Hi Steffen/Dan Thank you both for your quick responses and help.
I have just submitted another job and it looks like moscato2 is passing now. Which is great! However, I am now missing the mac morelia build completely, which is a bit strange.... - http://staging.bioconductor.org:8000/job/510/ There also seems to be a submission sent at April 21 2016, 11:15 am (server time) that passed all checks on all systems. I don't think I submitted this, I am guessing that this was from Dan testing something out? - http://staging.bioconductor.org:8000/job/507/ Thanks again for your help. Kind regards, Tom On Thu, Apr 21, 2016 at 4:22 PM, Dan Tenenbaum <dtene...@fredhutch.org> wrote: > > > ----- Original Message ----- > > From: "Steffen Neumann" <sneum...@ipb-halle.de> > > To: "Thomas Lawson" <thomas.nigel.law...@gmail.com>, "bioc-devel" < > Bioc-devel@r-project.org> > > Sent: Thursday, April 21, 2016 7:29:50 AM > > Subject: Re: [Bioc-devel] linking stage excessive runtime issue on > windows (was: New package submission) > > > 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. > > > > The package actually INSTALLs in less than 40 minutes (35m23s). And if you > look at where it's trying to build, it seems like it's done, and yet still > times out. I've seen this before. But also sometimes there are 'real' > timeouts in the build phase, where the build is not complete after 40 > minutes. > > I don't think this has anything to do with Thomas's issue. I think the > single package builder was installing dependencies without > INSTALL_opts="--merge-multiarch" which I have added and am trying now. > > Dan > > > > 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]] > >> > >> _______________________________________________ > >> Bioc-devel@r-project.org mailing list > >> https://stat.ethz.ch/mailman/listinfo/bioc-devel > > > > -- > > 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 > > > > _______________________________________________ > > Bioc-devel@r-project.org mailing list > > https://stat.ethz.ch/mailman/listinfo/bioc-devel > [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
