[GenABEL-dev] make check 2 PASS 4 FAIL

Mon Mar 3 22:16:16 CET 2014

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
-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-

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