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

[Steffen Neumann]

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]]
> 
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-- 
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