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