[Bioc-devel] Unable to install "msdata" package in current BioC 3.13 docker
Martin Morgan
mtmorg@n@b|oc @end|ng |rom gm@||@com
Thu Nov 5 17:56:41 CET 2020
...it would be useful to know whether 'timeout' settings, e.g., options(timeout = 180) improves things. I've introduced pull request on BiocManager to do this, at
https://github.com/Bioconductor/BiocManager/pull/81
Martin
On 11/5/20, 11:04 AM, "Martin Morgan" <mtmorgan.bioc using gmail.com> wrote:
I noticed in Johannes' message
> In addition: Warning messages:
...
> 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
I looked at ?download.file and saw
The timeout for many parts of the transfer can be set by the
option 'timeout' which defaults to 60 seconds. This is often
which goes on to say...
insufficient for downloads of large files (hundreds of MB or more)
and so should be increased when 'download.file' is used in
packages to do so.
so I'll investigate more and see if we can't get a more liberal default.
Martin
On 11/5/20, 10:06 AM, "Bioc-devel on behalf of Rainer Johannes" <bioc-devel-bounces using r-project.org on behalf of Johannes.Rainer using eurac.edu> wrote:
Thanks Mike!
that did the trick
cheers, jo
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
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> On 5 Nov 2020, at 14:02, Mike Smith <grimbough using gmail.com> wrote:
>
> 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.
>
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