Re: [Rd] R_HOME path getting munged in inst/doc/Makefile on Windows

From: Dan Tenenbaum <dtenenba_at_fhcrc.org>
Date: Mon, 21 Mar 2011 20:05:44 -0700

On Mon, Mar 21, 2011 at 7:22 PM, Simon Urbanek <simon.urbanek_at_r-project.org>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:
>
>
My R is from CRAN (built from source, though).

> 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.
>

Thanks...can you give me a tip as to how R_HOME should be set when building from source?
I didn't set it manually.

I admit to not knowing my way around Makevars....can you tell me exactly what you did, where you put Makevars (or should it be Makevars.win?) and what is omitted by [...], in other words, what command spits out R_HOME? I should RTFM, and I am, but haven't figured it out yet...

One additional piece of information: I went to inst\doc and ran "R CMD make" and it output the correct R_HOME. So maybe it's something about R CMD build that gets it wrong?

Thanks
Dan

>
> 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
> >
> >
>
>

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