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

Rainer Johannes Johannes.Rainer at eurac.edu
Wed Oct 11 13:14:11 CEST 2017

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.


> 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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