On Nov 5, 2020, at 7:21 AM, Rainer Johannes <Johannes.Rainer at 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:
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 at eurac.edu
github: jorainer
twitter: jo_rainer
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