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

[Neumann, Steffen]

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
> > > > > _______________________________________________
> > > > > Bioc-devel at r-project.org mailing list
> > > > > https://stat.ethz.ch/mailman/listinfo/bioc-devel
> > > > 
> > > > 
> > > > This email message may contain legally privileged and/or
> > > > confidential information.  If you are not the intended
> > > > recipient(s), or the employee or agent responsible for the
> > > > delivery of this message to the intended recipient(s), you are
> > > > hereby notified that any disclosure, copying, distribution, or
> > > > use of this email message is prohibited.  If you have received
> > > > this message in error, please notify the sender immediately by
> > > > e-mail and delete this email message from your computer. Thank
> > > > you.
> > > 
> > > _______________________________________________
> > > Bioc-devel at r-project.org mailing list
> > > https://stat.ethz.ch/mailman/listinfo/bioc-devel
> > 
> > 
> 
> 
> This email message may contain legally privileged
> and/or...{{dropped:2}}
> 
> _______________________________________________
> 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