[GenABEL-dev] make check 2 PASS 4 FAIL

Mon Mar 3 23:38:53 CET 2014

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"
> >>>
> >>>
> >>>
> >>>
> >>> _______________________________________________
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> >>> 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
> -*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-