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

[Dan Tenenbaum]

----- 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
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>                                  +49 (0) 345 5582 - 0
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> 
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