Re: Pique #986194 Bug closing

On Wed, Dec 13, 2023 at 1:40 AM Tony Travis <
[email protected]> wrote:

> On 13/12/2023 00:16, Tony Travis wrote:
> > On 12/12/2023 19:29, Komolehin Israel wrote:
> >> Hi Team,
> >>
> >> I worked on Pique package by providing autopkgtest and providing a
> >> patch to fix the smartpca command that blocks the upstream test from
> >> running successfully. CI was successful.
> >>
> >> This closes #986194 bug.
> >>
> >> I look forward to review and upload.
> >
> > Hi, Israel.
> >
> > I'm the upstream author of PIQUE: I was not aware of a problem with
> > "smartpca". Have you checked the version on GitHub?
> >
> >> https://github.com/tony-travis/PIQUE
> >
> > AFAIK, this version works correctly under Ubuntu 22.04 LTS but I've not
> > tested it under Debian.
>
> > Hi, Israel.
>
> > This is the version of EIGENSOFT that I have under Ubuntu-MATE 22.04:
>
> > root@wildcat:/usr/local/src/bioinformatics/PIQUE/master/test# apt
> policy eigensoft
> > eigensoft:
> >   Installed: 7.2.1+dfsg-3build1
> >   Candidate: 7.2.1+dfsg-3build1
> >   Version table:
> >  *** 7.2.1+dfsg-3build1 500
> >         500 http://gb.archive.ubuntu.com/ubuntu jammy/universe amd64
> Packages
> >         100 /var/lib/dpkg/status
>
> > PIQUE uses "smartpca" like this in the upstream test:
>
> > /usr/bin/smartpca -i sativas_GWAS.ped -a ../sativas413_recode12.map -b
> sativas_GWAS.ped -o sativas_GWAS -p sativas_GWAS -e sativas_GWAS.eval -k 5
> -l sativas_GWAS-smartpca.log
> > /usr/lib/eigensoft/smartpca -p sativas_GWAS.par
> >sativas_GWAS-smartpca.log
> > ploteig -i sativas_GWAS.evec -c 1:2  -p ???  -x  -y  -o sativas_GWAS.xtxt
> > evec2pca-ped.perl 5 sativas_GWAS.evec sativas_GWAS.ped sativas_GWAS
>
> > I've just run the upstream tests without error under Ubuntu-MATE 22.04
>
> > As you probably know, /usr/bin/smartpca is a Perl script that creates a
> > parameter file for /usr/lib/eigensoft/smartpca from its arguments.
>
> > Bye,
>
>   >  Tony.
>
>
>
Hi Tony,

Thanks for the followup on PIQUE test.

The eigensoft version installed on debian during the test is:
 > eigensoft:
> Installed: 8.0.0+dfsg-1
> Candidate: 8.0.0+dfsg -1
> Version table:
> *** 8.0.0+dfsg -1 500
> 500 http://deb.debian.org/debian sid/main amd64 Packages
> 100 /var/lib/dpkg/status

`run("smartpca -p $par_file > $out-smartpca.log");` looks up
/usr/bin/smartpca instead of /usr/lib/eigensoft/smartpca (I suppose) which
breaks the test with the following message:

 OOPS -1 flag not specified at /usr/bin/smartpca Line 21.

The fix was to circumvent this. However, could eigensoft recent version be
responsible for the behaviour ?

Regards,
Israel