Re: [Advent bug squashing] Re: PIQUE
On 04/12/2022 05:35, Andreas Tille wrote:
Hi Tony,
Am Sun, Dec 04, 2022 at 01:39:40AM +0000 schrieb Tony Travis:
Thanks for creating the "pique" package for my GWAS pipeline. I've just
installed it under Ubuntu 22.04 LTS and it installed quite a lot of
packages, but fails to run my tests with the error:
Error in library(multtest) : there is no package called ‘multtest’
Fixed in new upload.
I'll file a BUG report.
Since I want to fix a bug every day I simply take this one for today
even if not filed yet. ;-)
Hi, Andreas.
This is my BUG report:
https://bugs.launchpad.net/ubuntu/+source/pique/+bug/1998685
I filed it using "ubuntu-bug".
BTW, could you recommend some kind of test with some small example data
set? We could wrap this into a CI test and would be able to detect
these issues immediately.
There is a Makefile in the PIQUE "test" folder on the GitHub repo that
could be modified to test the installed version of PIQUE, rather than
testing the version of PIQUE in the source tree.
It downloads test data: We had a conversation about this previously and
I explained that GWAS requires quite a 'large' data-set to test it (44K
SNP's). In fact, the 'test' data is small by comparison to a typical
GWAS that we do with millions of SNP's. GWAS requires a genotype file
and a phenotype file. The phenotype file, and subsets, of it are in the
PIQUE "test" folder.
Thanks again for packaging "PIQUE",
Tony.
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