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

[Neumann, Steffen]

Hi,

On Sat, 2017-10-14 at 14:04 -0400, Kasper Daniel Hansen wrote:
> 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?

Currently I can't think of a way here. Basically, mzR uses 
one top-level object from "msdata" proteowizard, and we only include
and compile the minimum of dependencies for msdata. 

And indeed, today mzR finished in 1475 seconds on Windows, 
which is 1000 secs before the timeout would kick in. 

Not sure if upon the first compile after the fresh R installation
there is a cache built up by mingw somewhere, which would explain
why it is faster afterwards.

Yours,
Steffen



> 
> 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 rosw
> > ellp
> > > > > > 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
> > _______________________________________________
> > 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
06120 Halle                  Tel. +49 (0) 345 5582 - 1470
                                  +49 (0) 345 5582 - 0
sneumann(at)IPB-Halle.DE     Fax. +49 (0) 345 5582 - 1409