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

[Hervé Pagès]

Hi Steffen,

On 04/12/2017 04:22 AM, Neumann, Steffen wrote:
> Hi Martin and malbec2 admin(s):
>
> Some more digging revealed that malbec2
> https://urldefense.proofpoint.com/v2/url?u=http-3A__bioconductor.org_checkResults_devel_bioc-2DLATEST_malbec2-2DNodeInfo.html&d=DwIGaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=V9yGIrMq8w3mmdQPS2JnioJSKNG6iGCu1hurilsGY0I&s=l35mMJgBfX96wHZ0WjtJoTIFGDvA-IOLXMDy9TVtz6U&e=
> 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://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_sneumann_xcms_issues_150-23issuecomment-2D293545521&d=DwIGaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=V9yGIrMq8w3mmdQPS2JnioJSKNG6iGCu1hurilsGY0I&s=zvwRbtsHJd07tnGbqG5Cnj6SPzEQcadvufl5s_ir9sM&e=
>
> => 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 :-)

This is apparently the new default for R 3.4 beta. Don't know if that
was an intended change (someone might want to bring this up on R-devel),
but, if it was, then let's assume they had a good reason for it.

So I'm not too keen on touching this on the build machines. Might get
rid of the mzR and xcms warnings, but might also introduce other
problems.

Why not control the compilation flags at the package level?

Thanks,
H.

>
> 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://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_sneumann_xcms_issues_150&d=DwIGaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=V9yGIrMq8w3mmdQPS2JnioJSKNG6iGCu1hurilsGY0I&s=PgXl6YzkPCHh3_1B8D2N15A6-Aftsbr8Wx3bcMTwIQk&e=
> [...]
>>
>> 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
> https://urldefense.proofpoint.com/v2/url?u=http-3A__www.ipb-2Dhalle.de_en_public-2Drelations_3rd-2Dleibniz-2Dplant-2Dbiochemis&d=DwIGaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=V9yGIrMq8w3mmdQPS2JnioJSKNG6iGCu1hurilsGY0I&s=Za8ehpMewAbtvAcr0J0bV8O2S-SsaOwFzIQBfOF80n4&e=
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> --
> IPB Halle                    AG Massenspektrometrie &
> Bioinformatik
> Dr. Steffen Neumann          https://urldefense.proofpoint.com/v2/url?u=http-3A__www.IPB-2DHalle.DE&d=DwIGaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=V9yGIrMq8w3mmdQPS2JnioJSKNG6iGCu1hurilsGY0I&s=NiMolENKs_yTD3KviDw4AQR5KE4-Zo0wVy34JEO5r7k&e=
> 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
>

-- 
Hervé Pagès

Program in Computational Biology
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