On Wed, Dec 13, 2023 at 1:40 AM Tony Travis < tony.tra...@minke-informatics.co.uk> 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
