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

Kasper Daniel Hansen khansen at stat.Berkeley.EDU
Sun Sep 23 10:33:38 CEST 2007

On Sep 22, 2007, at 6:32 PM, Martin Morgan wrote:

> "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.

Somewhat tangential to this discussion: I have had cases where a  
vignette segfaults and R CMD check still reports it as fine... I  
think it was Rgraphviz quite a while ago - Herve was aware of it and  
we reported it to R-devel but never got an answer. It is a while ago,  
so I doubt we have a reproducible example.


> 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
> _______________________________________________
> Bioc-devel at stat.math.ethz.ch mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel

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