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 21 Haz 2016 14:43 tarihinde "Andreas Tille" <[email protected]> yazdı: > 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 <[email protected]>: > > > > > 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" <[email protected]> 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 <[email protected]>: > > >> > > > >> > > 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 <[email protected]> > > >> > > 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 <[email protected]>: > > >> > > > > > >> > > > > 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" <[email protected] > > > > >> 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 > > >> > > > > > -- > http://fam-tille.de > >
