From mtmorgan at fhcrc.org  Tue Mar 22 04:07:45 2011
From: mtmorgan at fhcrc.org (Martin Morgan)
Date: Mon, 21 Mar 2011 20:07:45 -0700
Subject: [Rd] R_HOME path getting munged in inst/doc/Makefile on Windows
In-Reply-To: <B6C2277E-8D69-491C-87B4-C8EF26C04D7D@r-project.org>
References: <AANLkTimOzb6Y4biwP9dCaT6goxyjXB7rgLhsnv3SMxjA@mail.gmail.com>
	<B6C2277E-8D69-491C-87B4-C8EF26C04D7D@r-project.org>
Message-ID: <4D881281.309@fhcrc.org>

On 03/21/2011 07:22 PM, Simon Urbanek wrote:
>
> On Mar 21, 2011, at 9:07 PM, Dan Tenenbaum wrote:
>
>> Hello,
>>
>> I have come across two separate packages that have a Makefile in inst/doc
>> which use the R_HOME variable.
>>
>> In both cases, the path to R_HOME gets munged in such a way that commands
>> that include R_HOME fail on Windows:
>>
>> For example, one Makefile, for the xmapcore package (
>> https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/xmapcore/username/password:
>> readonly) has this:
>>
>> R=${R_HOME}/bin/R
>> SUITE=../cookbook/delia.R
>> [...]
>> ${R} --vanilla --verbose<  ${SUITE}
>>
>> the output of trying to build this package includes:
>>
>> * creating vignettes ... ERROR
>> E:\biocbld\BBS-2~1.8-B\R/bin/R --vanilla --verbose<  ../cookbook/delia.R
>> E:biocbldBBS-2~1.8-BR/bin/R: not found
>> make: *** [pdf] Error 127
>> Error in tools::buildVignettes(dir = ".") : running 'make' failed
>> Execution halted
>>
>> It seems R_HOME is not getting resolved to a valid path. That's strange
>> because R CMD echo shows the right thing:
>>
>> E:\sandbox>\biocbld\bbs-2.8-bioc\R\bin\R CMD echo %R_HOME%
>> e:/biocbld/bbs-2.8-bioc/R
>>
>> That's a nice path with all forward slashes and no funny 8.3 paths with
>> tildes.  But it looks like when R_HOME is invoked in a Makefile, the
>> resulting path has a mix of forward and backslashes,
>
> Nope, at least not in R from CRAN:
>
> Makevars:
> all:
> 	echo R_HOME: $(R_HOME)
>
> [...]
> echo R_HOME: c:/PROGRA~1/R/R-212~1.2
> R_HOME: c:/PROGRA~1/R/R-212~1.2
>
> But I see that you have custom rhome setting (BBS...) so changes are that is the culprit - the rhome for that R build is set incorrectly to contain backslashes.

Not sure about the Makefile, but see

https://stat.ethz.ch/pipermail/r-devel/2011-March/060260.html

also on my own machine

Z:\> R CMD INSTALL Biobase
* installing to library 'C:\Users\User\Documents/R/win-library/2.13'
* installing *source* package 'Biobase' ...
...

** testing if installed package can be loaded
Error: '\U' used without hex digits in character string starting "C:\U"
Execution halted
ERROR: loading failed
* removing 'C:\Users\User\Documents/R/win-library/2.13/Biobase'
* restoring previous 'C:\Users\User\Documents/R/win-library/2.13/Rsamtools'

whereas under 2.12

Z:\>R CMD INSTALL Biobase
* installing to library 'C:\Users\User\Documents/R/win-library/2.12'
* installing *source* package 'Biobase' ...

and everything is fine.

Z:\> R --version
R version 2.13.0 alpha (2011-03-17 r54849)
Copyright (C) 2011 The R Foundation for Statistical Computing
ISBN 3-900051-07-0

>
> Cheers,
> Simon
>
>
>
>
>> and gets translated
>> into 8.3 style, and the resulting path is not valid for finding R
>> executables.
>>
>> Note that R_HOME is defined within R; I don't also have it defined at the
>> shell level:
>>
>> E:\sandbox>echo %R_HOME%
>> %R_HOME%
>>
>> Any ideas?
>> Thanks,
>> Dan
>>
>>> sessionInfo()
>> R version 2.13.0 alpha (2011-03-18 r54865)
>> Platform: i386-pc-mingw32/i386 (32-bit)
>>
>> locale:
>> [1] LC_COLLATE=English_United States.1252
>> [2] LC_CTYPE=English_United States.1252
>> [3] LC_MONETARY=English_United States.1252
>> [4] LC_NUMERIC=C
>> [5] LC_TIME=English_United States.1252
>>
>> attached base packages:
>> [1] stats     graphics  grDevices utils     datasets  methods   base
>>
>> 	[[alternative HTML version deleted]]
>>
>> ______________________________________________
>> R-devel at r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-devel
>>
>>
>
> ______________________________________________
> R-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel


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[Rd] R_HOME path getting munged in inst/doc/Makefile on Windows
Martin Morgan