[GenABEL-dev] make check 2 PASS 4 FAIL

Latchezar (Lucho) Dimitrov ldimitro at wakehealth.edu
Wed Mar 5 17:37:52 CET 2014 

Hi Lennart,

First of all thank you for considering my thoughts.

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 ;-))

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
> -*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-

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