Re: GSOC [Continuous Integration for all biological applications inside Debian]
Hello,
I have identified (some of the glitches) of the autodock tools and I
know upstream to already have worked on it, seriously. This is the pack
and grid on the same frame and incompatibility with the numeric library.
I'll send them a ping.
Best,
Steffen
On 07/04/16 23:58, Canberk Koç wrote:
> Hello Andreas,
>
> Thanks for rapid response again i talk with my friend he will send an
> introduction email to list. In test issue i'm confused about something
> if i delete dh_make section and run adt-run package do automatic test
> in built time and give no erors i notice that now but can't figure it
> out why already and working on it. Also i make set -e in unit test
> file but that fatal eror strings wont exit and work through the end it
> is another abnormality i found so i want to give you a little update
> about it.
> And CC issue i do it right now i think :-)
>
> Best Regards
>
> Canberk
>
> 2016-04-07 9:32 GMT+03:00 Andreas Tille <andreas@an3as.eu
> <mailto:andreas@an3as.eu>>:
>
> Hi Canberk,
>
> On Thu, Apr 07, 2016 at 04:42:56AM +0300, Canberk Koç wrote:
> > >[I think I gave a warning that non-private messages will be
> answered on
> > >the mailing list and I hereby doing so shamelessly violating
> netiquette.
> > >It would be great if you would answer on list as well.]
> >
> > Sorry for miss clicking i forget to reply all.
>
> No problem. BTW, the mailing list policy for Debian list is to not CC
> the original poster but just send to the mailing list. The mail
> client
> mutt supports "list-reply" (L) to do this efficiently. I have no idea
> about other mail clients and whether these might support this. Just
> telling you that if you might write on other Debian lists people might
> send angry replies for personal CCs. :-)
>
> > I committed the changes to exonerate package i hope i do it right.
>
> Yes. You did. :-) I turned your "NMU" into a "Team upload". The
> test
> suite can implemented in this way. However, when I actually run the
> test I get:
>
> ...
> /tmp/exonerate-test.nhNsuB/util/fastasplit.test.sh
> <http://fastasplit.test.sh>
> Split fastasplit.test.fasta OK
> Split into two files as expected
> Input len 2136
> Output len 2136
> Input and output lengths match
>
> /tmp/exonerate-test.nhNsuB/util/fastadiff.test.sh
> <http://fastadiff.test.sh>
> fastadiff: id mismatch: CALM_HUMAN P53_HUMAN
> Different seqs recognised as different
> Identity test OK
>
> /tmp/exonerate-test.nhNsuB/util/fastasubseq.test.sh
> <http://fastasubseq.test.sh>
> Generated correct subseq
>
> /tmp/exonerate-test.nhNsuB/util/fastavalidcds.test.sh
> <http://fastavalidcds.test.sh>
>
> ** (process:7647): WARNING **: odd_length length (7) not divisible
> by 3
>
> ** (process:7647): WARNING **: too_short length (4) not divisible by 3
>
> ** (process:7647): WARNING **: no_start missing start codon (has:AAA)
>
> ** (process:7647): WARNING **: no_end missing stop codon (has:TTT)
>
> ** (process:7647): WARNING **: in_frame_stop contains in-frame
> stop codon (pos:9, codon:TAG)
>
> ** (process:7647): WARNING **: non_acgt_base contains non-ACGT
> base: [pos: 5 base: N]
> Validiated CDS sequences OK
> >valid_seq
> ATGAAACCCGGGTTTTAA
> Validated correctly a single seq from input
>
> /tmp/exonerate-test.nhNsuB/util/fastaindex.fastafetch.test.sh
> <http://fastaindex.fastafetch.test.sh>
> Made index fastafetch.test.idx
> /usr/bin/fastafetch fastafetch.test.fasta fastafetch.test.idx
> CALM_HUMAN
> expect 0
> >CALM_HUMAN
> MADQLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADGNGTIDFPEFL
> TMMARKMKDTDSEEEIREAFRVFDKDGNGYISAAELRHVMTNLGEKLTDEEVDEMIREADIDGDGQVNYE
> EFVQMMTAK
> /usr/bin/fastafetch fastafetch.test.fasta fastafetch.test.idx
> P53_HUMAN
> expect 0
> >P53_HUMAN
> MEEPQSDPSVEPPLSQETFSDLWKLLPENNVLSPLPSQAMDDLMLSPDDIEQWFTEDPGPDEAPRMPEAA
> PPVAPAPAAPTPAAPAPAPSWPLSSSVPSQKTYQGSYGFRLGFLHSGTAKSVTCTYSPALNKMFCQLAKT
> CPVQLWVDSTPPPGTRVRAMAIYKQSQHMTEVVRRCPHHERCSDSDGLAPPQHLIRVEGNLRVEYLDDRN
> TFRHSVVVPYEPPEVGSDCTTIHYNYMCNSSCMGGMNRRPILTIITLEDSSGNLLGRNSFEVHVCACPGR
> DRRTEEENLRKKGEPHHELPPGSTKRALPNNTSSSPQPKKKPLDGEYFTLQIRGRERFEMFRELNEALEL
> KDAQAGKEPGGSRAHSSHLKSKKGQSTSRHKKLMFKTEGPDSD
> /usr/bin/fastafetch fastafetch.test.fasta fastafetch.test.idx
> A_MISSING_FROM_START
> expect 1
> ** FATAL ERROR **: Could not find identifier
> [A_MISSING_FROM_START] (missing -F ?)
> exiting ...
> /usr/bin/fastafetch fastafetch.test.fasta fastafetch.test.idx
> M_MISSING_FROM_MIDDLE
> expect 1
> ** FATAL ERROR **: Could not find identifier
> [M_MISSING_FROM_MIDDLE] (missing -F ?)
> exiting ...
> /usr/bin/fastafetch fastafetch.test.fasta fastafetch.test.idx
> z_MISSING_FROM_END
> expect 1
> ** FATAL ERROR **: Could not find identifier [z_MISSING_FROM_END]
> (missing -F ?)
> exiting ...
> fastaindex fastafetch test OK
>
> /tmp/exonerate-test.nhNsuB/util/fastaremove.test.sh
> <http://fastaremove.test.sh>
> Have calmodulin in input
> ** FATAL ERROR **: Could not open list for removal [CALM_HUMAN]
> exiting ...
> Calmodulin successfully removed
> PASS
>
>
> These "FATAL ERROR" strings in connection with "PASS" do not sound
> convincing. I wonder whether the build time tests are different
> in this aspect.
>
>
> > In MoM issue i want to do it but my mid-term exams start and
> they'll finish
> > 25 April i can do it after that date. And i want to ask you one
> friend of
> > mine wants to work it on too can we work together in that project.
>
> We'd be happy about any volunteer contributing to the Debian Med
> project.
>
> Kind regards
>
> Andreas.
>
> --
> http://fam-tille.de
>
>
>
>
> --
>
> --
>
> Canberk Koç
> https://about.me/canberkkoc
>
> <https://about.me/canberkkoc?promo=email_sig&utm_source=email_sig&utm_medium=email_sig&utm_campaign=external_links>
>
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