[Bioc-devel] FYI: Windows build of affyPLM devel has been broken for a while

[Henrik Bengtsson]

Hi,

I noticed that someone (you) fixed it recently.  Thanks.  Yes,
spawning ghostscript in a parallel thread/process in the background is
not easy to control.  I've once tried to control for this by probing
the output file for existence and file size and when the file size
wasn't changing for a certain time, I let the code assume that it was
ready.  I cannot remember if also tried to have a dummy file generated
afterwards that could check for.  It was a while ago, but there are
some hacks you can do beyond Sys.sleep().

However, in the bigger picture, have you/it been discussed to have
failed vignettes not to generate an error/stop the build of the
package, and instead let R CMD check give the error?  Is that even
possible?  A big tryCatch() around the vignette compiler?  In some
sense a broken vignette is like a broken example in a Rd file - it is
not critical for the package, but for the documentation, which is
something for R CMD check to "complain about".

Cheers

Henrik



On 9/22/07, Martin Morgan <mtmorgan at fhcrc.org> wrote:
> Hi Henrik --
>
> The problem appears to be that 'bitmaap / dev.off' on windows spawns
> ghostscript to perform the implied graphics file conversion. R does
> not wait for the process to return, and Sweave cleans up before
> ghostscript completes.
>
> The more-or-less ugly solution is to insert a Sys.sleep(10) in the
> vignette. Whether to insert this, and the duration of sleep, entirely
> depends on the build system and vignette. For instance, MAplots.Rnw
> uses bitmap and needs to sleep, but QualityAssess.Rnw uses bitmap but
> does not need to sleep.
>
> Martin
>
> "Henrik Bengtsson" <hb at stat.berkeley.edu> writes:
>
> > Hi,
> >
> > the affyPLM devel build for Windows has been broken for a while.  Last
> > successful build was/is v1.13.6 (2007-06-22) and now were on
> > v1.13.13(14).  Since there has recently been quite of bit of migration
> > from affyPLM to preprocessCore, code that relies on
> > affyPLM/preprocessCore is out of date on Windows.
> >
> > I'm not sure this is a package maintainer problem or a problem with
> > the BioC builds. From the build report:
> > http://bioconductor.org/checkResults/2.1/bioc-LATEST/affyPLM/liverpool-buildsrc.html
> >
> > texi2dvi.exe: Permission denied: MAplots.tex
> > Error in texi2dvi(file = bft, pdf = TRUE, clean = FALSE, quiet = quiet) :
> >   running 'texi2dvi' on 'MAplots.tex' failed
> > Calls: buildVignettes -> texi2dvi
> > Execution halted
> > Error: /undefinedfilename in
> > (E:\\biocbld\\bbs-2.1-bioc\\tmpdir\\RtmphbJVrR\\Rbit35182069)
> > Operand stack:
> >
> > Execution stack:
> >    %interp_exit   .runexec2   --nostringval--   --nostringval--
> > --nostringval--   2   %stopped_push   --nostringval--
> > --nostringval--   --nostringval--   false   1   %stopped_push
> > Dictionary stack:
> >    --dict:1126/1686(ro)(G)--   --dict:0/20(G)--   --dict:70/200(L)--
> > Current allocation mode is local
> > Last OS error: No such file or directory
> > AFPL Ghostscript 8.54: Unrecoverable error, exit code 1
> >
> > Cheers
> >
> > Henrik
> >
> > _______________________________________________
> > Bioc-devel at stat.math.ethz.ch mailing list
> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
>
> --
> Martin Morgan
> Bioconductor / Computational Biology
> http://bioconductor.org
>