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paola.lecca
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@paolalecca-11241
Last seen 8.7 years ago
On an ubuntu server, where ubuntu 14.04 LTS and R 3.3.1 are installed, I am not able to install the package
BSgenome.Mmusculus.UCSC.mm10
as I get the following error message:
Warning in .seqlengths_TwoBitFile(x) : End of file reading 4 bytes
Error : .onLoad failed in loadNamespace() for 'BSgenome.Mmusculus.UCSC.mm10', details:
call: .seqlengths_TwoBitFile(x)
error: UCSC library operation failed
Error: loading failed
Execution halted
ERROR: loading failed
* removing â/home/****/R-3.3.1/R-3.3.1/library/BSgenome.Mmusculus.UCSC.mm10â
The downloaded source packages are in
â/tmp/RtmpibMbXD/downloaded_packagesâ
Updating HTML index of packages in '.Library'
Making 'packages.html' ... done
Warning message:
In install.packages(pkgs = doing, lib = lib, ...) :
installation of package âBSgenome.Mmusculus.UCSC.mm10â had non-zero exit status
I would appreciate your help in fixing this issue.
Thanks in advance,
Paola.
Dear Martin,
thanks for your response. Here the results of the updates check:
library(BioInstaller)
Bioconductor version 3.4 (BiocInstaller 1.23.6), ?biocLite for help
biocValid()
Built ReposVer
AnnotationDbi "3.3.1" "1.35.4"
Biobase "3.3.1" "2.33.0"
BiocGenerics "3.3.1" "0.19.2"
BiocParallel "3.3.1" "1.7.5"
biomaRt "3.3.1" "2.29.2"
Biostrings "3.3.1" "2.41.4"
BSgenome "3.3.1" "1.41.2"
GenomeInfoDb "3.3.1" "1.9.4"
GenomicAlignments "3.3.1" "1.9.6"
GenomicFeatures "3.3.1" "1.25.16"
GenomicRanges "3.3.1" "1.25.93"
graph "3.3.1" "1.51.0"
IRanges "3.3.1" "2.7.12"
OrganismDbi "3.3.1" "1.15.1"
RBGL "3.3.1" "1.49.1"
Rsamtools "3.3.1" "1.25.1"
rtracklayer "3.3.1" "1.33.11"
S4Vectors "3.3.1" "0.11.10"
SummarizedExperiment "3.3.1" "1.3.81"
XVector "3.3.1" "0.13.7"
zlibbioc "3.3.1" "1.19.0"
Some other packages were outdated, but when I tried to update them I got this message:
Error in readRDS(nsInfoFilePath) : error reading from connection
Error: loading failed
Execution halted
ERROR: loading failed
* removing â/home/***/R-3.3.1/R-3.3.1/library/BiocGenericsâ
* restoring previous â/home/*****/R-3.3.1/R-3.3.1/library/BiocGenericsâ
Your code snippet is not enough to fully diagnose the problem. Start a new R session with no additional packages attached (e.g.,
R --vanilla), and report the full output ofBiocInstaller::biocLite("BiocGenerics")produce?