[ Started: 2025-01-30 13:31:27 CET ]
[ dorothea v1.7.4 for BioC-3.20 from https://github.com/saezlab/dorothea@master (1461fb7 2024-02-24 12:55:48) ]
[1] "Libraries: " "/home/omnipath/local/R/4.4-3.20"
[3] "/home/omnipath/local/R/4.4" "/usr/lib/R/library"
'getOption("repos")' replaces Bioconductor standard repositories, see
'help("repositories", package = "BiocManager")' for details.
Replacement repositories:
CRAN: https://cloud.r-project.org
Bioconductor version 3.20 (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 3.20 (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]
Summarize... (NA -> 1.32.0) [CRAN]
SingleCel... (NA -> 1.24.0) [CRAN]
Skipping 10 packages ahead of CRAN: zlibbioc, MatrixGenerics, BiocGenerics, GenomeInfoDbData, Biobase, viper, OmnipathR, BiocStyle, decoupleR, bcellViper
Installing 10 packages: XVector, SparseArray, S4Arrays, IRanges, S4Vectors, GenomeInfoDb, DelayedArray, GenomicRanges, SummarizedExperiment, SingleCellExperiment
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)
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downloaded 66 KB
trying URL 'https://bioconductor.org/packages/3.18/bioc/src/contrib/SparseArray_1.2.4.tar.gz'
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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)
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trying URL 'https://bioconductor.org/packages/3.18/bioc/src/contrib/IRanges_2.36.0.tar.gz'
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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)
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trying URL 'https://bioconductor.org/packages/3.18/bioc/src/contrib/GenomeInfoDb_1.38.8.tar.gz'
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trying URL 'https://bioconductor.org/packages/3.18/bioc/src/contrib/DelayedArray_0.28.0.tar.gz'
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trying URL 'https://bioconductor.org/packages/3.18/bioc/src/contrib/GenomicRanges_1.54.1.tar.gz'
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trying URL 'https://bioconductor.org/packages/3.18/bioc/src/contrib/SummarizedExperiment_1.32.0.tar.gz'
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trying URL 'https://bioconductor.org/packages/3.18/bioc/src/contrib/SingleCellExperiment_1.24.0.tar.gz'
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* installing *source* package ‘S4Vectors’ ...
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
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/4.4-3.20/S4Vectors’
ERROR: dependency ‘S4Vectors’ is not available for package ‘IRanges’
* removing ‘/home/omnipath/local/R/4.4-3.20/IRanges’
ERROR: dependencies ‘S4Vectors’, ‘IRanges’ are not available for package ‘XVector’
* removing ‘/home/omnipath/local/R/4.4-3.20/XVector’
ERROR: dependencies ‘S4Vectors’, ‘IRanges’ are not available for package ‘S4Arrays’
* removing ‘/home/omnipath/local/R/4.4-3.20/S4Arrays’
ERROR: dependencies ‘S4Vectors’, ‘IRanges’ are not available for package ‘GenomeInfoDb’
* removing ‘/home/omnipath/local/R/4.4-3.20/GenomeInfoDb’
ERROR: dependencies ‘S4Vectors’, ‘S4Arrays’, ‘IRanges’, ‘XVector’ are not available for package ‘SparseArray’
* removing ‘/home/omnipath/local/R/4.4-3.20/SparseArray’
ERROR: dependencies ‘S4Vectors’, ‘IRanges’, ‘GenomeInfoDb’, ‘XVector’ are not available for package ‘GenomicRanges’
* removing ‘/home/omnipath/local/R/4.4-3.20/GenomicRanges’
ERROR: dependencies ‘S4Vectors’, ‘IRanges’, ‘S4Arrays’, ‘SparseArray’ are not available for package ‘DelayedArray’
* removing ‘/home/omnipath/local/R/4.4-3.20/DelayedArray’
ERROR: dependencies ‘GenomicRanges’, ‘S4Vectors’, ‘IRanges’, ‘GenomeInfoDb’, ‘S4Arrays’, ‘DelayedArray’ are not available for package ‘SummarizedExperiment’
* removing ‘/home/omnipath/local/R/4.4-3.20/SummarizedExperiment’
ERROR: dependencies ‘SummarizedExperiment’, ‘S4Vectors’, ‘GenomicRanges’, ‘DelayedArray’ are not available for package ‘SingleCellExperiment’
* removing ‘/home/omnipath/local/R/4.4-3.20/SingleCellExperiment’
The downloaded source packages are in
‘/tmp/Rtmp8n9U4u/downloaded_packages’
Warning messages:
1: In i.p(...) :
installation of package ‘S4Vectors’ had non-zero exit status
2: In i.p(...) :
installation of package ‘IRanges’ had non-zero exit status
3: In i.p(...) :
installation of package ‘XVector’ had non-zero exit status
4: In i.p(...) :
installation of package ‘S4Arrays’ had non-zero exit status
5: In i.p(...) :
installation of package ‘GenomeInfoDb’ had non-zero exit status
6: In i.p(...) :
installation of package ‘SparseArray’ had non-zero exit status
7: In i.p(...) :
installation of package ‘GenomicRanges’ had non-zero exit status
8: In i.p(...) :
installation of package ‘DelayedArray’ had non-zero exit status
9: In i.p(...) :
installation of package ‘SummarizedExperiment’ had non-zero exit status
10: In i.p(...) :
installation of package ‘SingleCellExperiment’ had non-zero exit status
[ Finished: 2025-01-30 13:31:49 CET ]