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

[Martin Morgan]

"Henrik Bengtsson" <hb at stat.berkeley.edu> writes:

> 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().

Tom Short (responding off-list to my query on R-devel) also mentioned
hacking bitmap to call ghostscript directly, and using Cairo / GDD
(though Tom did not have direct experience in vignettes) which are
faster than ghostscript. A solution in R would warrant more thorough
approaches.

> 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

Not sure what the official position is on this, but vignettes serve,
for better or worse, as a kind of integration test. Failed vignettes
usually turn up meaningful errors. Of course a better practice would
exploit formal test structures.

Martin

> 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
>>

-- 
Martin Morgan
Bioconductor / Computational Biology
http://bioconductor.org