Possible issue with R-tools on Windows

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Possible issue with R-tools on Windows

Robert Baer
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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Re: Possible issue with R-tools on Windows

Uwe Ligges-3
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.
>
> ______________________________________________
> [hidden email] mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel

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Re: Possible issue with R-tools on Windows - Amend subject to RTerm issue

Robert Baer
Because my response is a little long and summarizes original thread is
at bottom.

Okay, I tried to implement your test (and the package is installed).  My
discovery is that it was RTerm and not
RTools giving me a problem.

Summary: RTerm starts fine if installed on C: even if there is a space
in the path.
RTerm starts fine on E: drive if there is no space in the path, but
fails to start if there is a space in the path.
Because of the R versions I happened to have, this was checked using a
combination of R-3.3.1, R-3.3.2, and R-3.3.3.
I know for surethat RTerm for R-3.3.2 and R-3.3.3 fails to start from
the command prompt in E:/prgram Files/R/R-3.3.x/bin
suggesting that R-dev should be tested.

For completeness here is what happened in a couple of circumstances:

Windows 10
I tried starting RTerm for various R versions in the following install
locations:
C:/program files/R/R-3.3.1/bin - Works
E:/Program Files/R/R-3.3.3/bin - Fails
E:/Program/R/R-3.3.3/bin/ - Works
C:/Program Files/R/R-3.3.1/bin - Works

Microsoft Windows [Version 10.0.14393]
(c) 2016 Microsoft Corporation. All rights reserved.

=====================================================================================
RTerm will start (at least an older version) in a path containing spaces ...

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

   Natural language support but running in an English locale

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

 > q()
Save workspace image? [y/n/c]: n
====================================================================================
Current RTerm won't start if on E: dirve in a path containing spaces ...
C:\Program Files\R\R-3.3.1\bin>e:

E:\Program Files\R\R-3.3.3\bin>R
'E:\Program' is not recognized as an internal or external command,
operable program or batch file.

E:\Program Files\R\R-3.3.3\bin>dir
  Volume in drive E is Baer_HardDrive
  Volume Serial Number is F890-9E98

  Directory of E:\Program Files\R\R-3.3.3\bin

03/11/2017  10:57 AM    <DIR>          .
03/11/2017  10:57 AM    <DIR>          ..
03/06/2017  04:00 PM             9,712 config.sh
03/11/2017  10:57 AM    <DIR>          i386
03/06/2017  04:07 PM            88,576 R.exe
03/06/2017  04:07 PM            88,576 Rscript.exe
03/11/2017  10:57 AM    <DIR>          x64
                3 File(s)        186,864 bytes
                4 Dir(s)  262,685,499,392 bytes free

E:\Program Files\R\R-3.3.3\bin>

=============================================================================
And finally current RTerm works on C: in a path with spaces ...


c:\Program Files\R\R-3.3.3\bin>R

R version 3.3.3 (2017-03-06) -- "Another Canoe"
Copyright (C) 2017 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

   Natural language support but running in an English locale

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.


On 3/12/2017 6:02 AM, Uwe Ligges wrote:

> 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.
>>
>> ______________________________________________
>> [hidden email] mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-devel

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