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

Laurent Gatto lg390 at cam.ac.uk
Wed Oct 11 14:29:27 CEST 2017

On 11 October 2017 11:14, Rainer Johannes wrote:

> Dear Martin,
>> On 11 Oct 2017, at 13:05, Martin Morgan <martin.morgan at roswellpark.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.


> 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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Laurent Gatto | @lgatt0

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