[GenABEL-dev] make check 2 PASS 4 FAIL

L.C. Karssen lennart at karssen.org
Wed Mar 5 22:26:09 CET 2014 

Hi Lucho,

On 05-03-14 17:37, Latchezar (Lucho) Dimitrov wrote:
> Hi Lennart,
> 
> First of all thank you for considering my thoughts.

Most welcome!

> 
> Secondly I'll leave the bug report to you ;-) since I/we are just
> considering using some of the functionality *ABEL provides and I
> seemingly have to subscribe or something in order to file a bug report.
> This (subscription) is something I will do if we get more involved. For
> now I am happy to be somewhat helpful and more importantly to have the
> software built successfully ;-))


Fair enough :-). Hope you'll enjoy working with the ABELs. If not, you
know how to find us.


Best,

Lennart.


P.S. The bug has been filed: Bug #5409,
https://r-forge.r-project.org/tracker/index.php?func=detail&aid=5409&group_id=505&atid=2058

> 
> Thanks again,
> Lucho
> 
>> -----Original Message-----
>> From: L.C. Karssen [mailto:lennart at karssen.org]
>> Sent: Wednesday, March 05, 2014 9:41 AM
>> To: Latchezar (Lucho) Dimitrov; 'genabel-devel at r-forge.wu-wien.ac.at'
>> Subject: Re: [GenABEL-dev] make check 2 PASS 4 FAIL
>>
>> Hi Lucho,
>>
>> On 04-03-14 01:14, Latchezar (Lucho) Dimitrov wrote:
>>> Dear Lennart,
>>>
>>> I had some time to spend and looked at possible solutions.
>>
>> Thanks for that!
>>
>>
>>> Unfortunately the more I look the more I realize:
>>>
>>> 1. why there is no -I in solaris diff ;-)) It's ugly kludge by itself
>>>
>>> 2. I am afraid the idea of having run_diff creates more problems than
>>> it solves. Sorry.
>>>
>>> If I am to implement it now I'd just:
>>>
>>> 1. have only the parts that should be identical in verified_results/
>>> 2. use appropriate diff directly in test_*.sh files - it's just
>>> replacing a proc. call with the actual one-liner
>>>
>>> like replacing, for example:
>>>
>>> run_diff linear_base_add.out.txt \
>>>     linear_ngp2_add.out.txt \
>>>     "QT check: dose vs. prob (additive model)" -I SNP
>>>
>>> if tail -n +2 linear_ngp2_add.out.txt |diff
>> linear_base_add.out.txt_1st_line_removed - ; then
>>>    echo -e "${name}${blanks:${#name}} OK"
>>> else
>>>    echo -e "${name}${blanks:${#name}} FAILED"
>>> #  exit 1   # replace this as appropriate
>>> fi
>>>
>>> This way it will be way more flexible and more importantly system
>>> independent - no autoconf and all that stuff.
>>
>> Autoconf has some nice features, but definitely isn't for the faint-of-
>> heart :-).
>>
>>>
>>> There are many variations of the approach but the idea should be
>> clear.
>>> More important question to me to resolve/answer, though, is "Do
>> really
>>> otherwise the same columns have to have different names in different
>>> files?". I'd rather put the differences in the file names and keep
>> the
>>> columns the same.
>>
>> That's a good suggestion! One of those things you overlook if you're
>> used to it for so long. Indeed the -I option is only used when
>> comparing output from dosage data to output from probability data (and
>> then only for the additive model). It makes sense to change the
>> headers, make the "dosage headers" equal to the "probability headers".
>> Especially since the "probability header" contains an explicit
>> reference to the SNP that is used as reference for calculating beta.
>>
>> I'll start up a conversation on the mailing list specifically for this
>> and add a bug report as well (unless you're willing to do so, of
>> course!).
>>
>>
>>>
>>>
>>> But ... this may be just me ;-))
>>
>> Always good to have a fresh pair of eyes looking at the code.
>>
>>
>> Best,
>>
>> Lennart.
>>
>>>
>>>
>>> Best regards,
>>> Lucho
>>>
>>>> -----Original Message-----
>>>> From: Latchezar (Lucho) Dimitrov
>>>> Sent: Monday, March 03, 2014 5:39 PM
>>>> To: 'L.C. Karssen'; 'genabel-devel at r-forge.wu-wien.ac.at'
>>>> Subject: RE: [GenABEL-dev] make check 2 PASS 4 FAIL
>>>>
>>>> Dear Lennart,
>>>>
>>>> As I said (or thought I had) it was ugly (quick & dirty) but worked
>>>> as a proof. 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.
>>>>
>>>> Sorry I do not have a nice solution. If I come across something I'll
>>>> let you know.
>>>>
>>>> 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
>> -*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-
> 
> 

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

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

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