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

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

--
Dr. Martin Morgan, PhD
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N.
PO Box 19024 Seattle, WA 98109