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

Robert Gentleman rgentlem at fhcrc.org
Sun Sep 23 03:35:09 CEST 2007

Henrik Bengtsson wrote:
> 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".

   We don't build on any error, and expect that package maintainers 
check the build page; we can help with fixes once alerted to the issue. 
  Having a package available for public use has some responsibilities, 
least among them is keeping it working on your own examples.  There is 
no way that we can start trying to decide which errors are serious and 
which are not.

   best wishes

> 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
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Robert Gentleman, PhD
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M2-B876
PO Box 19024
Seattle, Washington 98109-1024
rgentlem at fhcrc.org

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