Je viens de tester l’installation du package Bioconductor recount sur le serveur RStudio et j’ai un message d’erreur (ci-dessous).
-
Serait-il possible de l’installer par défaut pour tous les usagers (le package donne accès à la DB Recount2, qui est assez pratique pour obtenir rapidement des données RNA-seq humaines).
-
Comprenez-vous pourquoi il m’envoie ces messages d’erreur ? Je croyais qu’il allait tout bonnement installer Recount2 dans ma librairie perso .
Merci
Jacques
s’ does not exist and so has been treated as a topic
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning: no function found corresponding to methods exports from ‘XVector’ for: ‘concatenateObjects’
- DONE (GenomicRanges)
- installing source package ‘Biostrings’ …
** libs
Error: package ‘XVector’ 0.20.0 was found, but >= 0.21.4 is required by ‘Biostrings’ - removing ‘/shared/mfs/data/home/jvanhelden/R/x86_64-redhat-linux-gnu-library/3.5/Biostrings’
installation of package ‘Biostrings’ had non-zero exit statusERROR: dependency ‘Biostrings’ is not available for package ‘Rsamtools’ - removing ‘/shared/mfs/data/home/jvanhelden/R/x86_64-redhat-linux-gnu-library/3.5/Rsamtools’
installation of package ‘Rsamtools’ had non-zero exit statusERROR: dependencies ‘Biostrings’, ‘Rsamtools’ are not available for package ‘GenomicAlignments’ - removing ‘/shared/mfs/data/home/jvanhelden/R/x86_64-redhat-linux-gnu-library/3.5/GenomicAlignments’
installation of package ‘GenomicAlignments’ had non-zero exit statusERROR: dependencies ‘Biostrings’, ‘Rsamtools’, ‘GenomicAlignments’ are not available for package ‘rtracklayer’ - removing ‘/shared/mfs/data/home/jvanhelden/R/x86_64-redhat-linux-gnu-library/3.5/rtracklayer’
installation of package ‘rtracklayer’ had non-zero exit statusERROR: dependencies ‘Biostrings’, ‘rtracklayer’, ‘Rsamtools’ are not available for package ‘BSgenome’ - removing ‘/shared/mfs/data/home/jvanhelden/R/x86_64-redhat-linux-gnu-library/3.5/BSgenome’
installation of package ‘BSgenome’ had non-zero exit statusERROR: dependencies ‘Biostrings’, ‘rtracklayer’ are not available for package ‘GenomicFeatures’ - removing ‘/shared/mfs/data/home/jvanhelden/R/x86_64-redhat-linux-gnu-library/3.5/GenomicFeatures’
installation of package ‘GenomicFeatures’ had non-zero exit statusERROR: dependencies ‘Rsamtools’, ‘Biostrings’, ‘rtracklayer’, ‘BSgenome’, ‘GenomicFeatures’ are not available for package ‘VariantAnnotation’ - removing ‘/shared/mfs/data/home/jvanhelden/R/x86_64-redhat-linux-gnu-library/3.5/VariantAnnotation’
installation of package ‘VariantAnnotation’ had non-zero exit statusERROR: dependency ‘GenomicFeatures’ is not available for package ‘bumphunter’ - removing ‘/shared/mfs/data/home/jvanhelden/R/x86_64-redhat-linux-gnu-library/3.5/bumphunter’
installation of package ‘bumphunter’ had non-zero exit statusERROR: dependencies ‘Rsamtools’, ‘rtracklayer’, ‘GenomicAlignments’, ‘VariantAnnotation’ are not available for package ‘GenomicFiles’ - removing ‘/shared/mfs/data/home/jvanhelden/R/x86_64-redhat-linux-gnu-library/3.5/GenomicFiles’
installation of package ‘GenomicFiles’ had non-zero exit statusERROR: dependencies ‘bumphunter’, ‘GenomicAlignments’, ‘GenomicFeatures’, ‘GenomicFiles’, ‘Rsamtools’, ‘rtracklayer’ are not available for package ‘derfinder’ - removing ‘/shared/mfs/data/home/jvanhelden/R/x86_64-redhat-linux-gnu-library/3.5/derfinder’
installation of package ‘derfinder’ had non-zero exit statusERROR: dependencies ‘derfinder’, ‘rtracklayer’ are not available for package ‘recount’ - removing ‘/shared/mfs/data/home/jvanhelden/R/x86_64-redhat-linux-gnu-library/3.5/recount’
installation of package ‘recount’ had non-zero exit status
The downloaded source packages are in
‘/tmp/RtmpLPtZea/downloaded_packages’
installation path not writeable, unable to update packages: annotate, AnnotationDbi, Biobase, BiocGenerics,
BiocInstaller, BiocParallel, class, codetools, DelayedArray, DESeq2, evaluate, foreign, genefilter,
geneplotter, GenomeInfoDb, GenomeInfoDbData, GenomicRanges, igraph, IRanges, lattice, lme4, MASS, Matrix,
mgcv, modelr, MultiAssayExperiment, rhdf5, Rhdf5lib, S4Vectors, stringi, stringr, SummarizedExperiment,
survival, XML, XVector, zlibbioc