[ Started: 2025-01-28 13:43:39 CET ]
[ MetaProViz v2.1.4 for BioC-3.20 from https://github.com/saezlab/MetaProViz@development (2176ffc 2025-01-15 16:19:43) ]
[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)
Old packages: 'decoupleR'
trying URL 'https://bioconductor.org/packages/3.20/bioc/src/contrib/decoupleR_2.12.0.tar.gz'
Content type 'application/x-gzip' length 5238810 bytes (5.0 MB)
==================================================
downloaded 5.0 MB
* installing *source* package ‘decoupleR’ ...
** package ‘decoupleR’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (decoupleR)
The downloaded source packages are in
‘/tmp/RtmpAoRuiU/downloaded_packages’
'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'
OmnipathR (4ffd9ec5b... -> 872caf927...) [GitHub]
cosmosR (NA -> 81d1a7fe7...) [GitHub]
NA (NA -> 97a5846be...) [Git]
GenomeInfoDb (NA -> 1.38.8 ) [CRAN]
XVector (NA -> 0.42.0 ) [CRAN]
IRanges (NA -> 2.36.0 ) [CRAN]
S4Vectors (NA -> 0.40.2 ) [CRAN]
nloptr (NA -> 2.1.1 ) [CRAN]
lme4 (NA -> 1.1-36 ) [CRAN]
pbkrtest (NA -> 0.5.3 ) [CRAN]
car (NA -> 3.1-3 ) [CRAN]
rstatix (NA -> 0.7.2 ) [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]
GO.db (NA -> 3.18.0 ) [CRAN]
HDO.db (NA -> 0.99.1 ) [CRAN]
GOSemSim (NA -> 2.28.1 ) [CRAN]
DOSE (NA -> 3.28.2 ) [CRAN]
ggpubr (NA -> 0.6.0 ) [CRAN]
FactoMineR (NA -> 2.11 ) [CRAN]
GSEABase (NA -> 1.64.0 ) [CRAN]
enrichplot (NA -> 1.22.0 ) [CRAN]
factoextra (NA -> 1.0.7 ) [CRAN]
clusterPr... (NA -> 4.10.1 ) [CRAN]
Downloading GitHub repo saezlab/cosmosR@HEAD
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 9 packages ahead of CRAN: zlibbioc, GenomeInfoDbData, Biobase, BiocGenerics, graph, decoupleR, bcellViper, 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)
==================================================
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)
==================================================
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)
==================================================
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/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/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/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/annotate_1.80.0.tar.gz'
Content type 'application/gzip' length 1497628 bytes (1.4 MB)
==================================================
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)
==================================================
downloaded 292 KB
* 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 ‘GenomeInfoDb’
* removing ‘/home/omnipath/local/R/4.4-3.20/GenomeInfoDb’
ERROR: dependencies ‘S4Vectors’, ‘IRanges’ are not available for package ‘XVector’
* removing ‘/home/omnipath/local/R/4.4-3.20/XVector’
ERROR: dependencies ‘S4Vectors’, ‘IRanges’, ‘XVector’, ‘GenomeInfoDb’ are not available for package ‘Biostrings’
* removing ‘/home/omnipath/local/R/4.4-3.20/Biostrings’
ERROR: dependency ‘Biostrings’ is not available for package ‘KEGGREST’
* removing ‘/home/omnipath/local/R/4.4-3.20/KEGGREST’
ERROR: dependencies ‘IRanges’, ‘S4Vectors’, ‘KEGGREST’ are not available for package ‘AnnotationDbi’
* removing ‘/home/omnipath/local/R/4.4-3.20/AnnotationDbi’
ERROR: dependency ‘AnnotationDbi’ is not available for package ‘annotate’
* removing ‘/home/omnipath/local/R/4.4-3.20/annotate’
ERROR: dependencies ‘annotate’, ‘AnnotationDbi’ are not available for package ‘GSEABase’
* removing ‘/home/omnipath/local/R/4.4-3.20/GSEABase’
The downloaded source packages are in
‘/tmp/RtmpAoRuiU/downloaded_packages’
── R CMD build ─────────────────────────────────────────────────────────────────
* checking for file ‘/tmp/RtmpAoRuiU/remotes327d1b1af8f04a/saezlab-cosmosR-81d1a7f/DESCRIPTION’ ... OK
* preparing ‘cosmosR’:
* checking DESCRIPTION meta-information ... OK
* checking for LF line-endings in source and make files and shell scripts
* checking for empty or unneeded directories
* looking to see if a ‘data/datalist’ file should be added
* building ‘cosmosR_1.9.1.tar.gz’
Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L, :
storing paths of more than 100 bytes is not portable:
‘cosmosR/vignettes/net_compr_MOON_files/figure-markdown_strict/extract_subnetwork_from_scored_MOON_network_1.png’
ERROR: dependency ‘GSEABase’ is not available for package ‘cosmosR’
* removing ‘/home/omnipath/local/R/4.4-3.20/cosmosR’
Downloading git repo https://git.bioconductor.org/packages/limma.git
'/usr/bin/git' clone --depth 1 --no-hardlinks https://git.bioconductor.org/packages/limma.git /tmp/RtmpAoRuiU/file327d1b7814f1b9
Cloning into '/tmp/RtmpAoRuiU/file327d1b7814f1b9'...
── R CMD build ─────────────────────────────────────────────────────────────────
* checking for file ‘/tmp/RtmpAoRuiU/file327d1b7814f1b9/DESCRIPTION’ ... OK
* preparing ‘limma’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* checking for LF line-endings in source and make files and shell scripts
* checking for empty or unneeded directories
* building ‘limma_3.63.3.tar.gz’
* installing *source* package ‘limma’ ...
** 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 init.c -o init.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 normexp.c -o normexp.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 weighted_lowess.c -o weighted_lowess.o
gcc -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -o limma.so init.o normexp.o weighted_lowess.o -L/usr/lib/R/lib -lR
installing to /home/omnipath/local/R/4.4-3.20/00LOCK-limma/00new/limma/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (limma)
Skipping 15 packages ahead of CRAN: zlibbioc, GenomeInfoDbData, BiocGenerics, graph, Biobase, decoupleR, bcellViper, treeio, qvalue, BiocParallel, ggtree, dorothea, CARNIVAL, BiocStyle, EnhancedVolcano
Installing 23 packages: GenomeInfoDb, XVector, IRanges, S4Vectors, nloptr, lme4, pbkrtest, car, rstatix, Biostrings, KEGGREST, AnnotationDbi, annotate, GO.db, HDO.db, GOSemSim, DOSE, ggpubr, FactoMineR, GSEABase, enrichplot, factoextra, clusterProfiler
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/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/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://cran.uni-muenster.de/src/contrib/nloptr_2.1.1.tar.gz'
Content type 'application/x-gzip' length 2236635 bytes (2.1 MB)
==================================================
downloaded 2.1 MB
trying URL 'https://cran.uni-muenster.de/src/contrib/lme4_1.1-36.tar.gz'
Content type 'application/x-gzip' length 3294834 bytes (3.1 MB)
==================================================
downloaded 3.1 MB
trying URL 'https://cran.uni-muenster.de/src/contrib/pbkrtest_0.5.3.tar.gz'
Content type 'application/x-gzip' length 59013 bytes (57 KB)
==================================================
downloaded 57 KB
trying URL 'https://cran.uni-muenster.de/src/contrib/car_3.1-3.tar.gz'
Content type 'application/x-gzip' length 384407 bytes (375 KB)
==================================================
downloaded 375 KB
trying URL 'https://cran.uni-muenster.de/src/contrib/rstatix_0.7.2.tar.gz'
Content type 'application/x-gzip' length 405256 bytes (395 KB)
==================================================
downloaded 395 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)
==================================================
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/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/annotate_1.80.0.tar.gz'
Content type 'application/gzip' length 1497628 bytes (1.4 MB)
==================================================
downloaded 1.4 MB
trying URL 'https://bioconductor.org/packages/3.18/data/annotation/src/contrib/GO.db_3.18.0.tar.gz'
Content type 'application/gzip' length 29013599 bytes (27.7 MB)
==================================================
downloaded 27.7 MB
trying URL 'https://bioconductor.org/packages/3.18/data/annotation/src/contrib/HDO.db_0.99.1.tar.gz'
Content type 'application/gzip' length 1855560 bytes (1.8 MB)
==================================================
downloaded 1.8 MB
trying URL 'https://bioconductor.org/packages/3.18/bioc/src/contrib/GOSemSim_2.28.1.tar.gz'
Content type 'application/gzip' length 608119 bytes (593 KB)
==================================================
downloaded 593 KB
trying URL 'https://bioconductor.org/packages/3.18/bioc/src/contrib/DOSE_3.28.2.tar.gz'
Content type 'application/gzip' length 6807096 bytes (6.5 MB)
==================================================
downloaded 6.5 MB
trying URL 'https://cran.uni-muenster.de/src/contrib/ggpubr_0.6.0.tar.gz'
Content type 'application/x-gzip' length 1941659 bytes (1.9 MB)
==================================================
downloaded 1.9 MB
trying URL 'https://cran.uni-muenster.de/src/contrib/FactoMineR_2.11.tar.gz'
Content type 'application/x-gzip' length 2832656 bytes (2.7 MB)
==================================================
downloaded 2.7 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)
==================================================
downloaded 292 KB
trying URL 'https://bioconductor.org/packages/3.18/bioc/src/contrib/enrichplot_1.22.0.tar.gz'
Content type 'application/gzip' length 108617 bytes (106 KB)
==================================================
downloaded 106 KB
trying URL 'https://cran.uni-muenster.de/src/contrib/factoextra_1.0.7.tar.gz'
Content type 'application/x-gzip' length 1386480 bytes (1.3 MB)
==================================================
downloaded 1.3 MB
trying URL 'https://bioconductor.org/packages/3.18/bioc/src/contrib/clusterProfiler_4.10.1.tar.gz'
Content type 'application/gzip' length 624153 bytes (609 KB)
==================================================
downloaded 609 KB
* 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’
* installing *source* package ‘nloptr’ ...
** package ‘nloptr’ successfully unpacked and MD5 sums checked
** using staged installation
checking whether the C++ compiler works... yes
checking for C++ compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether the compiler supports GNU C++... yes
checking whether g++ -std=gnu++17 accepts -g... yes
checking for g++ -std=gnu++17 option to enable C++11 features... none needed
checking how to run the C++ preprocessor... g++ -std=gnu++17 -E
checking whether the compiler supports GNU C++... (cached) yes
checking whether g++ -std=gnu++17 accepts -g... (cached) yes
checking for g++ -std=gnu++17 option to enable C++11 features... (cached) none needed
checking for pkg-config... /usr/bin/pkg-config
checking if pkg-config knows NLopt... no
checking for cmake... no
------------------ CMAKE NOT FOUND --------------------
CMake was not found on the PATH. Please install CMake:
- sudo yum install cmake (Fedora/CentOS; inside a terminal)
- sudo apt install cmake (Debian/Ubuntu; inside a terminal).
- sudo pacman -S cmake (Arch Linux; inside a terminal).
- brew install --cask cmake (MacOS; inside a terminal with Homebrew)
- sudo port install cmake (MacOS; inside a terminal with MacPorts)
Alternatively install CMake from: <https://cmake.org/>
-------------------------------------------------------
ERROR: configuration failed for package ‘nloptr’
* removing ‘/home/omnipath/local/R/4.4-3.20/nloptr’
ERROR: dependency ‘S4Vectors’ is not available for package ‘IRanges’
* removing ‘/home/omnipath/local/R/4.4-3.20/IRanges’
ERROR: dependency ‘nloptr’ is not available for package ‘lme4’
* removing ‘/home/omnipath/local/R/4.4-3.20/lme4’
ERROR: dependencies ‘S4Vectors’, ‘IRanges’ are not available for package ‘GenomeInfoDb’
* removing ‘/home/omnipath/local/R/4.4-3.20/GenomeInfoDb’
ERROR: dependencies ‘S4Vectors’, ‘IRanges’ are not available for package ‘XVector’
* removing ‘/home/omnipath/local/R/4.4-3.20/XVector’
ERROR: dependency ‘lme4’ is not available for package ‘pbkrtest’
* removing ‘/home/omnipath/local/R/4.4-3.20/pbkrtest’
ERROR: dependencies ‘pbkrtest’, ‘lme4’ are not available for package ‘car’
* removing ‘/home/omnipath/local/R/4.4-3.20/car’
ERROR: dependencies ‘S4Vectors’, ‘IRanges’, ‘XVector’, ‘GenomeInfoDb’ are not available for package ‘Biostrings’
* removing ‘/home/omnipath/local/R/4.4-3.20/Biostrings’
ERROR: dependency ‘car’ is not available for package ‘rstatix’
* removing ‘/home/omnipath/local/R/4.4-3.20/rstatix’
ERROR: dependency ‘Biostrings’ is not available for package ‘KEGGREST’
* removing ‘/home/omnipath/local/R/4.4-3.20/KEGGREST’
ERROR: dependency ‘car’ is not available for package ‘FactoMineR’
* removing ‘/home/omnipath/local/R/4.4-3.20/FactoMineR’
ERROR: dependencies ‘IRanges’, ‘S4Vectors’, ‘KEGGREST’ are not available for package ‘AnnotationDbi’
* removing ‘/home/omnipath/local/R/4.4-3.20/AnnotationDbi’
ERROR: dependency ‘rstatix’ is not available for package ‘ggpubr’
* removing ‘/home/omnipath/local/R/4.4-3.20/ggpubr’
ERROR: dependency ‘AnnotationDbi’ is not available for package ‘annotate’
* removing ‘/home/omnipath/local/R/4.4-3.20/annotate’
ERROR: dependency ‘AnnotationDbi’ is not available for package ‘GO.db’
* removing ‘/home/omnipath/local/R/4.4-3.20/GO.db’
ERROR: dependency ‘AnnotationDbi’ is not available for package ‘HDO.db’
* removing ‘/home/omnipath/local/R/4.4-3.20/HDO.db’
ERROR: dependencies ‘FactoMineR’, ‘ggpubr’ are not available for package ‘factoextra’
* removing ‘/home/omnipath/local/R/4.4-3.20/factoextra’
ERROR: dependencies ‘AnnotationDbi’, ‘GO.db’ are not available for package ‘GOSemSim’
* removing ‘/home/omnipath/local/R/4.4-3.20/GOSemSim’
ERROR: dependencies ‘annotate’, ‘AnnotationDbi’ are not available for package ‘GSEABase’
* removing ‘/home/omnipath/local/R/4.4-3.20/GSEABase’
ERROR: dependencies ‘AnnotationDbi’, ‘HDO.db’, ‘GOSemSim’ are not available for package ‘DOSE’
* removing ‘/home/omnipath/local/R/4.4-3.20/DOSE’
ERROR: dependencies ‘DOSE’, ‘GOSemSim’ are not available for package ‘enrichplot’
* removing ‘/home/omnipath/local/R/4.4-3.20/enrichplot’
ERROR: dependencies ‘AnnotationDbi’, ‘DOSE’, ‘enrichplot’, ‘GO.db’, ‘GOSemSim’ are not available for package ‘clusterProfiler’
* removing ‘/home/omnipath/local/R/4.4-3.20/clusterProfiler’
The downloaded source packages are in
‘/tmp/RtmpAoRuiU/downloaded_packages’
Downloading GitHub repo saezlab/OmnipathR@devel
── R CMD build ─────────────────────────────────────────────────────────────────
* checking for file ‘/tmp/RtmpAoRuiU/remotes327d1b10f525cc/saezlab-OmnipathR-872caf9/DESCRIPTION’ ... OK
* preparing ‘OmnipathR’:
* checking DESCRIPTION meta-information ... OK
* checking for LF line-endings in source and make files and shell scripts
* checking for empty or unneeded directories
Removed empty directory ‘OmnipathR/.github’
* looking to see if a ‘data/datalist’ file should be added
* building ‘OmnipathR_3.15.2.tar.gz’
* installing *source* package ‘OmnipathR’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
[2025-01-28 13:45:15] [INFO] [OmnipathR] Setting up new cache directory `/home/omnipath/.cache/OmnipathR`.
[2025-01-28 13:45:15] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-28 13:45:15] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-28 13:45:15] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`.
[2025-01-28 13:45:15] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2025-01-28 13:45:15] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`.
[2025-01-28 13:45:15] [TRACE] [OmnipathR] Contains 1 files.
[2025-01-28 13:45:15] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2025-01-28 13:45:15] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-28 13:45:15] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-28 13:45:15] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`.
[2025-01-28 13:45:15] [TRACE] [OmnipathR] Pandoc version: `3.1.3`.
[2025-01-28 13:45:15] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.20/00LOCK-OmnipathR/00new/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-01-28 13:45:15] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-28 13:45:15] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.20/00LOCK-OmnipathR/00new/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-01-28 13:45:15] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-28 13:45:15] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.20/00LOCK-OmnipathR/00new/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-01-28 13:45:15] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-28 13:45:15] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.20/00LOCK-OmnipathR/00new/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-01-28 13:45:15] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-28 13:45:15] [TRACE] [OmnipathR] Cache locked: FALSE
** testing if installed package can be loaded from final location
[2025-01-28 13:45:16] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-28 13:45:16] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-28 13:45:16] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`.
[2025-01-28 13:45:16] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2025-01-28 13:45:16] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`.
[2025-01-28 13:45:16] [TRACE] [OmnipathR] Contains 1 files.
[2025-01-28 13:45:16] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2025-01-28 13:45:16] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-28 13:45:16] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-28 13:45:16] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`.
[2025-01-28 13:45:16] [TRACE] [OmnipathR] Pandoc version: `3.1.3`.
[2025-01-28 13:45:16] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.20/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-01-28 13:45:16] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-28 13:45:16] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.20/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-01-28 13:45:16] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-28 13:45:16] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.20/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-01-28 13:45:16] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-28 13:45:16] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.20/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-01-28 13:45:16] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-28 13:45:16] [TRACE] [OmnipathR] Cache locked: FALSE
** testing if installed package keeps a record of temporary installation path
* DONE (OmnipathR)
Downloading GitHub repo saezlab/cosmosR@HEAD
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 9 packages ahead of CRAN: zlibbioc, GenomeInfoDbData, Biobase, BiocGenerics, graph, decoupleR, bcellViper, 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)
==================================================
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)
==================================================
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)
==================================================
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/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/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/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/annotate_1.80.0.tar.gz'
Content type 'application/gzip' length 1497628 bytes (1.4 MB)
==================================================
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)
==================================================
downloaded 292 KB
* 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 ‘GenomeInfoDb’
* removing ‘/home/omnipath/local/R/4.4-3.20/GenomeInfoDb’
ERROR: dependencies ‘S4Vectors’, ‘IRanges’ are not available for package ‘XVector’
* removing ‘/home/omnipath/local/R/4.4-3.20/XVector’
ERROR: dependencies ‘S4Vectors’, ‘IRanges’, ‘XVector’, ‘GenomeInfoDb’ are not available for package ‘Biostrings’
* removing ‘/home/omnipath/local/R/4.4-3.20/Biostrings’
ERROR: dependency ‘Biostrings’ is not available for package ‘KEGGREST’
* removing ‘/home/omnipath/local/R/4.4-3.20/KEGGREST’
ERROR: dependencies ‘IRanges’, ‘S4Vectors’, ‘KEGGREST’ are not available for package ‘AnnotationDbi’
* removing ‘/home/omnipath/local/R/4.4-3.20/AnnotationDbi’
ERROR: dependency ‘AnnotationDbi’ is not available for package ‘annotate’
* removing ‘/home/omnipath/local/R/4.4-3.20/annotate’
ERROR: dependencies ‘annotate’, ‘AnnotationDbi’ are not available for package ‘GSEABase’
* removing ‘/home/omnipath/local/R/4.4-3.20/GSEABase’
The downloaded source packages are in
‘/tmp/RtmpAoRuiU/downloaded_packages’
── R CMD build ─────────────────────────────────────────────────────────────────
* checking for file ‘/tmp/RtmpAoRuiU/remotes327d1b8a6ae46/saezlab-cosmosR-81d1a7f/DESCRIPTION’ ... OK
* preparing ‘cosmosR’:
* checking DESCRIPTION meta-information ... OK
* checking for LF line-endings in source and make files and shell scripts
* checking for empty or unneeded directories
* looking to see if a ‘data/datalist’ file should be added
* building ‘cosmosR_1.9.1.tar.gz’
Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L, :
storing paths of more than 100 bytes is not portable:
‘cosmosR/vignettes/net_compr_MOON_files/figure-markdown_strict/extract_subnetwork_from_scored_MOON_network_1.png’
ERROR: dependency ‘GSEABase’ is not available for package ‘cosmosR’
* removing ‘/home/omnipath/local/R/4.4-3.20/cosmosR’
Downloading git repo https://git.bioconductor.org/packages/limma.git
'/usr/bin/git' clone --depth 1 --no-hardlinks https://git.bioconductor.org/packages/limma.git /tmp/RtmpAoRuiU/file327d1b6625dc2a
Cloning into '/tmp/RtmpAoRuiU/file327d1b6625dc2a'...
── R CMD build ─────────────────────────────────────────────────────────────────
* checking for file ‘/tmp/RtmpAoRuiU/file327d1b6625dc2a/DESCRIPTION’ ... OK
* preparing ‘limma’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* checking for LF line-endings in source and make files and shell scripts
* checking for empty or unneeded directories
* building ‘limma_3.63.3.tar.gz’
* installing *source* package ‘limma’ ...
** 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 init.c -o init.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 normexp.c -o normexp.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 weighted_lowess.c -o weighted_lowess.o
gcc -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -o limma.so init.o normexp.o weighted_lowess.o -L/usr/lib/R/lib -lR
installing to /home/omnipath/local/R/4.4-3.20/00LOCK-limma/00new/limma/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (limma)
There were 43 warnings (use warnings() to see them)
[ Finished: 2025-01-28 13:45:49 CET ]