Andreas Tille <ti...@debian.org> writes:
> Thanks for these helpful hints which I implemented and pushed.
No problem. I alas don't have time to take this package on fully, but
am happy to offer more hints.
> Unfortunately I'm now running into an error of the test suite:
Declaring a build dependency on the time package clears up these
immediate errors. However, several tests involve connecting to the
network, and blast_services_unit_test fails even when it can connect, I
think due to outdated assumptions about live data. You can adjust
debian/rules to tolerate test suite errors but report their details with
override_dh_auto_test:
-dh_auto_test || \
(cd c++/*/build && ./check.sh concat_err && cat check.sh.out_err)
With that problem out of the way, I see errors from dh_auto_install due
to lack of DESTDIR support upstream. I'd suggest substituting manual
installation of c++/*/bin/magicblast, which should be the only build
product you actually need here. (The upstream binary tarball includes
just magicblast and makeblastdb, for the latter of which you should
recommend or even depend on ncbi-blast+.)
Also, you can avoid the need to wildcard by adding a flag along the
lines of --with-build-root=BUILD, which will give the new c++
subdirectory a static name of BUILD.
> Moreover I've added unixodbc-dev to Build-Depends but I have no idea
> how to get rid of the code copy in
>
> c++/include/dbapi/driver/odbc/unix_odbc
Please try patching c++/src/dbapi/driver/dbapi_driver_utils.cpp to use
<sqlext.h> unconditionally, rather than only for NCBI_OS_MSWIN.
On a related note, please declare a build dependency on liblmdb-dev to
ensure building against the system installation rather than a
convenience copy. The existing build dependency on libncbi-vdb-dev
should indirectly take care of any other helpful lib*-dev dependencies;
I'm not sure what purpose the build dependency on sra-toolkit serves.
Thanks, and please feel free to consult me again if you have any other
questions.
--
Aaron M. Ucko, KB1CJC (amu at alum.mit.edu, ucko at debian.org)
http://www.mit.edu/~amu/ | http://stuff.mit.edu/cgi/finger/?a...@monk.mit.edu
