[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 
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

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

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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