[GenABEL-dev] make check 2 PASS 4 FAIL

[L.C. Karssen]

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

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

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