is package ‘Biostrings’ version ‘2.80.2’ ** using staged installation ** libs using C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0’ gcc -std=gnu2x -I"/usr/local/lib/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/S4Vectors/include' -I'/usr/local/lib/R/site-library/IRanges/include' -I'/usr/local/lib/R/site-library/XVector/include' -I/usr/local/include -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c BAB_class.c -o BAB_class.o gcc -std=gnu2x -I"/usr/local/lib/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/S4Vectors/include' -I'/usr/local/lib/R/site-library/IRanges/include' -I'/usr/local/lib/R/site-library/XVector/include' -I/usr/local/include -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c BitMatrix.c -o BitMatrix.o gcc -std=gnu2x -I"/usr/local/lib/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/S4Vectors/include' -I'/usr/local/lib/R/site-library/IRanges/include' -I'/usr/local/lib/R/site-library/XVector/include' -I/usr/local/include -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c IRanges_stubs.c -o IRanges_stubs.o gcc -std=gnu2x -I"/usr/local/lib/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/S4Vectors/include' -I'/usr/local/lib/R/site-library/IRanges/include' -I'/usr/local/lib/R/site-library/XVector/include' -I/usr/local/include -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c MIndex_class.c -o MIndex_class.o gcc -std=gnu2x -I"/usr/local/lib/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/S4Vectors/include' -I'/usr/local/lib/R/site-library/IRanges/include' -I'/usr/local/lib/R/site-library/XVector/include' -I/usr/local/include -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c PreprocessedTB_class.c -o PreprocessedTB_class.o gcc -std=gnu2x -I"/usr/local/lib/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/S4Vectors/include' -I'/usr/local/lib/R/site-library/IRanges/include' -I'/usr/local/lib/R/site-library/XVector/include' -I/usr/local/include -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c R_init_Biostrings.c -o R_init_Biostrings.o gcc -std=gnu2x -I"/usr/local/lib/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/S4Vectors/include' -I'/usr/local/lib/R/site-library/IRanges/include' -I'/usr/local/lib/R/site-library/XVector/include' -I/usr/local/include -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c RoSeqs_utils.c -o RoSeqs_utils.o gcc -std=gnu2x -I"/usr/local/lib/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/S4Vectors/include' -I'/usr/local/lib/R/site-library/IRanges/include' -I'/usr/local/lib/R/site-library/XVector/include' -I/usr/local/include -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c S4Vectors_stubs.c -o S4Vectors_stubs.o gcc -std=gnu2x -I"/usr/local/lib/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/S4Vectors/include' -I'/usr/local/lib/R/site-library/IRanges/include' -I'/usr/local/lib/R/site-library/XVector/include' -I/usr/local/include -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c XStringSetList_class.c -o XStringSetList_class.o gcc -std=gnu2x -I"/usr/local/lib/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/S4Vectors/include' -I'/usr/local/lib/R/site-library/IRanges/include' -I'/usr/local/lib/R/site-library/XVector/include' -I/usr/local/include -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c XStringSet_class.c -o XStringSet_class.o gcc -std=gnu2x -I"/usr/local/lib/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/S4Vectors/include' -I'/usr/local/lib/R/site-library/IRanges/include' -I'/usr/local/lib/R/site-library/XVector/include' -I/usr/local/include -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c XString_class.c -o XString_class.o gcc -std=gnu2x -I"/usr/local/lib/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/S4Vectors/include' -I'/usr/local/lib/R/site-library/IRanges/include' -I'/usr/local/lib/R/site-library/XVector/include' -I/usr/local/include -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c XVector_stubs.c -o XVector_stubs.o gcc -std=gnu2x -I"/usr/local/lib/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/S4Vectors/include' -I'/usr/local/lib/R/site-library/IRanges/include' -I'/usr/local/lib/R/site-library/XVector/include' -I/usr/local/include -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c find_palindromes.c -o find_palindromes.o gcc -std=gnu2x -I"/usr/local/lib/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/S4Vectors/include' -I'/usr/local/lib/R/site-library/IRanges/include' -I'/usr/local/lib/R/site-library/XVector/include' -I/usr/local/include -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c gtestsim.c -o gtestsim.o gcc -std=gnu2x -I"/usr/local/lib/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/S4Vectors/include' -I'/usr/local/lib/R/site-library/IRanges/include' -I'/usr/local/lib/R/site-library/XVector/include' -I/usr/local/include -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c inject_code.c -o inject_code.o gcc -std=gnu2x -I"/usr/local/lib/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/S4Vectors/include' -I'/usr/local/lib/R/site-library/IRanges/include' -I'/usr/local/lib/R/site-library/XVector/include' -I/usr/local/include -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c lcsuffix.c -o lcsuffix.o gcc -std=gnu2x -I"/usr/local/lib/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/S4Vectors/include' -I'/usr/local/lib/R/site-library/IRanges/include' -I'/usr/local/lib/R/site-library/XVector/include' -I/usr/local/include -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c letter_frequency.c -o letter_frequency.o gcc -std=gnu2x -I"/usr/local/lib/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/S4Vectors/include' -I'/usr/local/lib/R/site-library/IRanges/include' -I'/usr/local/lib/R/site-library/XVector/include' -I/usr/local/include -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c lowlevel_matching.c -o lowlevel_matching.o gcc -std=gnu2x -I"/usr/local/lib/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/S4Vectors/include' -I'/usr/local/lib/R/site-library/IRanges/include' -I'/usr/local/lib/R/site-library/XVector/include' -I/usr/local/include -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c match_PWM.c -o match_PWM.o gcc -std=gnu2x -I"/usr/local/lib/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/S4Vectors/include' -I'/usr/local/lib/R/site-library/IRanges/include' -I'/usr/local/lib/R/site-library/XVector/include' -I/usr/local/include -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c match_pattern.c -o match_pattern.o gcc -std=gnu2x -I"/usr/local/lib/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/S4Vectors/include' -I'/usr/local/lib/R/site-library/IRanges/include' -I'/usr/local/lib/R/site-library/XVector/include' -I/usr/local/include -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c match_pattern_boyermoore.c -o match_pattern_boyermoore.o gcc -std=gnu2x -I"/usr/local/lib/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/S4Vectors/include' -I'/usr/local/lib/R/site-library/IRanges/include' -I'/usr/local/lib/R/site-library/XVector/include' -I/usr/local/include -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c match_pattern_indels.c -o match_pattern_indels.o gcc -std=gnu2x -I"/usr/local/lib/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/S4Vectors/include' -I'/usr/local/lib/R/site-library/IRanges/include' -I'/usr/local/lib/R/site-library/XVector/include' -I/usr/local/include -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c match_pattern_shiftor.c -o match_pattern_shiftor.o gcc -std=gnu2x -I"/usr/local/lib/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/S4Vectors/include' -I'/usr/local/lib/R/site-library/IRanges/include' -I'/usr/local/lib/R/site-library/XVector/include' -I/usr/local/include -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c match_pdict.c -o match_pdict.o gcc -std=gnu2x -I"/usr/local/lib/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/S4Vectors/include' -I'/usr/local/lib/R/site-library/IRanges/include' -I'/usr/local/lib/R/site-library/XVector/include' -I/usr/local/include -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c match_pdict_ACtree2.c -o match_pdict_ACtree2.o gcc -std=gnu2x -I"/usr/local/lib/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/S4Vectors/include' -I'/usr/local/lib/R/site-library/IRanges/include' -I'/usr/local/lib/R/site-library/XVector/include' -I/usr/local/include -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c match_pdict_Twobit.c -o match_pdict_Twobit.o gcc -std=gnu2x -I"/usr/local/lib/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/S4Vectors/include' -I'/usr/local/lib/R/site-library/IRanges/include' -I'/usr/local/lib/R/site-library/XVector/include' -I/usr/local/include -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c match_pdict_utils.c -o match_pdict_utils.o gcc -std=gnu2x -I"/usr/local/lib/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/S4Vectors/include' -I'/usr/local/lib/R/site-library/IRanges/include' -I'/usr/local/lib/R/site-library/XVector/include' -I/usr/local/include -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c match_reporting.c -o match_reporting.o gcc -std=gnu2x -I"/usr/local/lib/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/S4Vectors/include' -I'/usr/local/lib/R/site-library/IRanges/include' -I'/usr/local/lib/R/site-library/XVector/include' -I/usr/local/include -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c read_fasta_files.c -o read_fasta_files.o gcc -std=gnu2x -I"/usr/local/lib/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/S4Vectors/include' -I'/usr/local/lib/R/site-library/IRanges/include' -I'/usr/local/lib/R/site-library/XVector/include' -I/usr/local/include -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c read_fastq_files.c -o read_fastq_files.o gcc -std=gnu2x -I"/usr/local/lib/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/S4Vectors/include' -I'/usr/local/lib/R/site-library/IRanges/include' -I'/usr/local/lib/R/site-library/XVector/include' -I/usr/local/include -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c replaceAt.c -o replaceAt.o gcc -std=gnu2x -I"/usr/local/lib/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/S4Vectors/include' -I'/usr/local/lib/R/site-library/IRanges/include' -I'/usr/local/lib/R/site-library/XVector/include' -I/usr/local/include -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c replace_letter_at.c -o replace_letter_at.o gcc -std=gnu2x -I"/usr/local/lib/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/S4Vectors/include' -I'/usr/local/lib/R/site-library/IRanges/include' -I'/usr/local/lib/R/site-library/XVector/include' -I/usr/local/include -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c strutils.c -o strutils.o gcc -std=gnu2x -I"/usr/local/lib/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/S4Vectors/include' -I'/usr/local/lib/R/site-library/IRanges/include' -I'/usr/local/lib/R/site-library/XVector/include' -I/usr/local/include -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c translate.c -o translate.o gcc -std=gnu2x -I"/usr/local/lib/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/S4Vectors/include' -I'/usr/local/lib/R/site-library/IRanges/include' -I'/usr/local/lib/R/site-library/XVector/include' -I/usr/local/include -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c unstrsplit_methods.c -o unstrsplit_methods.o gcc -std=gnu2x -I"/usr/local/lib/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/S4Vectors/include' -I'/usr/local/lib/R/site-library/IRanges/include' -I'/usr/local/lib/R/site-library/XVector/include' -I/usr/local/include -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c utils.c -o utils.o gcc -std=gnu2x -I"/usr/local/lib/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/S4Vectors/include' -I'/usr/local/lib/R/site-library/IRanges/include' -I'/usr/local/lib/R/site-library/XVector/include' -I/usr/local/include -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c xscat.c -o xscat.o gcc -std=gnu2x -shared -L/usr/local/lib/R/lib -L/usr/local/lib -o Biostrings.so BAB_class.o BitMatrix.o IRanges_stubs.o MIndex_class.o PreprocessedTB_class.o R_init_Biostrings.o RoSeqs_utils.o S4Vectors_stubs.o XStringSetList_class.o XStringSet_class.o XString_class.o XVector_stubs.o find_palindromes.o gtestsim.o inject_code.o lcsuffix.o letter_frequency.o lowlevel_matching.o match_PWM.o match_pattern.o match_pattern_boyermoore.o match_pattern_indels.o match_pattern_shiftor.o match_pdict.o match_pdict_ACtree2.o match_pdict_Twobit.o match_pdict_utils.o match_reporting.o read_fasta_files.o read_fastq_files.o replaceAt.o replace_letter_at.o strutils.o translate.o unstrsplit_methods.o utils.o xscat.o -L/usr/local/lib/R/lib -lR installing to /usr/local/lib/R/site-library/00LOCK-Biostrings/00new/Biostrings/libs ** R ** data ** inst ** byte-compile and prepare package for lazy loading in method for ‘twoWayAlphabetFrequencyByQuality’ with signature ‘"QualityScaledXStringSet"’: no definition for class “QualityScaledXStringSet” Creating a new generic function for ‘strsplit’ in package ‘Biostrings’ Creating a new generic function for ‘offset’ in package ‘Biostrings’ ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location Warning: multiple methods tables found for ‘detail’ ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location Warning: multiple methods tables found for ‘detail’ ** testing if installed package keeps a record of temporary installation path * DONE (Biostrings) * installing *binary* package ‘png’ ... * package ‘png’ successfully unpacked and SHA256 sums checked * DONE (png) * installing *binary* package ‘litedown’ ... * package ‘litedown’ successfully unpacked and SHA256 sums checked * DONE (litedown) * installing *binary* package ‘parallelly’ ... * package ‘parallelly’ successfully unpacked and SHA256 sums checked * DONE (parallelly) * installing *binary* package ‘rjson’ ... * package ‘rjson’ successfully unpacked and SHA256 sums checked * DONE (rjson) * installing *binary* package ‘lpSolve’ ... * package ‘lpSolve’ successfully unpacked and SHA256 sums checked * DONE (lpSolve) * installing *binary* package ‘visNetwork’ ... * package ‘visNetwork’ successfully unpacked and SHA256 sums checked * DONE (visNetwork) * installing *binary* package ‘lambda.r’ ... * package ‘lambda.r’ successfully unpacked and SHA256 sums checked * DONE (lambda.r) * installing *source* package ‘KEGGREST’ ... ** this is package ‘KEGGREST’ version ‘1.52.2’ ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading Warning: multiple methods tables found for ‘detail’ ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location Warning: multiple methods tables found for ‘detail’ ** testing if installed package can be loaded from final location Warning: multiple methods tables found for ‘detail’ ** testing if installed package keeps a record of temporary installation path * DONE (KEGGREST) * installing *binary* package ‘markdown’ ... * package ‘markdown’ successfully unpacked and SHA256 sums checked * DONE (markdown) * installing *source* package ‘CARNIVAL’ ... ** this is package ‘CARNIVAL’ version ‘2.22.0’ ** 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 (CARNIVAL) * installing *binary* package ‘futile.logger’ ... * package ‘futile.logger’ successfully unpacked and SHA256 sums checked * DONE (futile.logger) * installing *source* package ‘AnnotationDbi’ ... ** this is package ‘AnnotationDbi’ version ‘1.74.0’ ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading Warning: multiple methods tables found for ‘detail’ Creating a new generic function for ‘packageName’ in package ‘AnnotationDbi’ Creating a generic function for ‘ls’ from package ‘base’ in package ‘AnnotationDbi’ Creating a generic function for ‘eapply’ from package ‘base’ in package ‘AnnotationDbi’ Creating a generic function for ‘exists’ from package ‘base’ in package ‘AnnotationDbi’ Creating a generic function for ‘sample’ from package ‘base’ in package ‘AnnotationDbi’ ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location Warning: multiple methods tables found for ‘detail’ ** testing if installed package can be loaded from final location Warning: multiple methods tables found for ‘detail’ ** testing if installed package keeps a record of temporary installation path * DONE (AnnotationDbi) Warning: SystemRequirements specified C++11: support has been removed * installing *source* package ‘BiocParallel’ ... ** this is package ‘BiocParallel’ version ‘1.46.0’ ** using staged installation checking whether the C++ compiler works... yes checking for C++ compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether the compiler supports GNU C++... yes checking whether g++ -std=gnu++20 accepts -g... yes checking for g++ -std=gnu++20 option to enable C++11 features... none needed checking for library containing shm_open... none required checking for stdio.h... yes checking for stdlib.h... yes checking for string.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for strings.h... yes checking for sys/stat.h... yes checking for sys/types.h... yes checking for unistd.h... yes checking for sys/mman.h... yes configure: creating ./config.status config.status: creating src/Makevars ** libs specified C++11 using C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0’ g++ -std=gnu++20 -I"/usr/local/lib/R/include" -DNDEBUG -I"./" -I'/usr/local/lib/R/site-library/BH/include' -I'/usr/local/lib/R/site-library/cpp11/include' -I/usr/local/include -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c cpp11.cpp -o cpp11.o g++ -std=gnu++20 -I"/usr/local/lib/R/include" -DNDEBUG -I"./" -I'/usr/local/lib/R/site-library/BH/include' -I'/usr/local/lib/R/site-library/cpp11/include' -I/usr/local/include -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c ipcmutex.cpp -o ipcmutex.o g++ -std=gnu++20 -shared -L/usr/local/lib/R/lib -L/usr/local/lib -o BiocParallel.so cpp11.o ipcmutex.o -L/usr/local/lib/R/lib -lR installing to /usr/local/lib/R/site-library/00LOCK-BiocParallel/00new/BiocParallel/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 (BiocParallel) * installing *source* package ‘annotate’ ... ** this is package ‘annotate’ version ‘1.90.0’ ** using staged installation ** R ** data ** inst ** byte-compile and prepare package for lazy loading Warning message: multiple methods tables found for ‘detail’ ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location Warning: multiple methods tables found for ‘detail’ ** testing if installed package can be loaded from final location Warning: multiple methods tables found for ‘detail’ ** testing if installed package keeps a record of temporary installation path * DONE (annotate) * installing *source* package ‘decoupleR’ ... ** this is package ‘decoupleR’ version ‘2.17.0’ ** 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 (decoupleR) * installing *source* package ‘GSEABase’ ... ** this is package ‘GSEABase’ version ‘1.74.0’ ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading Warning message: multiple methods tables found for ‘detail’ ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location Warning: multiple methods tables found for ‘detail’ ** testing if installed package can be loaded from final location Warning: multiple methods tables found for ‘detail’ ** testing if installed package keeps a record of temporary installation path * DONE (GSEABase) The downloaded source packages are in ‘/tmp/RtmptTQfk1/downloaded_packages’ ── R CMD build ───────────────────────────────────────────────────────────────── * checking for file ‘/tmp/RtmptTQfk1/remotes14f2c8da788/saezlab-cosmosR-b2ed195/DESCRIPTION’ ... OK * preparing ‘cosmosR’: * checking DESCRIPTION meta-information ... OK * checking for LF line-endings in source and make files and shell scripts * checking for empty or unneeded directories * looking to see if a ‘data/datalist’ file should be added * building ‘cosmosR_1.21.2.tar.gz’ Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L, : storing paths of more than 100 bytes is not portable: ‘cosmosR/vignettes/net_compr_MOON_files/figure-markdown_strict/extract_subnetwork_from_scored_MOON_network_1.png’ Installing package into ‘/usr/local/lib/R/site-library’ (as ‘lib’ is unspecified) * installing *source* package ‘cosmosR’ ... ** this is package ‘cosmosR’ version ‘1.21.2’ ** using staged installation ** R ** data ** 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 (cosmosR) Override from GitHub: saezlab/OmnipathR@devel Downloading GitHub repo saezlab/OmnipathR@devel Installing 15 packages: data.table, fastmatch, BBmisc, ParamHelpers, parallelMap, deSolve, lhs, smoof, mlr, plotly, sigmajs, SBMLR, R.matlab, mlrMBO, gprofiler2 Installing packages into ‘/usr/local/lib/R/site-library’ (as ‘lib’ is unspecified) trying URL 'https://p3m.dev/cran/__linux__/noble/latest/src/contrib/data.table_1.18.6.1.tar.gz' trying URL 'https://p3m.dev/cran/__linux__/noble/latest/src/contrib/fastmatch_1.1-8.tar.gz' trying URL 'https://p3m.dev/cran/__linux__/noble/latest/src/contrib/BBmisc_1.13.1.tar.gz' trying URL 'https://p3m.dev/cran/__linux__/noble/latest/src/contrib/ParamHelpers_1.14.2.tar.gz' trying URL 'https://p3m.dev/cran/__linux__/noble/latest/src/contrib/parallelMap_1.5.1.tar.gz' trying URL 'https://p3m.dev/cran/__linux__/noble/latest/src/contrib/deSolve_1.42.tar.gz' trying URL 'https://p3m.dev/cran/__linux__/noble/latest/src/contrib/lhs_1.3.0.tar.gz' trying URL 'https://p3m.dev/cran/__linux__/noble/latest/src/contrib/smoof_1.7.0.tar.gz' trying URL 'https://p3m.dev/cran/__linux__/noble/latest/src/contrib/mlr_2.19.3.tar.gz' trying URL 'https://p3m.dev/cran/__linux__/noble/latest/src/contrib/plotly_4.12.1.tar.gz' trying URL 'https://p3m.dev/cran/__linux__/noble/latest/src/contrib/sigmajs_0.1.5.tar.gz' trying URL 'https://bioconductor.org/packages/3.23/bioc/src/contrib/SBMLR_2.8.0.tar.gz' trying URL 'https://p3m.dev/cran/__linux__/noble/latest/src/contrib/R.matlab_3.8.1.tar.gz' trying URL 'https://p3m.dev/cran/__linux__/noble/latest/src/contrib/mlrMBO_1.1.6.tar.gz' trying URL 'https://p3m.dev/cran/__linux__/noble/latest/src/contrib/gprofiler2_0.2.4.tar.gz' * installing *binary* package ‘data.table’ ... * package ‘data.table’ successfully unpacked and SHA256 sums checked * DONE (data.table) * installing *binary* package ‘fastmatch’ ... * package ‘fastmatch’ successfully unpacked and SHA256 sums checked * DONE (fastmatch) * installing *binary* package ‘deSolve’ ... * package ‘deSolve’ successfully unpacked and SHA256 sums checked * DONE (deSolve) * installing *binary* package ‘lhs’ ... * package ‘lhs’ successfully unpacked and SHA256 sums checked * DONE (lhs) * installing *binary* package ‘sigmajs’ ... * package ‘sigmajs’ successfully unpacked and SHA256 sums checked * DONE (sigmajs) * installing *binary* package ‘R.matlab’ ... * package ‘R.matlab’ successfully unpacked and SHA256 sums checked * DONE (R.matlab) * installing *binary* package ‘BBmisc’ ... * package ‘BBmisc’ successfully unpacked and SHA256 sums checked * DONE (BBmisc) * installing *binary* package ‘plotly’ ... * package ‘plotly’ successfully unpacked and SHA256 sums checked * DONE (plotly) * installing *source* package ‘SBMLR’ ... ** this is package ‘SBMLR’ version ‘2.8.0’ ** using staged installation ** 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 ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (SBMLR) * installing *binary* package ‘ParamHelpers’ ... * package ‘ParamHelpers’ successfully unpacked and SHA256 sums checked * DONE (ParamHelpers) * installing *binary* package ‘parallelMap’ ... * package ‘parallelMap’ successfully unpacked and SHA256 sums checked * DONE (parallelMap) * installing *binary* package ‘gprofiler2’ ... * package ‘gprofiler2’ successfully unpacked and SHA256 sums checked * DONE (gprofiler2) * installing *binary* package ‘smoof’ ... * package ‘smoof’ successfully unpacked and SHA256 sums checked * DONE (smoof) * installing *binary* package ‘mlr’ ... * package ‘mlr’ successfully unpacked and SHA256 sums checked * DONE (mlr) * installing *binary* package ‘mlrMBO’ ... * package ‘mlrMBO’ successfully unpacked and SHA256 sums checked * DONE (mlrMBO) The downloaded source packages are in ‘/tmp/RtmptTQfk1/downloaded_packages’ ── R CMD build ───────────────────────────────────────────────────────────────── * checking for file ‘/tmp/RtmptTQfk1/remotes14f60d7997b/saezlab-OmnipathR-a7c05f9/DESCRIPTION’ ... OK * preparing ‘OmnipathR’: * checking DESCRIPTION meta-information ... OK * checking for LF line-endings in source and make files and shell scripts * checking for empty or unneeded directories Removed empty directory ‘OmnipathR/.github’ * looking to see if a ‘data/datalist’ file should be added * building ‘OmnipathR_4.1.0.tar.gz’ Installing package into ‘/usr/local/lib/R/site-library’ (as ‘lib’ is unspecified) * installing *source* package ‘OmnipathR’ ... ** this is package ‘OmnipathR’ version ‘4.1.0’ ** using staged installation ** 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 ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (OmnipathR) 'getOption("repos")' replaces Bioconductor standard repositories, see 'help("repositories", package = "BiocManager")' for details. Replacement repositories: CRAN: https://p3m.dev/cran/__linux__/noble/latest * sessionInfo() R version 4.6.1 (2026-06-24) Platform: x86_64-pc-linux-gnu Running under: Ubuntu 24.04.4 LTS Matrix products: default BLAS: /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3 LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.26.so; LAPACK version 3.12.0 locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=en_US.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C time zone: Europe/Berlin tzcode source: system (glibc) attached base packages: [1] stats graphics grDevices utils datasets methods base loaded via a namespace (and not attached): [1] processx_3.9.0 BiocManager_1.30.27 compiler_4.6.1 [4] R6_2.6.1 cli_3.6.6 tools_4.6.1 [7] otel_0.2.0 curl_8.0.0 remotes_2.5.0 [10] desc_1.4.3 callr_3.8.0 ps_1.9.3 [13] pkgbuild_1.4.8 Bioconductor version '3.24' * 8 packages out-of-date * 0 packages too new create a valid installation with BiocManager::install(c( "annotate", "AnnotationDbi", "BiocParallel", "Biostrings", "CARNIVAL", "GSEABase", "KEGGREST", "SBMLR" ), update = TRUE, ask = FALSE, force = TRUE) more details: BiocManager::valid()$too_new, BiocManager::valid()$out_of_date Warning message: 8 packages out-of-date; 0 packages too new [ Finished: 2026-10-02 15:00:31 CEST ]