[Bioc-devel] evaluation of C post-increments changed in GCC 4.8.2

[Robert Castelo]

hi Nathaniel cc Dan,

thanks a lot for clearing up completely the entire story. I'm afraid 
that one or two cycles ago of our conversation i did a simple reply 
instead of a reply-all and the bioc-devel list wasn't included anymore 
in the recipients of these emails.

since what you say below sounds like a relevant piece of information for 
anyone working with C code i'm cc'ing the bioc-devel list again.

cheers,
robert.

On 6/16/14 11:15 PM, Nathaniel Hayden wrote:
> Hi, Robert. You are correct. zin2 and petty failed to emit warnings 
> for the problematic code. After some digging we discovered that for 
> gcc, any optimization level above 0 prevents emission of the 
> -Wsequence-point warning in this case. But the optimizations must stay 
> for production code.
>
> As a follow-up to the recommendations before about flags to use during 
> package development, we have added content to the Package Guidelines 
> page on our website: 
> http://www.bioconductor.org/developers/package-guidelines/#c-code
>
> The failure of some build machines to emit the warning under 
> production conditions underscores the importance of the original 
> recommendation to enable as many warnings as possible during development.
>
> Thanks for bringing it up!
> Nate
>
> On Mon 16 Jun 2014 07:42:36 AM PDT, Robert Castelo wrote:
>>
>> hi Nathaniel,
>>
>> On 06/14/2014 01:01 AM, Nathaniel Hayden wrote:
>>>
>>> Hi, Robert. You're welcome.
>>>
>>> It sounds like something isn't happening, but you think it
>>> should. Could you be more precise about what you expect to happen (the
>>> conditions that *should* lead to the warning, but do not)? There are
>>> lots of variables floating around:
>>> - devel or release? (I see similar commits to devel and release so
>>> unclear which I should look at; current devel version looks like it
>>> fails before it has a chance to give the warning.)
>>
>>
>> yes, this was an unrelated error, which actually Dan warned me about
>> and for which i sent a fix yesterday. the situation i was describing
>> was occurring in both, devel and release, but both are fixed by now.
>>
>>>
>>> - it sounds like you're talking about a Mavericks machine in the Bioc
>>> build system; can you confirm which one?
>>>
>>> Both the devel and release Mavericks build machines use clang, and
>>> both linux machines (zin1/zin2) use gcc with -Wall.
>>
>>
>> so, for instance, the release version from VariantFiltering 1.0.1 was
>> giving these warnings i was talking about:
>>
>> Found the following significant warnings:
>> methods-WeightMatrix.c:256:19: warning: unsequenced modification and
>> access to 'q' [-Wunsequenced]
>> methods-WeightMatrix.c:638:17: warning: unsequenced modification and
>> access to 'q' [-Wunsequenced]
>>
>> *only* in the R CMD check from 'morelia' and not from 'petty' or
>> 'zin2', while all three machines in principle have the -Wall option
>> activated.
>>
>> currently, because i submitted the fix, version 1.0.2 does not give
>> these warnings anymore. however, i have just committed a new version
>> to de release branch, 1.0.3, that has this problem back in line 256:
>>
>> while ((*q++=tolower(*q)));
>>
>> and should recreate the odd situation i saw, that only 'morelia' warns
>> about this line, but not 'petty' or 'zin2'.
>>
>>
>> thanks!
>> robert.
>>
>>
>>
>>>
>>> Thanks,
>>> Nate
>>>
>>> On 06/13/2014 12:54 AM, Robert Castelo wrote:
>>>>
>>>> hi Nathaniel,
>>>>
>>>> thanks for the very clear examples. after all, probably it is just my
>>>> package which may have this problem. one further question below..
>>>>
>>>> On 06/12/2014 07:12 PM, Nathaniel Hayden wrote:
>>>>>
>>>>> Hi, Robert. C++ is my area so I can't speak as knowledgeably about C,
>>>>
>>>> [...]
>>>>>
>>>>> I confirm that using your test file gcc 4.6.3 indeed warns about
>>>>> unsequenced shenanigans with -Wall 'warning: operation on ‘p’ may be
>>>>> undefined [-Wsequence-point]'. I would add it's also a good idea
>>>>> during
>>>>> the development cycle to use -Wextra and -pedantic flags. (You can
>>>>> read
>>>>> about them here:
>>>>> http://gcc.gnu.org/onlinedocs/gcc/Warning-Options.html)
>>>>
>>>>
>>>> the strange things is that the only machine at the building pipeline
>>>> of BioC that warned about this in my package was the one running Mac
>>>> OSX Mavericks with gcc 4.8.2 and not also the Linux zin2 which is
>>>> running gcc 4.6.3
>>>>
>>>> you can see it if the 1.0.1 version of VariantFiltering is still at
>>>> the check report.
>>>>
>>>> anyway, i'll use those options during development and that should
>>>> avoid me this kind of problems in the future.
>>>>
>>>> thanks!
>>>> robert.
>>>>
>>>
>>>
>>>
>>