[Bioc-devel] texmf error on 7 packages on devel winXP build nodes
Hi,
Seth Falcon wrote:
Martin Morgan <mtmorgan at fhcrc.org> writes:
To make things work, you can remove \usepackage{Sweave} from your
vignette (but then you won't be able to build the vignette except by
building the R package). Alternatively, you can configuring tex to
find Sweave.sty. How to actually configure tex depends on your
installation. On Windows using MiKTeX there's a graphical interface to
set MiKTeX options. You can add a 'Root' path to point to the file
system location where R has a copy of Sweave.sty (R_HOME\share\texmf)
and then 'Refresh' the file name data base. On linux the strategy is
usually to define an environment variable TEXINPUTS to include the
path.
The preferred fix, IMO, is to remove the \usepackage{Sweave} line from
the vignettes. Why?
Well, if we let R find/set the path to Sweave.sty, we will always get
the latest version of it and do not have to change any additional
configuration on the build systems when we upgrade R.
I vote for this fix too (i.e. removing the \usepackage{Sweave}) because:
- The Sweave.sty is not part of the "standard" MikTeX distribution.
By removing \usepackage{Sweave} then everybody can easily
build the vignette without having to play with TEXINPUTS or copying
R_HOME\share\texmf\Sweave.sty around.
- Better consistency and reproducibility: by having all vignettes in the
1.9 builds using the same Sweave.sty file (the "official" one) we are
more consistent. Also other people can try to re-build the vignettes on
their own machine and expect to get the same thing. Eventually, it makes
tracking down build problems easier.
For example, on lemming, are we sure that we are getting the "right" Sweave.sty?
No we are not. Packages that don't include \usepackage{Sweave} get
the "right" one (R_HOME\share\texmf\Sweave.sty) but packages that
include it get C:\localtexmf\tex\Sweave.sty instead.
And of course, they are different (the diff shows a few changes
between the files).
Granted, the style file does not change often, but I'm concerned about it because Robert and I have recently discussed some additions to it. OTOH, perhaps Herve will have a clever way to automate/trick the configuration such that we always get the right Sweave.sty when R is upgraded.
Easy: let's remove C:\localtexmf\tex\Sweave.sty so we break
packages that include \usepackage{Sweave} on lemming too ;-)
H.
------------------------ Herv? Pag?s E-mail: hpages at fhcrc.org Phone: (206) 667-5791 Fax: (206) 667-1319