Re: [Bioc-devel] linking stage excessive runtime issue on windows (was: New package submission)
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. > >&g
Re: [Bioc-devel] linking stage excessive runtime issue on windows (was: New package submission)
- 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: >> >> >> >> --- >> >>
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? - 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 >
Re: [Bioc-devel] linking stage excessive runtime issue on windows (was: New package submission)
- 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 HalleAG 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
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. 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 HalleAG 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
