[Bioc-devel] R CMD check without WARNING: g++ and STL issue for xcms and mzR

[Vincent Carey]

Suppose you had a handler for SIGABRT in your code.  Could CMD check check
for that and, if found, refrain from warning?  That is somewhat involved
and goes beyond Bioc but it seems a principled way of dealing with
operations in binary infrastructure whose behavior we cannot control.  The
problem will surely arise in other settings.  Could BiocCheck prototype the
approach?

On Wed, Apr 12, 2017 at 9:12 AM, Kasper Daniel Hansen <
kasperdanielhansen at gmail.com> wrote:

> I think "we" have to appreciate that the warning about abort/etc and others
> is really hard to deal with when you're including (large) external source
> as you do in mzR and for example affxparser / Rgraphviz.  Generally fixing
> those in external code requires a lot of effort, and the further effort to
> document that the included sources in the package are different from the
> official sources.  I have had warnings about this in affxparser for a long,
> long time and no-one has bothered me over it.
>
> What might be nice is (somehow) setting a flag saying this should be
> ignored in the check process, but of course we don't want that flag to be
> set by the developer, because usually, these issues should be dealt with.
> So perhaps there is nothing to do and I always have to click on each build
> report to verify that there is only 1 warning from this issues and not
> others.
>
> Best,
> Kasper
>
> On Wed, Apr 12, 2017 at 7:22 AM, Neumann, Steffen <sneumann at ipb-halle.de>
> wrote:
>
> > Hi Martin and malbec2 admin(s):
> >
> > Some more digging revealed that malbec2
> > http://bioconductor.org/checkResults/devel/bioc-
> > LATEST/malbec2-NodeInfo.html
> > is using "CFLAGS=-g -O2 -Wall" but only "CXXFLAGS=-Wall"
> > while e.g. tokay2 uses "CXXFLAGS=-O2 -Wall -mtune=core2"
> >
> > The -O2 optimisation is getting rid of the abort() symbol,
> > as shown in https://github.com/sneumann/xcms/issues/150#
> > issuecomment-293545521
> >
> > => Is there a way to get -O2 back on the BioC build machines ?
> >    This should fix our WARNING. Bonus: will fix the same issue in mzR :-)
> >
> > Yours,
> > Steffen
> >
> > On So, 2017-04-02 at 10:01 -0400, Martin Morgan wrote:
> > >
> > > On 04/02/2017 06:52 AM, Neumann, Steffen wrote:
> > > >
> > > > [...]
> > > > in preparation for the release, we are hunting down WARNINGS
> > > > "Found ‘abort’, possibly from ‘abort’ (C)" in xcms/mzR.
> > > > The abort() call is not coming from XCMS, but rather
> > > > from the C++ code in the STL, and we have no idea
> > [...]
> > >
> > > >
> > > > We are tracking this in:
> > > > https://github.com/sneumann/xcms/issues/150
> > [...]
> > >
> > > I don't think Bioconductor can help with this; maybe the Rcpp or R-
> > > devel mailing lists?
> > --
> > 3rd Leibniz Plant Biochemistry Symposium, 22.-23. of June 2017
> > http://www.ipb-halle.de/en/public-relations/3rd-leibniz-plant-biochemis
> > try-symposium/
> > --
> > IPB Halle                    AG Massenspektrometrie &
> > Bioinformatik
> > Dr. Steffen Neumann          http://www.IPB-Halle.DE
> > Weinberg 3                   Tel. +49 (0) 345 5582 - 1470
> > 06120 Halle                       +49 (0) 345 5582 - 0
> > sneumann(at)IPB-Halle.DE     Fax. +49 (0) 345 5582 - 1409
> >
> > --
> > 3rd Leibniz Plant Biochemistry Symposium, 22.-23. of June 2017
> > http://www.ipb-halle.de/en/public-relations/3rd-leibniz-plant-biochemis
> > try-symposium/
> > --
> > IPB Halle                    AG Massenspektrometrie &
> > Bioinformatik
> > Dr. Steffen Neumann          http://www.IPB-Halle.DE
> > Weinberg 3                   Tel. +49 (0) 345 5582 - 1470
> > 06120 Halle                       +49 (0) 345 5582 - 0
> > sneumann(at)IPB-Halle.DE     Fax. +49 (0) 345 5582 - 1409
> >
> > _______________________________________________
> > Bioc-devel at r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
> >
>
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