[ Started: 2024-10-17 12:26:12 CEST ]
[ cosmosR v1.12.0 for BioC-3.19 from https://git.bioconductor.org/packages/cosmosR@RELEASE_3_19 (51923e9 2024-04-30 11:34:23) ]

[1] "Libraries: "                     "/home/omnipath/local/R/4.4-3.19"
[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 3.19 (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' 
GenomeInfoDb (NA -> 1.38.8) [CRAN]
XVector      (NA -> 0.42.0) [CRAN]
Biostrings   (NA -> 2.70.3) [CRAN]
KEGGREST     (NA -> 1.42.0) [CRAN]
S4Vectors    (NA -> 0.40.2) [CRAN]
IRanges      (NA -> 2.36.0) [CRAN]
Annotatio... (NA -> 1.64.1) [CRAN]
annotate     (NA -> 1.80.0) [CRAN]
GSEABase     (NA -> 1.64.0) [CRAN]
Skipping 14 packages ahead of CRAN: BiocParallel, limma, BiocGenerics, zlibbioc, GenomeInfoDbData, Biobase, fgsea, marray, graph, decoupleR, bcellViper, piano, dorothea, CARNIVAL
Installing 9 packages: GenomeInfoDb, XVector, Biostrings, KEGGREST, S4Vectors, IRanges, AnnotationDbi, annotate, GSEABase
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)
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downloaded 3.4 MB

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/Biostrings_2.70.3.tar.gz'
Content type 'application/gzip' length 12740728 bytes (12.2 MB)
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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)
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downloaded 21 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)
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downloaded 818 KB

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)
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downloaded 469 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)
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downloaded 4.2 MB

trying URL 'https://bioconductor.org/packages/3.18/bioc/src/contrib/annotate_1.80.0.tar.gz'
Content type 'application/gzip' length 1497628 bytes (1.4 MB)
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downloaded 1.4 MB

trying URL 'https://bioconductor.org/packages/3.18/bioc/src/contrib/GSEABase_1.64.0.tar.gz'
Content type 'application/gzip' length 299035 bytes (292 KB)
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downloaded 292 KB

* 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 ‘GenomeInfoDb’
* removing ‘/home/omnipath/local/R/4.4-3.19/GenomeInfoDb’
ERROR: dependencies ‘S4Vectors’, ‘IRanges’ are not available for package ‘XVector’
* removing ‘/home/omnipath/local/R/4.4-3.19/XVector’
ERROR: dependencies ‘S4Vectors’, ‘IRanges’, ‘XVector’, ‘GenomeInfoDb’ are not available for package ‘Biostrings’
* removing ‘/home/omnipath/local/R/4.4-3.19/Biostrings’
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: dependency ‘AnnotationDbi’ is not available for package ‘annotate’
* removing ‘/home/omnipath/local/R/4.4-3.19/annotate’
ERROR: dependencies ‘annotate’, ‘AnnotationDbi’ are not available for package ‘GSEABase’
* removing ‘/home/omnipath/local/R/4.4-3.19/GSEABase’

The downloaded source packages are in
	‘/tmp/Rtmp8hPXOc/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 ‘GenomeInfoDb’ had non-zero exit status
4: In i.p(...) :
  installation of package ‘XVector’ had non-zero exit status
5: In i.p(...) :
  installation of package ‘Biostrings’ had non-zero exit status
6: In i.p(...) :
  installation of package ‘KEGGREST’ had non-zero exit status
7: In i.p(...) :
  installation of package ‘AnnotationDbi’ had non-zero exit status
8: In i.p(...) :
  installation of package ‘annotate’ had non-zero exit status
9: In i.p(...) :
  installation of package ‘GSEABase’ had non-zero exit status
[ Finished: 2024-10-17 12:26:34 CEST ]