[Bioc-devel] Unable to install "msdata" package in current BioC 3.13 docker

Rainer Johannes Joh@nne@@R@|ner @end|ng |rom eur@c@edu
Thu Nov 5 13:21:14 CET 2020

Dear all,

I'm unable to install the "msdata" package for the current BioC 3.13 release. I keep getting the following error:

> BiocManager::install("msdata")
Bioconductor version 3.13 (BiocManager 1.30.10), R Under development (unstable)
  (2020-10-24 r79367)
Installing package(s) 'msdata'
trying URL 'https://bioconductor.org/packages/3.13/data/experiment/src/contrib/msdata_0.31.0.tar.gz'
Content type 'application/x-gzip' length 446179202 bytes (425.5 MB)
downloaded 274.7 MB

Error in download.file(url, destfile, method, mode = "wb", ...) : 
  download from 'https://bioconductor.org/packages/3.13/data/experiment/src/contrib/msdata_0.31.0.tar.gz' failed
In addition: Warning messages:
1: In download.file(url, destfile, method, mode = "wb", ...) :
  downloaded length 288082900 != reported length 446179202
2: In download.file(url, destfile, method, mode = "wb", ...) :
  URL 'https://bioconductor.org/packages/3.13/data/experiment/src/contrib/msdata_0.31.0.tar.gz': Timeout of 60 seconds was reached
Warning in download.packages(pkgs, destdir = tmpd, available = available,  :
  download of package ‘msdata’ failed
Installation path not writeable, unable to update packages: codetools

I'm using the docker image (bioconductor/bioconducto_docker:devel), sessionInfo below - so this error should be reproducible

thanks for any hints/suggestion how I could solve this



> sessionInfo()
R Under development (unstable) (2020-10-24 r79367)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 20.04 LTS

Matrix products: default
BLAS/LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.8.so

 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=C             
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] BiocManager_1.30.10

loaded via a namespace (and not attached):
[1] compiler_4.1.0 tools_4.1.0   

Johannes Rainer, PhD
Eurac Research

Institute for Biomedicine
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email: johannes.rainer using eurac.edu
github: jorainer
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