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!
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Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
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