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

[Nitesh Turaga]

Hi Johannes,

I’ll take a look at this and get back to you.

Best,

Nitesh 

> On Nov 5, 2020, at 7:21 AM, 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
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> 
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