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

[Dan Tenenbaum]

----- 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