Re: [Outreachy] Hi all!
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-a54519f15bc3c06b1500f7c238715fc793b4a7db_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
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