[Bioc-devel] BiocStyle on windows with spaces in path names

[Henrik Bengtsson]

Maybe you could use

\RequirePackage{Bioconductor}

and then set the TEXINPUTS environment variable via Sys.setenv().
Internally tools::texi2dvi() is used that that "listens to" TEXINPUTS.

Just FYI: I use this trick in
https://github.com/HenrikBengtsson/R.rsp/blob/master/R/compileLaTeX.R
to set/fix/update TEXINPUTS temporarily, but for somewhat different
reasons.  There you also see take extra precautions to drop duplicates
etc.

/Henrik

On Mon, Oct 6, 2014 at 3:21 PM, Martin Morgan <mtmorgan at fhcrc.org> wrote:
> On 10/6/2014 2:44 PM, James W. MacDonald wrote:
>>
>> Hi Steffen,
>>
>> It looks like you are running R as an administrator, rather than as a
>> regular user (or you are on something really old like XP). By default R
>> should try to create a user-level library directory in your Documents
>> folder. It is probably not such a good idea to run R as administrator if
>> you are on a more modern version of Windows.
>>
>> Note that system.file (which BiocStyle::latex()  calls to find the package
>> path) will in the case of base packages use .Library to construct the
>> path:
>>
>>> system.file()
>>
>> [1] "C:/PROGRA~1/R/R-31~1.0/library/base"
>>
>> Which being an 8.1 path, will work for MikTex. But if I run as an
>
>
> It would be great for BiocStyle to return a functional path under all
> circumstances.
>
> I'm not sure that MikTex handles ~ in paths? or at least not the way
> BiocStyle currently uses this, as
>
> \RequirePackage{C:/PROGRA~1/R/R-31~1.0/library/BiocStyle/sty/Bioconductor}
>
> When I try to mock this up it looks like the ~ are being processed as latex
> -- there is a latex file not found error with the ~ replaced by
> \unhbox\voidb at x \penalty \@m \{}.
>
> I thought there might be some hints with the Sweave sty file use by all
> vignettes. This is found with
>
>         styfile <- file.path(R.home("share"), "texmf", "tex", "latex",
> "Sweave")
>         if (.Platform$OS.type == "windows")
>             styfile <- chartr("\\", "/", styfile)
>         if (length(grep(" ", styfile)))
>             warning(gettextf("path to %s contains spaces,\n",
> sQuote(styfile)),
>                     gettext("this may cause problems when running LaTeX"),
>                     domain = NA)
>
> but R.home() (eventually find.package()) uses .Library for the special case
> when the path to a single package from the base distribution is being sought
>
>> find.package("stats")
> [1] "C:/PROGRA~1/R/R-31~1.1/library/stats"
>> find.package(c("stats", "stats"))[1]
> [1] "C:/Program Files/R/R-3.1.1/library/stats"
>
> So I'm not sure how to get at a working path to Bioconductor.sty in the face
> of spaces in the installed path name (the warning hints that R has similar
> problems).
>
>
>> administrator and put BiocStyle in my Program Files library, I get
>>
>>> latex()
>>
>> \RequirePackage{C:/Program
>> Files/R/R-3.1.0/library/BiocStyle/sty/Bioconductor}
>>
>> \AtBeginDocument{\bibliographystyle{C:/Program
>> Files/R/R-3.1.0/library/BiocStyle/sty/unsrturl}}
>>
>> Which of course will fail. So the best option is to stop running R as an
>> administrator, and install packages in your Documents folder in a path
>> with
>> no spaces.
>>
>> Best,
>>
>> Jim
>>
>>
>>
>> On Mon, Oct 6, 2014 at 4:34 PM, Neumann, Steffen <sneumann at ipb-halle.de>
>> wrote:
>>
>>> Hi,
>>>
>>> sometimes I am forced to R CMD check packages on windows,
>>> and my problem is that both the system-wide library and
>>> the personal library with BiocStyle contain spaces, so that
>>> BiocStyle::latex() results in:
>>> \RequirePackage{C:/Program
>>> Files/R/R-3.1.0/library/BiocStyle/sty/Bioconductor}
>>>
>>> which causes MiKTeX to fail with
>>> ! LaTeX Error: File
>>> `C:/ProgramFiles/R/R-3.1.0/library/BiocStyle/sty/Bioconductor.sty' not
>>> found.
>>> (This is with BiocStyles-1.3.15)
>>>
>>> What is the recommended solution here ? Installing R to a non-standard
>>> location ?
>>> Use texlive instead of miktex (does that make a difference ?) Or
>>> something
>>> else ?
>>>
>>> Yours,
>>> Steffen
>>>
>>>
>>>
>>>
>>>
>>> _______________________________________________
>>> Bioc-devel at r-project.org mailing list
>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>>
>>
>>
>>
>
>
> --
> Dr. Martin Morgan, PhD
> Fred Hutchinson Cancer Research Center
> 1100 Fairview Ave. N.
> PO Box 19024 Seattle, WA 98109
>
>
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