Great! Thank you. Tom
On Thu, Apr 21, 2016 at 9:41 PM, Dan Tenenbaum <dtene...@fredhutch.org> wrote: > > > ----- 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 > [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
