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

Hi.
"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.
Yes, I am aware of that, but all other test cases are validated by R
CMD check not R CMD build.

I believe allowing vignettes to fail during build comes down to how
vignette is important for the service the package provides.  For
instance, I can definitely see how code and data (possibly not example
data but is currently no such separation) should be valid in order to
install a package.  Documentation, however, is not critical for a
package's operation.  To me a vignette is just another documentation
format just like the TeX, HTML, CHTML, man pages, ...

Don't get me wrong, I do believe packages should build and pass all
builds and checks without errors and warnings.

Cheers

Henrik
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

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

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

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

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