[Rd] Possible issue with R-tools on Windows
Uwe Ligges
ligges at statistik.tu-dortmund.de
Sun Mar 12 12:02:12 CET 2017
Hmmm, you may know winbuilder: It has R not installed oin drive C: and
works well. Even with R installed on a network share I can easily
install packages.
using R-devel binary in, e.g. for 64 bit: in d:/RCompile/recent/R/bin/x64
working directory: d:/library-devel
specified library: c:/tmp
> install.packages("GO.db", lib="c:/tmp")
installing the source package ‘GO.db’
trying URL
'https://bioconductor.org/packages/3.5/data/annotation/src/contrib/GO.db_3.4.0.tar.gz'
Content type 'application/x-gzip' length 31897756 bytes (30.4 MB)
downloaded 30.4 MB
* installing *source* package 'GO.db' ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
*** arch - i386
*** arch - x64
* DONE (GO.db)
The downloaded source packages are in
‘d:\temp\RtmpKaYI2t\downloaded_packages’
So we really need the full log.
Can you please run the installation from the OS shell, i.e. something like:
R CMD INSTALL --library=c:/tmp GO.db_3.4.0.tar.gz
and send us the install.log
Best,
Uwe Ligges
On 11.03.2017 18:17, Robert Baer wrote:
> This is a bit of a cross-post but I've encountered what appears to be a
> parsing error with RTools on Windows in a couple of different contexts
> on Widows when R is installed on a secondary drive to avoid using
> precious space on my c:/ solid state drive.
>
> This type of apparent parsing error has has occurred several times
> previously when install source code from GitHub, and most recently when
> installing Bioconductor code. It occurred that this list might have
> input directed at RTools on Windows, if this is indeed my problem
>
> Here's the full example of my most recent encounter posted to
> bioconductor: https://support.bioconductor.org/p/93731/
>
> In brief the parsing seems to break in the space in the path name:
>
> The downloaded source packages are in
> ‘C:\Users\Rob Baer\AppData\Local\Temp\RtmpagJM0a\downloaded_packages’
> Warning messages:
> 1: running command '"E:/Program Files/R/R-3.3.3/bin/x64/R" CMD INSTALL
> -l "C:\Users\Rob Baer\R\win-library\3.3"
> C:\Users\ROBBAE~1\AppData\Local\Temp\RtmpagJM0a/downloaded_packages/GO.db_3.4.0.tar.gz'
> had status 1
> 2: In install.packages(update[instlib == l, "Package"], l, repos =
> repos, :
> installation of package ‘GO.db’ had non-zero exit status
>
> Is there something going on with my RTools installation I should
> upgrade? My apologies if this is too off-topic for this list.
>
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