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.mor...@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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