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

Henrik Bengtsson hb at biostat.ucsf.edu
Tue Oct 7 04:03:31 CEST 2014 

On Mon, Oct 6, 2014 at 6:48 PM, Henrik Bengtsson <hb at biostat.ucsf.edu> wrote:
> On Mon, Oct 6, 2014 at 5:33 PM, Martin Morgan <mtmorgan at fhcrc.org> wrote:
>> On 10/06/2014 04:52 PM, Henrik Bengtsson wrote:
>>>
>>> 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.
>>
>>
>> Thanks; I think that would require 'us' to run texi2dvi (otherwise the
>> environment variable isn't seen by texi2dvi) and that sounds like writing a
>> Sweave driver, or worse. latex() could be modified to be passed a flag or
>> path indicating a TEXINPUTS directory where bioconductor.sty could be found,
>> but that doesn't sound like a robust strategy (e.g., because the
>> specially-installed sty file becomes out of sync with the version in the
>> package). Hopefully there is a simpler solution.
>
> I haven't tried, but it's possible that if you do
> Sys.setenv(TEXINPUTS=...) when the BiocStyle is loaded/attached that
> it will stick/survive until the vignette is built.

It works to set environment variables in either .onLoad() or
.onAttach().  I verified with:

.onLoad <- function(libname, pkgname) {
  Sys.setenv(FOO="hello")
}

.onAttach <- function(libname, pkgname) {
  Sys.setenv(BAR="world")
}

that both environment variables 'FOO' and 'BAR' are available to the
vignette itself and have their values set as expected.  I've tried
with vignette engines knitr::Rmd and R.rsp::rsp and in both cases the
build and installed vignettes show FOO=hello and BAR=world.

Given that this works, I would be surprised if you cannot set
TEXINPUTS such that texi2dvi() et al. won't see it.

/Henrik

>
> /Henrik
>
>>
>> Martin
>>
>>
>>>
>>> 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
>>>>
>>>>
>>>> _______________________________________________
>>>> Bioc-devel at r-project.org mailing list
>>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>
>>
>>
>> --
>> Computational Biology / Fred Hutchinson Cancer Research Center
>> 1100 Fairview Ave. N.
>> PO Box 19024 Seattle, WA 98109
>>
>> Location: Arnold Building M1 B861
>> Phone: (206) 667-2793

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