Dear all, I am sorry for the long absence , i had unexpected turnarounds with the experiment i am running for my thesis ;)
However in my free time i kept trying to build the above mentioned packages from source - and i think i am more successful than before. Running sudo apt-get source bwa cd bwa-0.7.12 sudo apt-get build-dep bwa sudo apt-get upgrade debuild -i -us -uc -b produced the desired bwa_0.7.12-5_amd64.deb file. I also build the other the packages ' primer3' , 'maq' and 'tophat' (which builds fine as well) for some more practice. However , i cannot find the */debian/tests/' file - i'm running the 'apt-file list bwa_0.7.12-5_amd64.deb' command - so maybe there is still some mistake in the build? Or maybe i should use another command? Thank you all again for your help :) Kind regards, Kate On Fri, Oct 20, 2017 at 11:28 AM, Andreas Tille <[email protected]> wrote: > Hi Katerina, > > On Thu, Oct 19, 2017 at 07:05:39PM +0300, ka lou wrote: > > I am sorry for the late answer! This is just an update on my last tries > to > > get the source of tophat and run a test with sbuild ;) > > Good you hit the list with your question. > > > As Diane suggested in the last email , i downloaded and installed (at > least > > tried too) the sbuild package on my linux mint machine. I followed the > > instructions of the Debian wiki > > <https://wiki.debian.org/sbuild#CA-a54519f15bc3c06b1500f7c238715f > c793b4a7db_1> > > and > > i also installed the libsbuild-dev > > <https://community.linuxmint.com/software/view/libsbuild-dev>. Things > > seemed to work up until that point. > > Good. I admit I *personally* was never happy with sbuild (in contrast > to others who like it) since I was always running into trouble. > > > I then followed the commands 'apt source tophat' , 'apt build-dep > > tophat', 'cd usr/source/tophat', 'dpkg-buildpackage', which went also > > well. > > Are you sure that you went to usr/source/tophat? Apt source extracts the > source to > > ./tophat-<packageversion> > > at this point I would suggest to use debuild (from devscripts package). > This is the most simple way to create a Debian package on your local > machine. For this to work you did right with `apt build-dep tophat` > (which is not needed in a chroot as sbuild is creating). > > Could you confirm that this creates a tophat*.deb package? > > > However, when i tried 'sudo sbuild -d unstable' , after running for a > while > > i get an error : 'E: Build failure (dpkg-buildpackage died)'. > > I think the error connected to that (last lines of the log) is that : > > '/usr/include/c++/7/bits/stl_pair.h:519:5: note: template argument > > deduction/substitution failed: > > tophat_reports.cpp:2707:128: note: cannot convert ‘junction_stat’ (type > > ‘JunctionStats’) to type ‘JunctionStats&&’ > > gtf_junctions.insert(make_pair<Junction, > > JunctionStats>(Junction(ref_id, left_coord, right_coord, antisense), > > junction_stat));' > > I admit I'm not aware that tophat fails to build from source. To save you > some trouble from this actual package which was a pretty random example > here are some other example packages featuring autopkgtests. Just forget > tophat and use either > > bwa > primer3 > maq > > as examples. There is no point in wasting your time with tophat. > > > I can also send you more details if you wish (e.g the summary) , i am > sorry > > i do not know very well how to report all these. > > > > Finally , i would like to tell you that since my PhD thesis deadline is > > postponed to the end of January , i will probably won't make it to apply > to > > the Outreach program for this round... which is really sad. However , > with > > your permission, i would like to keep on working on running tests and get > > more familiar with the whole process. And hopefully i will be able to > apply > > for Outreach's next round! > > There is absolutely no need to ask for permission to help inside the > Debian Med team. Everybody is perfectly welcome to join the project and > help us making the best operating system for life sciences and medicine. > > Kind regards > > Andreas. > > -- > http://fam-tille.de > >
