Hi BioConductor community, I have recently submitted my new R package into BioConductor tracker (issue 1455) that carries out some data pre-processing for MS/MS spectra. I seem to be having trouble with the moscato2 Windows build though. The package is fine on Linux and Mac but I get an error message (see below) for windows. Also, I was not receiving the error last night. It looks like it has something to do with the BioConductor package that I import called "mzR" and an associated DLL it uses. The error message: ------------------------------------------- Installing package prior to check... install for i386 * installing *source* package 'msPurity' ... ** R ** inst ** preparing package for lazy loading Error in library.dynam(lib, package, package.lib) : DLL 'mzR' not found: maybe not installed for this architecture? ERROR: lazy loading failed for package 'msPurity' * removing 'E:/packagebuilder/workers/jobs/msPurity_20160421061423/msPurity. buildbin-libdir/msPurity' Warning: running command 'E:/packagebuilder/R/bin/i386/Rcmd.exe INSTALL --library=msPurity.buildbin-libdir msPurity_0.99.0.tar.gz --no-multiarch' had status 1 ------------------------------------------- For more information see: http://staging.bioconductor.org:8000/job/506/ Any help would be really appreciated. Kind regards, Tom
[Bioc-devel] New package submission
2 messages · Thomas Lawson, Neumann, Steffen
Hi Thomas,? mzR has been in stormy waters since the new Windows toolchain? was used. While now all compile errors are gone: http://bioconductor.org/checkResults/devel/bioc-LATEST/mzR/ The build still timeouts on windows, because for reasons completely? unknown to me the linking step into mzR.dll takes a whopping 20 minutes on windows, and that twice to create the mzR.dll for both i386 and x64. It is somehow an issue in the mingw compiler. We even tried? an alternative linker (see issue threads linked below). I don't know if this could be helped with CFLAGS/LDFLAGS. => If there is anyone who knows why and if there is any way? ? ?to speed this up, any suggestions would be greatly appreciated. ? ?This has been a pain for a long time, and I am sorry? ? ?for the turbulences caused. Yours, Steffen We track this issue here: https://github.com/sneumann/mzR/issues/21#issuecomment-87801932
On Do, 2016-04-21 at 14:37 +0100, Thomas Lawson wrote:
Hi BioConductor community, I have recently submitted my new R package into BioConductor tracker (issue 1455) that carries out some data pre-processing for MS/MS spectra. I seem to be having trouble with the moscato2 Windows build though. The package is fine on Linux and Mac but I get an error message (see below) for windows. Also, I was not receiving the error last night. It looks like it has something to do with the BioConductor package that I import called "mzR" and an associated DLL it uses. The error message: ------------------------------------------- Installing package prior to check... install for i386 * installing *source* package 'msPurity' ... ** R ** inst ** preparing package for lazy loading Error in library.dynam(lib, package, package.lib) : ? DLL 'mzR' not found: maybe not installed for this architecture? ERROR: lazy loading failed for package 'msPurity' * removing 'E:/packagebuilder/workers/jobs/msPurity_20160421061423/msPurity. buildbin-libdir/msPurity' Warning: running command 'E:/packagebuilder/R/bin/i386/Rcmd.exe INSTALL --library=msPurity.buildbin-libdir msPurity_0.99.0.tar.gz --no- multiarch' had status 1 ------------------------------------------- For more information see: http://staging.bioconductor.org:8000/job/50 6/ Any help would be really appreciated. Kind regards, Tom [[alternative HTML version deleted]]
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IPB Halle AG Massenspektrometrie & Bioinformatik Dr. Steffen Neumann http://www.IPB-Halle.DE Weinberg 3 http://msbi.bic-gh.de 06120 Halle Tel. +49 (0) 345 5582 - 1470 +49 (0) 345 5582 - 0 sneumann(at)IPB-Halle.DE Fax. +49 (0) 345 5582 - 1409