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

[Neumann, Steffen]

Hi,

certainly these are good suggestions, but I would tend 
to simply add some whitelisting functionality if the 
cause is beyond the package's control. 

In this case I doubt it is a handler for SIGABRT, 
since that would not go away with -O2, or would it ?

For now, just adding -O2 on Linux would fix this issue. 

Yours,
Steffen


On Mi, 2017-04-12 at 10:07 -0400, Vincent Carey wrote:
> 
> 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 <kasperdanielha
> nsen 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-hal
> > le.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-bio
> > chemis
> > > 
> > > 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-bio
> > chemis
> > > 
> > > 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
> > > 
> >         [[alternative HTML version deleted]]
> > 
> > _______________________________________________
> > Bioc-devel at r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
> > 
-- 
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