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 <sneum...@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@roswellp > > > > > 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 > > > > > > _______________________________________________ > > > > > > Bioc-devel@r-project.org mailing list > > > > > > https://stat.ethz.ch/mailman/listinfo/bioc-devel > > > > > > > > > > > > > > > This email message may contain legally privileged and/or > > > > > confidential information. If you are not the intended > > > > > recipient(s), or the employee or agent responsible for the > > > > > delivery of this message to the intended recipient(s), you are > > > > > hereby notified that any disclosure, copying, distribution, or > > > > > use of this email message is prohibited. If you have received > > > > > this message in error, please notify the sender immediately by > > > > > e-mail and delete this email message from your computer. Thank > > > > > you. > > > > > > > > _______________________________________________ > > > > Bioc-devel@r-project.org mailing list > > > > https://stat.ethz.ch/mailman/listinfo/bioc-devel > > > > > > > > > > > > This email message may contain legally privileged > > and/or...{{dropped:2}} > > > > _______________________________________________ > > Bioc-devel@r-project.org mailing list > > https://stat.ethz.ch/mailman/listinfo/bioc-devel > -- > > IPB Halle AG Massenspektrometrie & Bioinformatik > Dr. Steffen Neumann http://www.IPB-Halle.DE > Weinberg 3 http://msbi.bic-gh.de > 06120 Halle Tel. +49 (0) 345 5582 - 1470 > +49 (0) 345 5582 - 0 > sneumann(at)IPB-Halle.DE Fax. +49 (0) 345 5582 - 1409 > _______________________________________________ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel > [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel