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

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
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

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James W. MacDonald, M.S.
Biostatistician
University of Washington
Environmental and Occupational Health Sciences
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