[GenABEL-dev] make check 2 PASS 4 FAIL

[Latchezar (Lucho) Dimitrov]

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.

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'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 :-))


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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> > evel
> >
> 
> --
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> L.C. Karssen
> Utrecht
> The Netherlands
> 
> lennart at karssen.org
> http://blog.karssen.org
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