Re: PIQUE packaging (Was: request for r-cran packages) [correction]
Hi Tony,
On Wed, Jul 22, 2020 at 11:46:03PM +0100, Tony Travis wrote:
> > Analysis finished: Mon Jul 20 13:56:47 2020
> >
> > Create sativas_GWAS.covar file...
> > smartpca -p sativas_GWAS.par > sativas_GWAS-smartpca.log
> > OOPS -i flag not specified at /usr/bin/smartpca line 21.
> > pique: error - Can't read sativas_GWAS.evec
> > make: *** [Makefile:29: input] Fehler 255
>
> I created a pristine Ubuntu-MATE 20.04 VM, installed "med-bio" and
> "med-bio-dev" into it, then installed PIQUE from GitHub without any tar-ball
> dependencies. The only missing dependency was
> "libparallel-forkmanager-perl", which I installed, and then the PIQUE test
> ran without error.
libparallel-forkmanager-perl is in the list of Depends of the pique
package uploaded to new - so this should be settled.
> I'll update PIQUE on Github and remove the tar-ball dependencies from it now
> that everything I need is available in "med-bio" or "med-bio-dev".
Well, "everything you need" is (hopefully) specified as Depends of the
pique package - if not that should be fixed. IMHO we need to sort out
the details of the error above. Could you please check with a recent
version of eigensoft the issue behing the
OOPS -i flag not specified at /usr/bin/smartpca line 21.
message? The version that was used in this test is 7.2.1+dfsg-1.
> Thanks again for your work packaging PIQUE,
Regarding testing I'd like to refresh my mail from March of last
year which I somehow can not find inside the web archive, so
I'm copying its content here:
Regarding testing pique (and to find such missing depends): test/Makefile
also uses wget to download data. Could you provide a simple shell script
that is using only the available data to test the functionality of pique
a) in a build time test
b) as autopkgtest
?
Kind regards
Andreas.
--
http://fam-tille.de
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