[Bioc-devel] Build error on Moscato2 for mzR

[Kasper Daniel Hansen]

And if not fixed on Sunday, surely Monday.  Everyone has been working hard
to get this to work; so just hang tight.

Best,
Kasper

On Sat, Apr 16, 2016 at 5:35 AM, Laurent Gatto <lg390 at cam.ac.uk> wrote:

>
> On 16 April 2016 09:42, Blattmann Peter wrote:
>
> > 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?
>
> The problem has been fixed by Dan with help from Kasper and Jim and the
> Rcpp team. Confirmation on Bioc build servers on Sunday.
>
> Details here
>
>  https://github.com/sneumann/mzR/issues/36
>
> Best wishes,
>
> Laurent
>
> > Best
> >
> > Peter
> >
> > -----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 onhttps://github.com/sneumann/mzR/issues/36
> >
> > I know one person who was able to build mzR on the new toolchainhttps://
> github.com/sneumann/mzR/issues/34#issuecomment-190231
> > 559
> >
> > 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,
> > yours,
> > Steffen
>
>
> --
> Laurent Gatto | @lgatt0
> http://cpu.sysbiol.cam.ac.uk/
> http://lgatto.github.io/
>
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