----- Original Message ----- > From: "Thomas Lawson" <thomas.nigel.law...@gmail.com> > To: "Dan Tenenbaum" <dtene...@fredhutch.org> > Cc: "Steffen Neumann" <sneum...@ipb-halle.de>, "bioc-devel" > <Bioc-devel@r-project.org> > Sent: Thursday, April 21, 2016 1:37:15 PM > Subject: Re: [Bioc-devel] linking stage excessive runtime issue on windows > (was: New package submission)
> 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? > Yes. > > - http://staging.bioconductor.org:8000/job/507/ > You should not be looking at reports on staging.bioconductor.org, just the ones that are provided to you in the tracker. According to that (https://bioconductor.org/spb_reports/msPurity_0.99.0_buildreport_20160421114005.html), the last build was totally clean. Dan > > 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 _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
