[Bioc-devel] R CMD check without WARNING: g++ and STL issue for xcms and mzR
Hervé Pagès
hpages at fredhutch.org
Wed Apr 19 21:45:07 CEST 2017
Thanks Steffen for bringing this to the R-devel list. I only
see the fix in trunk for now. They'll need to port it to the 3.4
branch if we want to see it propagate to our BioC 3.5 builds.
Just to clarify, by default R doesn't use the -Wall flag to
compile packages on Linux. It's something we add on our Linux
builders.
Cheers,
H.
On 04/19/2017 11:52 AM, Neumann, Steffen wrote:
> Hi,
>
> just a quick report, I followed this up to r-devel,
> and a fix adding -O2 back to default CXXFLAGS
> has been committed (r72549, see [1]) to R by Martyn Plummer,
> thus "fixing" the abort() related WARNING in mzR/xcms
> once this gets into the R version used on malbec2.
>
> Yours,
> Steffen
>
> [1] https://urldefense.proofpoint.com/v2/url?u=http-3A__developer.r-2Dproject.org_R-5Fsvnlog-5F2013&d=DwIGaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=YE8GxLGaWhq-2Zt3n3yIFSqX3K1hSlEQgyUpXjLaYPg&s=nRu69QAXHm0lBKf9Al-8KvSvfGAqLrzp1uWirvd6XF0&e=
>
> On Mi, 2017-04-12 at 22:07 -0400, Martin Morgan wrote:
>> On 04/12/2017 11:31 AM, Neumann, Steffen wrote:
>>>
>>> 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.
>> The code is compiled on the user machine, so twiddling with the
>> build
>> system masks the problem from the developer while leaving the user
>> vulnerable.
>>
>> Calling abort() is certainly a serious problem, abruptly ending the
>> user
>> session.
>>
>> Optimization could either eliminate a dead code path, or it could
>> compile the call to abort in a way that R no longer recognizes it --
>> R
>> is doing the equivalent of nm *.o |grep abort.
>>
>> It would be appropriate to ignore the warning about abort() if it
>> were
>> never reached; one would only know this by careful code analysis
>> rather
>> than adjusting optimization flags.
>>
>> Rsamtools re-defines abort (before including offending headers), and
>> avoids the warning (and crash), with the equivalent of
>>
>> PKG_CFLAGS=-D__builtin_abort=_samtools_abort
>>
>> where _samtools_abort is my own implementation to signal an R error
>> telling the user that an unrecoverable error has occurred and they
>> should stop what they are doing. Unfortunately this requires
>> -U_FORTIFY_SOURCE and doesn't actually address the reason for the
>> abort,
>> and is hardly ideal.
>>
>> I don't think the developer can set the optimization flag in a way
>> that
>> overrides the R or user setting (the PKG_CXXFLAGS is inserted before
>> the
>> R flags). And it doesn't address the underlying problem anyway.
>>
>> Kasper's pragmatic approach (it's a very unlikely situation, and
>> difficult to fix, so live with the warning) seems like it would often
>> be
>> a reasonable one.
>>
>> FWIW this little bit of C++ seems to be enough to include abort
>>
>> tmp.cpp:
>> -------
>> #include <list>
>>
>> int foo(int argc, const char *argv[]) {
>> std::list<int> l1, l2;
>> std::list<int>::iterator it;
>>
>> it = l1.begin();
>> l1.splice (it, l2); // mylist1: 1 10 20 30 2 3 4
>>
>> return 0;
>> }
>> -------
>>
>> Test with
>>
>> rm -f tmp.o && R CMD SHLIB tmp.cpp && nm tmp.o | grep abort
>>
>> with compiler settings in
>>
>> ~/.R/Makevars
>> -------------
>> CXXFLAGS = -g -O0
>> -------------
>>
>>
>> Martin
>>
>>>
>>>
>>> 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
>>>>>> https://urldefense.proofpoint.com/v2/url?u=http-3A__bioconductor.org_checkResults_devel_bioc-2D&d=DwIGaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=YE8GxLGaWhq-2Zt3n3yIFSqX3K1hSlEQgyUpXjLaYPg&s=kUGjYuMkhD3e-WsuG6IAuE_MTjPtNkrZw9B4I-9xpwM&e=
>>>>>> 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://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_sneumann_xcms_issues_150-23&d=DwIGaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=YE8GxLGaWhq-2Zt3n3yIFSqX3K1hSlEQgyUpXjLaYPg&s=Bzp4j1sYGGHCblnhv2xferniQzw1BPE-wmoHi0zWSLM&e=
>>>>>> 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://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_sneumann_xcms_issues_150&d=DwIGaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=YE8GxLGaWhq-2Zt3n3yIFSqX3K1hSlEQgyUpXjLaYPg&s=RJrwRqEKnRJOw5M0FS7za46JPhrG2vKflu80XCWzxVI&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&d=DwIGaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=YE8GxLGaWhq-2Zt3n3yIFSqX3K1hSlEQgyUpXjLaYPg&s=JV-QoY63QkPHNGmis61NuX2JS_4rxBN6c7oFCQFGvm8&e=
>>>>>> -bio
>>>>> chemis
>>>>>>
>>>>>>
>>>>>> try-symposium/
>>>>>> --
>>>>>> 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=YE8GxLGaWhq-2Zt3n3yIFSqX3K1hSlEQgyUpXjLaYPg&s=tW4jM8Um0HwJ4_bkERUrB4C0DfUfjiz0ikU8_6I5Dho&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
>>>>>>
>>>>>> --
>>>>>> 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&d=DwIGaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=YE8GxLGaWhq-2Zt3n3yIFSqX3K1hSlEQgyUpXjLaYPg&s=JV-QoY63QkPHNGmis61NuX2JS_4rxBN6c7oFCQFGvm8&e=
>>>>>> -bio
>>>>> chemis
>>>>>>
>>>>>>
>>>>>> try-symposium/
>>>>>> --
>>>>>> 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=YE8GxLGaWhq-2Zt3n3yIFSqX3K1hSlEQgyUpXjLaYPg&s=tW4jM8Um0HwJ4_bkERUrB4C0DfUfjiz0ikU8_6I5Dho&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
>>>>>>
>>>>>> _______________________________________________
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>>>>>>
>>>>> [[alternative HTML version deleted]]
>>>>>
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--
Hervé Pagès
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
P.O. Box 19024
Seattle, WA 98109-1024
E-mail: hpages at fredhutch.org
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Fax: (206) 667-1319
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