[GenABEL-dev] make check 2 PASS 4 FAIL

L.C. Karssen lennart at karssen.org
Wed Mar 5 15:16:55 CET 2014 

Dear Lucho,

On 03-03-14 23:38, Latchezar (Lucho) Dimitrov wrote:
> Dear Lennart,
> 
> As I said (or thought I had) it was ugly (quick & dirty) but worked
> as a proof.

You did mention that. I was hoping it wasn't as ugly as you said :-).


> I used, e.g., 'tail -n +2 $file1 >f1' to make a copy of each of
> the two files with first line removed and then 'diff'. The ugliest part
> is it is the same for all diff's, i.e., it does not take -I into account
> at all just blindly compares the two files w/o the first line. But it
> worked for me as a proof my build is correct.

Not too bad a solution. Excluding the headers will not be too much of a
problem, although the current implementation has the advantage that it
excludes the headers only when they are expected to be different.

> 
> Sorry I do not have a nice solution. If I come across something I'll
> let you know.


Thanks a lot,

Lennart.

> 
> Thanks,
> Lucho
> 
>> -----Original Message-----
>> From: L.C. Karssen [mailto:lennart at karssen.org]
>> Sent: Monday, March 03, 2014 4:16 PM
>> To: Latchezar (Lucho) Dimitrov; 'genabel-devel at r-forge.wu-wien.ac.at'
>> Subject: Re: [GenABEL-dev] make check 2 PASS 4 FAIL
>>
>> Dear Lucho,
>>
>>
>> On 03-03-14 21:38, Latchezar (Lucho) Dimitrov wrote:
>>> Dear Lennart,
>>>
>>> Yeah, I know. Solaris is not for the faint of heart ;-) however it is
>>> rewarding! Anyway, I have built some of the gnu utils on solaris but
>>> diff is not amongst them. GCC is though. I looked more carefully at
>>> the diff's (pun intended) between gnu(linux) diff and the one I have
>>> and figured it is -I option missing in mine. I changed run_diff my
>> way
>>> to skip first line in all comparisons and it worked. Now that I
>>> confirmed it is 'make check' issue and not the build itself one I am
>> happy.
>>
>> Glad to hear it all worked out! From your remark below it seems that
>> you modified run_diff a bit in order to ignor ethe first line. If so,
>> would you consider sending a patch? Ths would bring Solaris support
>> (and portability in general) one step closer.
>>
>>>
>>> BTW, I couldn't find a quick nice replacement for your -I option to
>>> share so it might be a good idea at least to mention the case and the
>>> requirement for diff to support -I for 'make check' to work properly.
>>
>> I'll see if I can find a way to let autoconf figure out if a certain
>> option is accepted by a command. It seems that the
>> AC_PATH_PROGS_FEATURE_CHECK macro can do this. That may be helpful for
>> other cases as well.
>>
>>> I'd also suggest changing
>>>
>>> if diff "$file1" "$file2" $args; then
>>>
>>> to the canonical
>>>
>>> if diff $args "$file1" "$file2" ; then
>>>
>>> which actually quickly showed me where the problems was and might be
>>> helpful to ones who do not read the readme files :-))
>>>
>>
>> Done, thanks for the suggestion. It's in SVN r1603.
>>
>>
>> Thanks,
>>
>> Lennart.
>>
>>>
>>> Thank you very much,
>>> Lucho
>>>
>>> PS. I may decide to make a module gnu in my solaris systems ;-)))
>>>
>>>
>>>> -----Original Message-----
>>>> From: L.C. Karssen [mailto:lennart at karssen.org]
>>>> Sent: Monday, March 03, 2014 4:13 AM
>>>> To: Latchezar (Lucho) Dimitrov; 'genabel-devel at r-forge.wu-
>> wien.ac.at'
>>>> Subject: Re: [GenABEL-dev] make check 2 PASS 4 FAIL
>>>>
>>>> Dear Lucho,
>>>>
>>>> Thanks for your interest in ProbABEL. I think you are one of the
>>>> (very?) few users using ProbABEL on Solaris, so we are very
>>>> interested in your feedback.
>>>>
>>>> Could you send us the config.log file created when running
>> ./configure?
>>>> That may give us some more hints on how your system is configured.
>>>>
>>>> My first hunch is that the diff utility in Solaris has some
>> different
>>>> options from the GNU version. When comparing the outputs from dosage
>>>> inputs with probability input files the checks use the -I option to
>>>> ignore the header line. Does your version of diff have that option?
>>>>
>>>> My knowledge of Solaris is a bit rusty, but I seem to remember that
>>>> some of the GNU tools are available (or at least in principle
>>>> installable) on Solaris. I think they are then prefixed with a g. Do
>>>> you have gdiff on your system (maybe in /usr/bin/ or /usr/sfw/bin/)?
>>>>
>>>>
>>>> Best regards,
>>>>
>>>> Lennart Karssen.
>>>>
>>>> On 02-03-14 01:10, Latchezar (Lucho) Dimitrov wrote:
>>>>> Dear genABEL developers,
>>>>>
>>>>> I have successfully built probABEL v.0.4.2 using gcc-4.1.1 on
>> ORACLE
>>>>> Solaris 10 x86 but when I ran
>>>>>
>>>>>   make check
>>>>>
>>>>> I got the subj. results. I went and manually ran one of the failing
>>>> check:
>>>>>
>>>>> run_diff coxph_dose_add.out.txt coxph_prob_add.out.txt \
>>>>>      "pacoxph check: dose vs. prob" -I SNP
>>>>> diff: two filename arguments required pacoxph check: dose vs. prob
>>>> FAILED
>>>>>
>>>>> Then I manually compared the two fails:
>>>>>
>>>>> diff coxph_dose_add.out.txt coxph_prob_add.out.txt
>>>>> 1c1
>>>>> < name A1 A2 Freq1 MAF Quality Rsq n Mean_predictor_allele chrom
>>>>> position beta_SNP_add sebeta_SNP_add chi2_SNP
>>>>> ---
>>>>>> name A1 A2 Freq1 MAF Quality Rsq n Mean_predictor_allele chrom
>>>>>> position beta_SNP_addA1 sebeta_SNP_addA1 chi2_SNP_A1
>>>>>
>>>>> Finally, I compared the two files w/o their first lines and they
>> are
>>>> the same.
>>>>>
>>>>>
>>>>> Any help highly appreciated. Please find the log file attached
>>>>>
>>>>>
>>>>> Thank you very much,
>>>>> Latchezar (Lucho) "Speaking w/ computers" Dimitrov
>>>>>
>>>>> Analyst/Programmer IV,
>>>>> Center for Genomics and Personalized Medicine Research
>>>>> Wake Forest University School of Medicine      fax:  (336)713-7566
>>>>> Medical Center Blvd.                           work: (336)713-7137
>>>>> Winston-Salem, NC 27157
>>>>>
>>>>> -- A computer lets you make more mistakes faster than any invention
>>>> in human history --
>>>>>    with the possible exceptions of handguns and tequila.
>>>>>                                            --Mitch Ratliffe,
>>>> "Technology Review"
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> _______________________________________________
>>>>> genabel-devel mailing list
>>>>> genabel-devel at lists.r-forge.r-project.org
>>>>> https://lists.r-forge.r-project.org/cgi-
>> bin/mailman/listinfo/genabel-
>>>> d
>>>>> evel
>>>>>
>>>>
>>>> --
>>>> *-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*
>>>> L.C. Karssen
>>>> Utrecht
>>>> The Netherlands
>>>>
>>>> lennart at karssen.org
>>>> http://blog.karssen.org
>>>> GPG key ID: A88F554A
>>>> -*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-
>>>
>>>
>>
>> --
>> *-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*
>> L.C. Karssen
>> Utrecht
>> The Netherlands
>>
>> lennart at karssen.org
>> http://blog.karssen.org
>> GPG key ID: A88F554A
>> -*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-
> 
> 

-- 
*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*
L.C. Karssen
Utrecht
The Netherlands

lennart at karssen.org
http://blog.karssen.org
GPG key ID: A88F554A
-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-

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