[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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