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

[Neumann, Steffen]

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