[Bioc-devel] texmf error on 7 packages on devel winXP build nodes

[Herve Pages]

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.


-- 
------------------------
Hervé Pagès
E-mail: hpages at fhcrc.org
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