[Bioc-devel] linking stage excessive runtime issue on windows (was: New package submission)

Thomas Lawson thomas.nigel.lawson at gmail.com
Thu Apr 21 22:47:13 CEST 2016 

Great! Thank you.

Tom

On Thu, Apr 21, 2016 at 9:41 PM, Dan Tenenbaum <dtenenba at fredhutch.org>
wrote:

>
>
> ----- Original Message -----
> > From: "Thomas Lawson" <thomas.nigel.lawson at gmail.com>
> > To: "Dan Tenenbaum" <dtenenba at fredhutch.org>
> > Cc: "Steffen Neumann" <sneumann at ipb-halle.de>, "bioc-devel" <
> Bioc-devel at 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 <dtenenba at fredhutch.org>
> > wrote:
> >
> >>
> >>
> >> ----- Original Message -----
> >> > From: "Steffen Neumann" <sneumann at ipb-halle.de>
> >> > To: "Thomas Lawson" <thomas.nigel.lawson at gmail.com>, "bioc-devel" <
> >> Bioc-devel at 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 at 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 at r-project.org mailing list
> >> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
>

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