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

[Martin Morgan]

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 affyPLM/preprocessCore is out of date on Windows.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