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.
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]]
>
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>
>
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