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

[Hervé Pagès]

Hi,

Note that the BUILD and CHECK steps also have to compile mzR
but they always manage to finish in time so obviously something
else is going on.

Here is what we've observed: for some obscure reasons these INSTALL
TIMEOUTs happen only after a *fresh install of R* on the Windows
builders (Val updated R from 3.4.1 to 3.4.2 Patched on Monday).
In "normal times", INSTALL takes about 25 min there so finishes in
time. This should be the case today when the report gets updated.

We've no idea why this would happen.

Cheers,
H.


On 10/11/2017 06:39 AM, 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 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.
>
> 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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-- 
Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
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