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

I recognize that the code base is pretty complex (and that mass spec
libraries are a mess at times), but could there be advantages to
modularizing the code into more than 1 package, with a mzR master
package. Could that help with linking etc?

Best,
Kasper

On Fri, Oct 13, 2017 at 4:24 PM, Neumann, Steffen <sneumann at ipb-halle
.de> wrote:

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 rosw

ellp

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

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