Hello Andreas,
Actually i dont have a solution because program dont work like they offer. I can manage to solve this fault it is a bit trick. If i wrote the section names in a file and give file path to program it is working .
Their mention is :
Fastaremove FASTAFİLE (PATH or STDIN)
But PATH works STDIN dont.
Best regards
Canberk Koç
www.about.me/canberkkoc
Hi Canberk,
thanks for checking. Unfortunately I do not really understand what you
want to express. You quoted a section from src/util/fastaremove.c but
what exactly would be your solution to fix the problem? Could you
provide a quilt patch which would lead to proper operation of the code?
Kind regards
Andreas.
On Fri, Jun 10, 2016 at 02:29:04AM +0300, Canberk Koç wrote:
> Hİ All,
>
> I tried to patch file tonight but i found i make a mistake about typo
> mistake . fastaremove script wont work on stdin.
> For example
> I made a.txt file and wrote the header of fasta sequences it worked but
> when i give it stdin not a path program gives error. I think it may occur
> because of deprecated g_strcasecmp function below i give you error line .
> I think it is a bug situation here.
>
> if(!g_strcasecmp(remove_path, "stdin")){
> remove_fp = stdin;
> } else {
> remove_fp = fopen(remove_path, "r");
> if(!remove_fp)
> g_error("Could not open list for removal [%s]",
> remove_path);
> }
>
> Best Regards
>
>
>
> Canberk Koç
> [image: https://]about.me/canberkkoc
> <https://about.me/canberkkoc?promo=email_sig&utm_source=email_sig&utm_medium=email_sig&utm_campaign=external_links>
>
> 2016-06-08 17:25 GMT+03:00 Canberk Koç <canberkkoc@gmail.com>:
>
> > Hello Andreas,
> >
> > Thanks for your understanding. I'll focus fully now i'll upload quilt
> > patches by tommorrow and pick another package.
> >
> > Best Regards
> >
> > Canberk Koç
> > www.about.me/canberkkoc
> > 8 Haz 2016 16:26 tarihinde "Andreas Tille" <andreas@an3as.eu> yazdı:
> >
> > Hi Canberk,
> >>
> >> I hope you were luckily passing your exams. Please make sure to
> >> increase your activity from now on. Midterm evaluations are approaching
> >> at end of June and so far there is nothing mentionable done. I confirm
> >> that I understand your situation and the importance of your exams but if
> >> there is no mentionable activity I can not lie in the evaluation.
> >>
> >> Please also note: I'll be basically offline from 10.-17. of June. I
> >> trust my team mates for helping you when writing to the list and thus
> >> you are not alone in case of trouble.
> >>
> >> Kind regards
> >>
> >> Andreas.
> >>
> >> On Wed, Jun 01, 2016 at 06:34:14AM +0300, Canberk Koç wrote:
> >> > Hello Andreas,
> >> >
> >> > Due to my final exams i'll be passive to 8 June when if it will be a
> >> > problem i try to do work also patches.
> >> > İf it's not it will be very good for me .
> >> >
> >> > Best Regards
> >> >
> >> >
> >> >
> >> > Canberk Koç
> >> > [image: https://]about.me/canberkkoc
> >> > <
> >> https://about.me/canberkkoc?promo=email_sig&utm_source=email_sig&utm_medium=email_sig&utm_campaign=external_links
> >> >
> >> >
> >> > 2016-05-31 9:41 GMT+03:00 Andreas Tille <andreas@an3as.eu>:
> >> >
> >> > > Hi Canberk,
> >> > >
> >> > > On Tue, May 31, 2016 at 04:43:45AM +0300, Canberk Koç wrote:
> >> > > >
> >> > > > Finally i manage to figure out what is wrong in tests.
> >> > >
> >> > > :-)
> >> > >
> >> > > > At last resort i run tests manually and find out these results.
> >> > >
> >> > > I admit I *always* try to design the tests that it can be run manually
> >> > > on the local machine. I also usually install the tests into
> >> > > /usr/share/doc/<packagename>
> >> > > and add a README.test there to inform users how they can test the
> >> > > package manually. This serves in most cases as an informative example
> >> > > how to use the software.
> >> > >
> >> > > > First:
> >> > > >
> >> > > > *fastaremove.test.sh <http://fastaremove.test.sh>line no: 25*
> >> > > >
> >> > > > *$FASTAREMOVE $INPUTFILE CALM_HUMAN(ARGUMENT PART) > $OUTPUTFILE*
> >> > > >
> >> > > > Upper test fails because upstream package have a little bug in
> >> test.sh.
> >> > > > There must be >CALM_HUMAN for input argument but they forget ">"
> >> > > character :-)
> >> > >
> >> > > Please forward this upstream (address is in debian/copyright) but
> >> > > see below first.
> >> > >
> >> > > > *fastaindex.fastafetch.test.sh <
> >> http://fastaindex.fastafetch.test.sh>
> >> > > >
> >> > > > line no: 34
> >> > > > $FASTAFETCH $INPUTFILE $INDEXFILE $IDENTIFIER
> >> > > >
> >> > > > line no:52
> >> > > > run_fastafetch A_MISSING_FROM_START 1
> >> > > > run_fastafetch M_MISSING_FROM_MIDDLE 1
> >> > > > run_fastafetch z_MISSING_FROM_END 1*
> >> > > >
> >> > > > Upper test fail because in source file it take an argument -1 for
> >> > > > fail and in test.sh they use -1 parameter for showing fail
> >> situation.
> >> > > > At these lines they test for what program act when there is a
> >> missing
> >> > > > part in fasta file so test working correct actually :-)
> >> > > > if you need more info i can show c.file line numbers too .
> >> > > >
> >> > > > Now what we do for correct these mistakes :)
> >> > >
> >> > > quilt push -a
> >> > > # this applies all previous patches
> >> > > quilt new fix_test1.patch
> >> > > # this creates a new patch
> >> > > quilt edit <path_to>/test.sh
> >> > > Add the missing ">"
> >> > > quilt refresh
> >> > > # this tells quilt you are done with the patch
> >> > > quilt new fix_test2.patch
> >> > > # this creates another patch (feel free to leave
> >> > > # this out and block-fix everything in one patch
> >> > > quilt edit <broken_c_file_with_wrong_return_code>
> >> > > Fix the return code
> >> > > quilt refresh
> >> > > # done with patching
> >> > > quilt pop -a
> >> > > # unapply all patches
> >> > > editor debian/patches/fix_test1.patch
> >> > > Add the DEP3 fields:
> >> > >
> >> > > Author: Canberk Koç <canberkkoc@gmail.com>
> >> > > Last-Update: <timestamp>
> >> > > Description: <explain what you explained above
> >> > > to make upstream understand the problem>
> >> > > editor debian/patches/fix_test2.patch
> >> > > If you decided to use two patches add DEP3 header as well
> >> > > git add debian/patches/fix_test*.patch
> >> > > git commit -a -m 'Fix testsuite'
> >> > > git push
> >> > >
> >> > > Once you are done with this I can check. Then we can point upstream
> >> to
> >> > > our patches to enable inclusion into next release.
> >> > >
> >> > > Please do not hesitate to ask if the advise above is to short.
> >> > >
> >> > > Kind regards
> >> > >
> >> > > Andreas.
> >> > >
> >> > > > Best regards
> >> > > >
> >> > > >
> >> > > >
> >> > > >
> >> > > > Canberk Koç
> >> > > > [image: https://]about.me/canberkkoc
> >> > > > <
> >> > >
> >> https://about.me/canberkkoc?promo=email_sig&utm_source=email_sig&utm_medium=email_sig&utm_campaign=external_links
> >> > > >
> >> > > >
> >> > > > 2016-05-26 13:10 GMT+03:00 Canberk Koç <canberkkoc@gmail.com>:
> >> > > >
> >> > > > > Hello Andreas,
> >> > > > >
> >> > > > > Actually hints give me some ideas but i am struggling with
> >> > > understanding
> >> > > > > what is wrong. Package do these tests in building by itself no
> >> problem
> >> > > > > occurs but adt-run give 2 test failure though one test works once
> >> also
> >> > > :-)
> >> > > > > I look at build log see some warnings about deprecated methods
> >> i'll
> >> > > gather
> >> > > > > all together and turn back to you.
> >> > > > >
> >> > > > > Best regards
> >> > > > >
> >> > > > > Canberk Koç
> >> > > > > www.about.me/canberkkoc
> >> > > > > 26 May 2016 12:50 tarihinde "Andreas Tille" <andreas@an3as.eu>
> >> yazdı:
> >> > > > >
> >> > > > > Hi Canberk,
> >> > > > >>
> >> > > > >> since you did not sent any answer I assume the hints were helpful
> >> > > > >> enough. Is this assumption true?
> >> > > > >>
> >> > > > >> Kind regards
> >> > > > >>
> >> > > > >> Andreas.
> >> > > > >>
> >> > > > >> On Tue, May 24, 2016 at 08:09:11AM +0200, Andreas Tille wrote:
> >> > > > >> > Hi Tanya,
> >> > > > >> >
> >> > > > >> > > ...
> >> > > > >> >
> >> > > > >> > thanks for your verbose and (without testing sounding) sensible
> >> > > input.
> >> > > > >> >
> >> > > > >> > On Tue, May 24, 2016 at 05:26:06AM +0300, merlettaia wrote:
> >> > > > >> > > Hope this helps.
> >> > > > >> > > Please, somebody correct me if my interpretation is wrong.
> >> > > > >> >
> >> > > > >> > Canberk, please let us know here if you need some further help
> >> or
> >> > > > >> > testing.
> >> > > > >> >
> >> > > > >> > Kind regards
> >> > > > >> >
> >> > > > >> > Andreas.
> >> > > > >> >
> >> > > > >> > --
> >> > > > >> > http://fam-tille.de
> >> > > > >> >
> >> > > > >> >
> >> > > > >>
> >> > > > >> --
> >> > > > >> http://fam-tille.de
> >> > > > >>
> >> > > > >>
> >> > >
> >> > > --
> >> > > http://fam-tille.de
> >> > >
> >> > >
> >>
> >> --
> >> http://fam-tille.de
> >>
> >
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