problems in installing BSgenome.Mmusculus.UCSC.mm10
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@paolalecca-11241
Last seen 7.6 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.

software error bioconductor • 1.7k views
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@martin-morgan-1513
Last seen 6 weeks ago
United States

Are your software packages up-to-date

BiocInstaller::biocValid()

?

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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Some other packages were outdated, but when I tried to update them I got this message: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

 

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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 of

BiocInstaller::biocLite("BiocGenerics")

produce?

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