Re: [MoM] Packaging mindthegap (Was: [MoM] Packaging mindthemap)
Hi Andrius and Shayan,
On Thu, Jul 04, 2019 at 09:31:05AM +0300, merkys@debian.org wrote:
> On 2019-07-04 09:19, Andreas Tille wrote:
> > can you please push?
>
> Sure. I sometimes don't feel comfortable by pushing onto someone's
> active development. My problem.
Not really a problem. To my observation chances for racing conditions
in development of one Debian Med package are pretty low. If you've found
a solution for a problem somebody has mentioned here it makes sense to
push frequently to enable the team member continue to work.
@Shayan
Thanks to Andrius' contribution the cmake issue should be solved. At
least in my pbuilder the build process is starting. Now I was stumbling
upon missing Build-Depends. Generally there are two ways to find out
Build-Depends:
[Educated approach]: Reading upstream docs or even upstream code
[Lazy approach]: Try building and see what's missing
I personally usually follow the lazy approach. ;-) That way I've found
that libboost-dev and zlib1g-dev were missing since the typical header
files were not found. I simply added these since I wanted to make some
progress. However, that's not good from an educational point of view
and thus I stopped here. Currently my build ends with:
...
/usr/bin/c++ -I/build/mindthegap-2.2.0/src -g -O2 -fdebug-prefix-map=/build/mindthegap-2.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/MindTheGap.dir/src/GraphAnalysis.cpp.o -c /build/mindthegap-2.2.0/src/GraphAnalysis.cpp
In file included from /usr/include/gatb/tools/collections/impl/Bloom.hpp:33,
from /usr/include/gatb/gatb_core.hpp:40,
from /build/mindthegap-2.2.0/src/Filler.hpp:25,
from /build/mindthegap-2.2.0/src/Filler.cpp:21:
/usr/include/gatb/tools/math/LargeInt.hpp:38:10: fatal error: hdf5/serial/hdf5.h: No such file or directory
#include <hdf5/serial/hdf5.h>
^~~~~~~~~~~~~~~~~~~~
compilation terminated.
In file included from /usr/include/gatb/tools/collections/impl/Bloom.hpp:33,
from /usr/include/gatb/gatb_core.hpp:40,
from /build/mindthegap-2.2.0/src/Finder.hpp:25,
from /build/mindthegap-2.2.0/src/Finder.cpp:21:
/usr/include/gatb/tools/math/LargeInt.hpp:38:10: fatal error: hdf5/serial/hdf5.h: No such file or directory
#include <hdf5/serial/hdf5.h>
^~~~~~~~~~~~~~~~~~~~
compilation terminated.
In file included from /usr/include/gatb/tools/collections/impl/Bloom.hpp:33,
from /usr/include/gatb/gatb_core.hpp:40,
from /build/mindthegap-2.2.0/src/Finder.hpp:25,
from /build/mindthegap-2.2.0/src/main.cpp:22:
/usr/include/gatb/tools/math/LargeInt.hpp:38:10: fatal error: hdf5/serial/hdf5.h: No such file or directory
#include <hdf5/serial/hdf5.h>
^~~~~~~~~~~~~~~~~~~~
compilation terminated.
make[3]: *** [CMakeFiles/MindTheGap.dir/build.make:92: CMakeFiles/MindTheGap.dir/src/Finder.cpp.o] Error 1
make[3]: *** Waiting for unfinished jobs....
make[3]: *** [CMakeFiles/MindTheGap.dir/build.make:66: CMakeFiles/MindTheGap.dir/src/main.cpp.o] Error 1
make[3]: *** [CMakeFiles/MindTheGap.dir/build.make:79: CMakeFiles/MindTheGap.dir/src/Filler.cpp.o] Error 1
In file included from /usr/include/gatb/tools/collections/impl/Bloom.hpp:33,
from /usr/include/gatb/gatb_core.hpp:40,
from /build/mindthegap-2.2.0/src/Filler.hpp:25,
from /build/mindthegap-2.2.0/src/GraphAnalysis.hpp:32,
from /build/mindthegap-2.2.0/src/GraphAnalysis.cpp:20:
/usr/include/gatb/tools/math/LargeInt.hpp:38:10: fatal error: hdf5/serial/hdf5.h: No such file or directory
#include <hdf5/serial/hdf5.h>
^~~~~~~~~~~~~~~~~~~~
compilation terminated.
What to do next (or how did I found the missing Build-Depends). I'm
using apt-file. If you never used it do
sudo apt install apt-file
sudo apt-file update
(the latter is needed only once if you want to use it right now. The
daily update is done via cron.)
Than you can do
$ apt-file search hdf5/serial/hdf5.h
libhdf5-dev: /usr/include/hdf5/serial/hdf5.h
and you know that you need to add libhdf5-dev as Build-Depends. Try
next build and see what else might be missing.
Further hint: I've looked into your debian/control file. The
formatting of the long description should be not exceed 80 characters.
There is no point in doing the reformatting manually. Just use
cme fix dpkg-control
See Debian Med policy what packages need to be installed to use cme!
It also does some other re-arrangements (one (Build-)Depends per line
and so on). That's the formatting your team mates are comfortable
with. Just trust cme to do the right thing.
> I've fixed minia and uploaded it.
Cool!
Kind regards
Andreas.
--
http://fam-tille.de
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