[ Started: 2024-12-09 12:58:02 CET ]
[ decoupleR v2.10.0 for BioC-3.19 from https://git.bioconductor.org/packages/decoupleR@RELEASE_3_19 (7e6c106 2024-04-30 11:34:47) ]
[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Bioconductor version '3.19' is out-of-date; the current release version '3.20'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]
S4Arrays (NA -> 1.2.1 ) [CRAN]
IRanges (NA -> 2.36.0) [CRAN]
S4Vectors (NA -> 0.40.2) [CRAN]
GenomeInfoDb (NA -> 1.38.8) [CRAN]
DelayedArray (NA -> 0.28.0) [CRAN]
GenomicRa... (NA -> 1.54.1) [CRAN]
Biostrings (NA -> 2.70.3) [CRAN]
KEGGREST (NA -> 1.42.0) [CRAN]
Annotatio... (NA -> 1.64.1) [CRAN]
annotate (NA -> 1.80.0) [CRAN]
beachmat (NA -> 2.18.1) [CRAN]
ScaledMatrix (NA -> 1.10.0) [CRAN]
rhdf5 (NA -> 2.46.1) [CRAN]
Summarize... (NA -> 1.32.0) [CRAN]
GSEABase (NA -> 1.64.0) [CRAN]
DelayedMa... (NA -> 1.24.0) [CRAN]
BiocSingular (NA -> 1.18.0) [CRAN]
HDF5Array (NA -> 1.30.1) [CRAN]
SingleCel... (NA -> 1.24.0) [CRAN]
AUCell (NA -> 1.24.0) [CRAN]
GSVA (NA -> 1.50.5) [CRAN]
Skipping 14 packages ahead of CRAN: zlibbioc, MatrixGenerics, BiocGenerics, GenomeInfoDbData, Biobase, graph, sparseMatrixStats, BiocParallel, Rhdf5lib, rhdf5filters, OmnipathR, BiocStyle, fgsea, viper
Installing 23 packages: XVector, SparseArray, S4Arrays, IRanges, S4Vectors, GenomeInfoDb, DelayedArray, GenomicRanges, Biostrings, KEGGREST, AnnotationDbi, annotate, beachmat, ScaledMatrix, rhdf5, SummarizedExperiment, GSEABase, DelayedMatrixStats, BiocSingular, HDF5Array, SingleCellExperiment, AUCell, GSVA
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* 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: dependency ‘S4Vectors’ is not available for package ‘rhdf5’
* removing ‘/home/omnipath/local/R/4.4-3.19/rhdf5’
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 ‘IRanges’, ‘S4Vectors’, ‘KEGGREST’ are not available for package ‘AnnotationDbi’
* removing ‘/home/omnipath/local/R/4.4-3.19/AnnotationDbi’
ERROR: dependencies ‘DelayedArray’, ‘SparseArray’ are not available for package ‘beachmat’
* removing ‘/home/omnipath/local/R/4.4-3.19/beachmat’
ERROR: dependencies ‘S4Vectors’, ‘DelayedArray’ are not available for package ‘ScaledMatrix’
* removing ‘/home/omnipath/local/R/4.4-3.19/ScaledMatrix’
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 ‘DelayedArray’, ‘S4Vectors’, ‘IRanges’ are not available for package ‘DelayedMatrixStats’
* removing ‘/home/omnipath/local/R/4.4-3.19/DelayedMatrixStats’
ERROR: dependencies ‘DelayedArray’, ‘rhdf5’, ‘S4Vectors’, ‘IRanges’, ‘S4Arrays’ are not available for package ‘HDF5Array’
* removing ‘/home/omnipath/local/R/4.4-3.19/HDF5Array’
ERROR: dependency ‘AnnotationDbi’ is not available for package ‘annotate’
* removing ‘/home/omnipath/local/R/4.4-3.19/annotate’
ERROR: dependencies ‘S4Vectors’, ‘DelayedArray’, ‘ScaledMatrix’, ‘beachmat’ are not available for package ‘BiocSingular’
* removing ‘/home/omnipath/local/R/4.4-3.19/BiocSingular’
ERROR: dependencies ‘SummarizedExperiment’, ‘S4Vectors’, ‘GenomicRanges’, ‘DelayedArray’ are not available for package ‘SingleCellExperiment’
* removing ‘/home/omnipath/local/R/4.4-3.19/SingleCellExperiment’
ERROR: dependencies ‘annotate’, ‘AnnotationDbi’ are not available for package ‘GSEABase’
* removing ‘/home/omnipath/local/R/4.4-3.19/GSEABase’
ERROR: dependencies ‘DelayedArray’, ‘DelayedMatrixStats’, ‘GSEABase’, ‘SummarizedExperiment’ are not available for package ‘AUCell’
* removing ‘/home/omnipath/local/R/4.4-3.19/AUCell’
ERROR: dependencies ‘S4Vectors’, ‘IRanges’, ‘SummarizedExperiment’, ‘GSEABase’, ‘SingleCellExperiment’, ‘DelayedArray’, ‘DelayedMatrixStats’, ‘HDF5Array’, ‘BiocSingular’ are not available for package ‘GSVA’
* removing ‘/home/omnipath/local/R/4.4-3.19/GSVA’
The downloaded source packages are in
‘/tmp/Rtmpj6JSh5/downloaded_packages’
There were 23 warnings (use warnings() to see them)
[ Finished: 2024-12-09 12:58:44 CET ]