[Bioc-devel] EXTERNAL: Increase timeout for mzR on Windows?

[Kasper Daniel Hansen]

I recognize that the code base is pretty complex (and that mass spec
libraries are a mess at times), but could there be advantages to
modularizing the code into more than 1 package, with a mzR master package.
Could that help with linking etc?

Best,
Kasper

On Fri, Oct 13, 2017 at 4:24 PM, Neumann, Steffen <sneumann at ipb-halle.de>
wrote:

> Hi,
>
> we've had binary compiles a while ago, but we were glad
> when we could revert that to "normal" compilation a long time ago.
>
> Another observation from years ago was that the linker step
> was what took the longest, and even with a precompiled libpwiz.a
> this took very long.
>
> Thanks Herve for the observation about normal build times
> vs. the "fresh R" case. This might show that, in general,
> mzR does build in <40 minutes.
>
> yours,
> Steffen
>
> On Wed, 2017-10-11 at 09:39 -0400, Martin Morgan wrote:
> > On 10/11/2017 08:29 AM, Laurent Gatto wrote:
> > >
> > > On 11 October 2017 11:14, Rainer Johannes wrote:
> > >
> > > > Dear Martin,
> > > >
> > > > > On 11 Oct 2017, at 13:05, Martin Morgan <martin.morgan at roswellp
> > > > > ark.org> wrote:
> > > > >
> > > > > On 10/11/2017 03:48 AM, Rainer Johannes wrote:
> > > > > > Hi,
> > > > > > would it be possible to increase the allowed build and check
> > > > > > times for mzR on Windows? Building mzR takes very long due to
> > > > > > the compilation of the included proteowizard (and boost?)
> > > > > > code so there is not much we can do to speed that up.
> > > > >
> > > > > what's the role of proteowizard in mzR? is it required in its
> > > > > entirety, or can it be more selectively included? I agree that
> > > > > mzR is often problematic because of the excessive compilation
> > > > > time.
> > > > >
> > > >
> > > > mzR uses Rcpp modules to directly call/use the C++ code from
> > > > proteowizard to read mzML, mzXML and other MS file formats.
> > > > Regarding
> > > > selective includes: I believe Steffen Neumann and Laurent Gatto
> > > > spent
> > > > already a great deal of time to reduce the amount of code that
> > > > needs
> > > > to be included for mzR to compile/work. I think there is not much
> > > > more
> > > > that can be done here, unfortunately.
> > >
> > > Steffen (he should get the credit for this) has indeed tried to be
> > > as
> > > selective as possible, yes. There might be more to be done, but I
> > > don't
> > > think we could gain anything really substantial.
> >
> > probably we have been down this road before but is another option to
> > pre-compile and distribute the Windows binaries?
> >
> > Martin
> >
> > >
> > > Laurent
> > >
> > > > jo
> > > >
> > > > > Martin
> > > > >
> > > > > > On linux and macOS all is fine, but we get TIMEOUT errors on
> > > > > > a regular basis on Windows (I guess because it has to be
> > > > > > compiled for i386 and x86_64). The problem is that a failing
> > > > > > mzR causes all packages depending on it (like MSnbase and
> > > > > > xcms) to fail too.
> > > > > > cheers, jo
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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
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