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

[Mike Smith]

Hi Jo,

There was some discussion of a similar issue on the support forum at
https://support.bioconductor.org/p/p132470/

The suggestion there was to try changing  R's download.file.method option
e.g. options(download.file.method = "curl")

Best,
Mike

On Thu, 5 Nov 2020 at 13:21, Rainer Johannes <Johannes.Rainer using eurac.edu>
wrote:

> 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
>
> jo
>
>
> sessionInfo:
>
> > 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
>
> locale:
>  [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
> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=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
> Via Galvani 31, I-39100 Bolzano, Italy
> M +39 327 4075490
> T +39 0471 055 491
> email: johannes.rainer using eurac.edu
> github: jorainer
> twitter: jo_rainer
>
> Legal Seat
> Viale Druso 1, I-39100 Bolzano, Italy
> www.eurac.edu
>
> This transmission is intended only for the use of the addressee and may
> contain confidential or legally privileged information.
> If you receive this transmission by error, please notify the author
> immediately by mail and delete all copies of this transmission and any
> attachments.
> Any use or dissemination of this commu­nication is strictly prohibited by
> the „Privacy-Code“, D.Lgs. 196/2003, and may lead to penal prosecution and
> liability for damages.
>
> _______________________________________________
> Bioc-devel using r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>

	[[alternative HTML version deleted]]