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

[Martin Morgan]

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!


This email message may contain legally privileged and/or...{{dropped:2}}