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

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

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

Thread (10 messages)