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[Bioc-devel] Linking to zlibbioc results in erroneous BUILD report

3 messages · Johannes Helmuth, Martin Morgan, Hervé Pagès

Johannes Helmuth
# 
Dear Bioconductor Developers,

The build of `Rhtslib` and `bamsignals` on moscato1 (Windows) is erroneous at stage "build" because 
of a missing `zlibbioc` dependency. Both packages link to `zlibbioc`:

http://bioconductor.org/checkResults/devel/bioc-LATEST/Rhtslib/moscato1-buildsrc.html :
Warning: running command '"D:/biocbld/bbs-3.4-bioc/R/bin/x64/Rcmd.exe" INSTALL -l 
"D:\biocbld\bbs-3.4-bioc\tmpdir\RtmpgvG0DD\Rinst14ec6d5d6fb1" --no-multiarch 
"D:/biocbld/bbs-3.4-bioc/tmpdir/RtmpgvG0DD/Rbuild14ec4fb25dc6/Rhtslib"' had status 1
       -----------------------------------
ERROR: dependency 'zlibbioc' is not available for package 'Rhtslib'
* removing 'D:/biocbld/bbs-3.4-bioc/tmpdir/RtmpgvG0DD/Rinst14ec6d5d6fb1/Rhtslib'
       -----------------------------------
ERROR: package installation failed

http://bioconductor.org/checkResults/devel/bioc-LATEST/bamsignals/moscato1-buildsrc.html :
Warning: running command '"D:/biocbld/bbs-3.4-bioc/R/bin/x64/Rcmd.exe" INSTALL -l 
"D:\biocbld\bbs-3.4-bioc\tmpdir\Rtmpio5vfR\Rinstb98d0068cd" --no-multiarch 
"D:/biocbld/bbs-3.4-bioc/tmpdir/Rtmpio5vfR/Rbuildb985bbc52dd/bamsignals"' had status 1
       -----------------------------------
ERROR: dependency 'zlibbioc' is not available for package 'bamsignals'
* removing 'D:/biocbld/bbs-3.4-bioc/tmpdir/Rtmpio5vfR/Rinstb98d0068cd/bamsignals'
       -----------------------------------
ERROR: package installation failed


However, the `zlibbioc` build and installation did not report an error on moscato1 (Windows):
  http://bioconductor.org/checkResults/devel/bioc-LATEST/zlibbioc/moscato1-install.html

Can you identify the problem here?

Thanks in advance for clarification!
Martin Morgan
#
On 07/28/2016 06:12 AM, Johannes Helmuth wrote:
This is a problem that is plaguing the build system. Notice the last 
line of the zlibbioc build report

   Warning: cannot remove prior installation of package 'zlibbioc'

and also the large number of windows failures here

   http://bioconductor.org/checkResults/devel/bioc-LATEST/

The build system starts by removing all packages, then building up from 
scratch. But the removal of zlibbioc failed (most of the package was 
removed, but not all) because a rogue process is holding a reference to 
the dll. The rogue process continues to hold a reference to zlibbioc, 
and the installation of the new version of zlibbioc also fails. So the 
build system is left without zlibbioc.

There is nothing the individual developer can do; we will take more 
drastic measures to address this on our side.

Martin
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Hervé Pagès
# 
Hi guys,
On 07/28/2016 03:45 AM, Martin Morgan wrote:
BTW, not that it would solve the rogue process problem, but it would
help if 'R CMD INSTALL' was not reporting success here. Since the
installation clearly failed, it should return a non-zero code. Then
we would see an INSTALL error on the build report, which would reflect
the truth.

H.