[ Started: 2024-11-06 13:55:52 CET ] [ progeny v1.26.0 for BioC-3.19 from https://git.bioconductor.org/packages/progeny@RELEASE_3_19 (4643a88 2024-04-30 11:01:43) ] [1] "Libraries: " "/home/omnipath/local/R/4.4-3.19" [3] "/home/omnipath/local/R/4.4" "/usr/lib/R/library" Bioconductor version '3.19' is out-of-date; the current release version '3.20' is available with R version '4.4'; see https://bioconductor.org/install 'getOption("repos")' replaces Bioconductor standard repositories, see 'help("repositories", package = "BiocManager")' for details. Replacement repositories: CRAN: https://cloud.r-project.org Bioconductor version 3.19 (BiocManager 1.30.25), R 4.4.1 (2024-06-14) 'getOption("repos")' replaces Bioconductor standard repositories, see 'help("repositories", package = "BiocManager")' for details. Replacement repositories: CRAN: https://cloud.r-project.org Bioconductor version 3.19 (BiocManager 1.30.25), R 4.4.1 (2024-06-14) Warning message: package(s) not installed when version(s) same as or greater than current; use `force = TRUE` to re-install: 'BiocCheck' XVector (NA -> 0.42.0) [CRAN] SparseArray (NA -> 1.2.4 ) [CRAN] DelayedArray (NA -> 0.28.0) [CRAN] S4Arrays (NA -> 1.2.1 ) [CRAN] GenomeInfoDb (NA -> 1.38.8) [CRAN] IRanges (NA -> 2.36.0) [CRAN] S4Vectors (NA -> 0.40.2) [CRAN] GenomicRa... (NA -> 1.54.1) [CRAN] Biostrings (NA -> 2.70.3) [CRAN] KEGGREST (NA -> 1.42.0) [CRAN] Summarize... (NA -> 1.32.0) [CRAN] Annotatio... (NA -> 1.64.1) [CRAN] DESeq2 (NA -> 1.42.1) [CRAN] SingleCel... (NA -> 1.24.0) [CRAN] biomaRt (NA -> 2.58.2) [CRAN] airway (NA -> 1.22.0) [CRAN] Skipping 9 packages ahead of CRAN: BiocGenerics, zlibbioc, GenomeInfoDbData, Biobase, MatrixGenerics, BiocParallel, BiocFileCache, BiocStyle, decoupleR Installing 16 packages: XVector, SparseArray, DelayedArray, S4Arrays, GenomeInfoDb, IRanges, S4Vectors, GenomicRanges, Biostrings, KEGGREST, SummarizedExperiment, AnnotationDbi, DESeq2, SingleCellExperiment, biomaRt, airway trying URL 'https://bioconductor.org/packages/3.18/bioc/src/contrib/XVector_0.42.0.tar.gz' Content type 'application/gzip' length 67825 bytes (66 KB) ================================================== downloaded 66 KB trying URL 'https://bioconductor.org/packages/3.18/bioc/src/contrib/SparseArray_1.2.4.tar.gz' Content type 'application/gzip' length 367778 bytes (359 KB) ================================================== downloaded 359 KB trying URL 'https://bioconductor.org/packages/3.18/bioc/src/contrib/DelayedArray_0.28.0.tar.gz' Content type 'application/gzip' length 624166 bytes (609 KB) ================================================== downloaded 609 KB trying URL 'https://bioconductor.org/packages/3.18/bioc/src/contrib/S4Arrays_1.2.1.tar.gz' Content type 'application/gzip' length 282089 bytes (275 KB) ================================================== downloaded 275 KB trying URL 'https://bioconductor.org/packages/3.18/bioc/src/contrib/GenomeInfoDb_1.38.8.tar.gz' Content type 'application/gzip' length 3581806 bytes (3.4 MB) ================================================== downloaded 3.4 MB trying URL 'https://bioconductor.org/packages/3.18/bioc/src/contrib/IRanges_2.36.0.tar.gz' Content type 'application/gzip' length 481055 bytes (469 KB) ================================================== downloaded 469 KB trying URL 'https://bioconductor.org/packages/3.18/bioc/src/contrib/S4Vectors_0.40.2.tar.gz' Content type 'application/gzip' length 838187 bytes (818 KB) ================================================== downloaded 818 KB trying URL 'https://bioconductor.org/packages/3.18/bioc/src/contrib/GenomicRanges_1.54.1.tar.gz' Content type 'application/gzip' length 1140246 bytes (1.1 MB) ================================================== downloaded 1.1 MB trying URL 'https://bioconductor.org/packages/3.18/bioc/src/contrib/Biostrings_2.70.3.tar.gz' Content type 'application/gzip' length 12740728 bytes (12.2 MB) ================================================== downloaded 12.2 MB trying URL 'https://bioconductor.org/packages/3.18/bioc/src/contrib/KEGGREST_1.42.0.tar.gz' Content type 'application/gzip' length 22412 bytes (21 KB) ================================================== downloaded 21 KB trying URL 'https://bioconductor.org/packages/3.18/bioc/src/contrib/SummarizedExperiment_1.32.0.tar.gz' Content type 'application/gzip' length 686052 bytes (669 KB) ================================================== downloaded 669 KB trying URL 'https://bioconductor.org/packages/3.18/bioc/src/contrib/AnnotationDbi_1.64.1.tar.gz' Content type 'application/gzip' length 4359564 bytes (4.2 MB) ================================================== downloaded 4.2 MB trying URL 'https://bioconductor.org/packages/3.18/bioc/src/contrib/DESeq2_1.42.1.tar.gz' Content type 'application/gzip' length 2098789 bytes (2.0 MB) ================================================== downloaded 2.0 MB trying URL 'https://bioconductor.org/packages/3.18/bioc/src/contrib/SingleCellExperiment_1.24.0.tar.gz' Content type 'application/gzip' length 985002 bytes (961 KB) ================================================== downloaded 961 KB trying URL 'https://bioconductor.org/packages/3.18/bioc/src/contrib/biomaRt_2.58.2.tar.gz' Content type 'application/gzip' length 670061 bytes (654 KB) ================================================== downloaded 654 KB trying URL 'https://bioconductor.org/packages/3.18/data/experiment/src/contrib/airway_1.22.0.tar.gz' Content type 'application/gzip' length 24755612 bytes (23.6 MB) ================================================== downloaded 23.6 MB * installing *source* package ‘S4Vectors’ ... ** using staged installation ** libs using C compiler: ‘gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0’ gcc -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c AEbufs.c -o AEbufs.o gcc -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c DataFrame_class.c -o DataFrame_class.o gcc -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c Hits_class.c -o Hits_class.o gcc -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c LLint_class.c -o LLint_class.o gcc -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c List_class.c -o List_class.o gcc -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c R_init_S4Vectors.c -o R_init_S4Vectors.o gcc -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c Rle_class.c -o Rle_class.o Rle_class.c: In function ‘_subset_Rle_by_ranges’: Rle_class.c:1136:17: error: format not a string literal and no format arguments [-Werror=format-security] 1136 | error(errmsg); | ^~~~~ Rle_class.c: In function ‘_subset_Rle_by_positions’: Rle_class.c:1161:17: error: format not a string literal and no format arguments [-Werror=format-security] 1161 | error(errmsg); | ^~~~~ Rle_class.c: In function ‘Rle_extract_range’: Rle_class.c:1190:17: error: format not a string literal and no format arguments [-Werror=format-security] 1190 | error(errmsg); | ^~~~~ cc1: some warnings being treated as errors make: *** [/usr/lib/R/etc/Makeconf:195: Rle_class.o] Error 1 ERROR: compilation failed for package ‘S4Vectors’ * removing ‘/home/omnipath/local/R/4.4-3.19/S4Vectors’ ERROR: dependency ‘S4Vectors’ is not available for package ‘IRanges’ * removing ‘/home/omnipath/local/R/4.4-3.19/IRanges’ ERROR: dependencies ‘S4Vectors’, ‘IRanges’ are not available for package ‘XVector’ * removing ‘/home/omnipath/local/R/4.4-3.19/XVector’ ERROR: dependencies ‘S4Vectors’, ‘IRanges’ are not available for package ‘S4Arrays’ * removing ‘/home/omnipath/local/R/4.4-3.19/S4Arrays’ ERROR: dependencies ‘S4Vectors’, ‘IRanges’ are not available for package ‘GenomeInfoDb’ * removing ‘/home/omnipath/local/R/4.4-3.19/GenomeInfoDb’ ERROR: dependencies ‘S4Vectors’, ‘S4Arrays’, ‘IRanges’, ‘XVector’ are not available for package ‘SparseArray’ * removing ‘/home/omnipath/local/R/4.4-3.19/SparseArray’ ERROR: dependencies ‘S4Vectors’, ‘IRanges’, ‘GenomeInfoDb’, ‘XVector’ are not available for package ‘GenomicRanges’ * removing ‘/home/omnipath/local/R/4.4-3.19/GenomicRanges’ ERROR: dependencies ‘S4Vectors’, ‘IRanges’, ‘XVector’, ‘GenomeInfoDb’ are not available for package ‘Biostrings’ * removing ‘/home/omnipath/local/R/4.4-3.19/Biostrings’ ERROR: dependencies ‘S4Vectors’, ‘IRanges’, ‘S4Arrays’, ‘SparseArray’ are not available for package ‘DelayedArray’ * removing ‘/home/omnipath/local/R/4.4-3.19/DelayedArray’ ERROR: dependency ‘Biostrings’ is not available for package ‘KEGGREST’ * removing ‘/home/omnipath/local/R/4.4-3.19/KEGGREST’ ERROR: dependencies ‘GenomicRanges’, ‘S4Vectors’, ‘IRanges’, ‘GenomeInfoDb’, ‘S4Arrays’, ‘DelayedArray’ are not available for package ‘SummarizedExperiment’ * removing ‘/home/omnipath/local/R/4.4-3.19/SummarizedExperiment’ ERROR: dependencies ‘IRanges’, ‘S4Vectors’, ‘KEGGREST’ are not available for package ‘AnnotationDbi’ * removing ‘/home/omnipath/local/R/4.4-3.19/AnnotationDbi’ ERROR: dependencies ‘S4Vectors’, ‘IRanges’, ‘GenomicRanges’, ‘SummarizedExperiment’ are not available for package ‘DESeq2’ * removing ‘/home/omnipath/local/R/4.4-3.19/DESeq2’ ERROR: dependencies ‘SummarizedExperiment’, ‘S4Vectors’, ‘GenomicRanges’, ‘DelayedArray’ are not available for package ‘SingleCellExperiment’ * removing ‘/home/omnipath/local/R/4.4-3.19/SingleCellExperiment’ ERROR: dependency ‘AnnotationDbi’ is not available for package ‘biomaRt’ * removing ‘/home/omnipath/local/R/4.4-3.19/biomaRt’ ERROR: dependency ‘SummarizedExperiment’ is not available for package ‘airway’ * removing ‘/home/omnipath/local/R/4.4-3.19/airway’ The downloaded source packages are in ‘/tmp/RtmpkGBVNm/downloaded_packages’ There were 16 warnings (use warnings() to see them) [ Finished: 2024-11-06 13:56:24 CET ]