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

On 07/28/2016 06:12 AM, Johannes Helmuth wrote:

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?

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

Thanks in advance for clarification!

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