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

[Hervé Pagès]

Hi guys,

On 07/28/2016 03:45 AM, Martin Morgan wrote:
> 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.

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.

>
> Martin
>
>>
>> Thanks in advance for clarification!
>
>
> This email message may contain legally privileged and/or...{{dropped:2}}
>
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-- 
Hervé Pagès

Program in Computational Biology
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