On Mon, Oct 6, 2014 at 5:33 PM, Martin Morgan <mtmor...@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. /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 <mtmor...@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@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 <sneum...@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@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@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 _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
