[ Started: 2025-03-11 01:27:12 CET ]
[ progeny v1.28.0 for BioC-3.20 from https://git.bioconductor.org/packages/progeny@RELEASE_3_20 (cbdfaf7 2024-10-29 10:23:15) ]
[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]
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
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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’, ‘XVector’, ‘GenomeInfoDb’ are not available for package ‘Biostrings’
* removing ‘/home/omnipath/local/R/4.4-3.20/Biostrings’
ERROR: dependencies ‘S4Vectors’, ‘IRanges’, ‘S4Arrays’, ‘SparseArray’ are not available for package ‘DelayedArray’
* removing ‘/home/omnipath/local/R/4.4-3.20/DelayedArray’
ERROR: dependency ‘Biostrings’ is not available for package ‘KEGGREST’
* removing ‘/home/omnipath/local/R/4.4-3.20/KEGGREST’
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 ‘IRanges’, ‘S4Vectors’, ‘KEGGREST’ are not available for package ‘AnnotationDbi’
* removing ‘/home/omnipath/local/R/4.4-3.20/AnnotationDbi’
ERROR: dependencies ‘S4Vectors’, ‘IRanges’, ‘GenomicRanges’, ‘SummarizedExperiment’ are not available for package ‘DESeq2’
* removing ‘/home/omnipath/local/R/4.4-3.20/DESeq2’
ERROR: dependencies ‘SummarizedExperiment’, ‘S4Vectors’, ‘GenomicRanges’, ‘DelayedArray’ are not available for package ‘SingleCellExperiment’
* removing ‘/home/omnipath/local/R/4.4-3.20/SingleCellExperiment’
ERROR: dependency ‘AnnotationDbi’ is not available for package ‘biomaRt’
* removing ‘/home/omnipath/local/R/4.4-3.20/biomaRt’
ERROR: dependency ‘SummarizedExperiment’ is not available for package ‘airway’
* removing ‘/home/omnipath/local/R/4.4-3.20/airway’
The downloaded source packages are in
‘/tmp/Rtmpn5tTVA/downloaded_packages’
There were 16 warnings (use warnings() to see them)
[ Finished: 2025-03-11 01:27:48 CET ]