[Bioc-devel] Build error on Moscato2 for mzR

Blattmann Peter blattmann at imsb.biol.ethz.ch
Sat Apr 16 10:42:42 CEST 2016

Dear all, 

I'm maintaining the SWATH2stats package and we just use the MSstats package in the vignette for showing an example workflow. As MSstats depends on MSnbase and this depends on mzR we receive an error to build our SWATH2stats package now. 

In light of the release schedule (where packages should pass R cmd build and check by April 15) how shall we proceed? 
Is it no problem that our package is included in the current release if we have install and build errors only on moscato2 but it builds correctly on the other operating systems? Or should we at one point take out the example workflow from the vignette? Or will the problem in mzR be solved in time and we don't have to worry?



-----Original Message-----
From: Bioc-devel [mailto:bioc-devel-bounces at r-project.org] On Behalf Of Steffen Neumann
Sent: Thursday, April 07, 2016 11:03 AM
To: Samuel Wieczorek; mailman, bioc-devel
Subject: Re: [Bioc-devel] Build error on Moscato2 for mzR

Hi Samuel, 

On Do, 2016-04-07 at 10:28 +0200, Samuel Wieczorek wrote:
> which needs the mzR package.
> The latter package has build error since a few days and this 
> propagates errors on the other packages.
We're painfully aware of the build failure of mzR. I opened an issue for it on https://github.com/sneumann/mzR/issues/36

I know one person who was able to build mzR on the new toolchain https://github.com/sneumann/mzR/issues/34#issuecomment-190231

Unfortunately none of us is a Windows wizard, and I even failed to install a working development environment on a virtual machine. If you or someone else would help out with a patch for issue #36, that would be awesome. I am currently unsure if we need to modify the CFLAGS so that only one of the files contains the std symbols, or the LDFLAGS so that the linker realises that it can chose one of the symbols. 

Please head over to the github issue and continue discussion for fixes there, I can also test and upload any suggested patches to the SinglePackageBuilder.

Thanks for any help,

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

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