Re: What is the relation ncbi-magicblast and magicblast
Hi Aaron,
On Fri, Jun 19, 2020 at 12:09:56PM -0400, Aaron M. Ucko wrote:
> 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 think due to outdated assumptions about live data.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)
I did this. I'm a bit worried about those errors but if you say so
I think we can go with this.
> 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+.)
Is there any chance to skip the build of makeblastdb to save computing
power and time if we ignore the build result anyway?
> 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.
Done.
> 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.
Droping sra-toolkit works fine.
> Thanks, and please feel free to consult me again if you have any other
> questions.
Yes, there are remaining questions raised by lintian:
E: ncbi-magicblast: custom-library-search-path usr/bin/magicblast /lib/x86_64-linux-gnu
E: ncbi-magicblast source: license-problem-json-evil c++/include/misc/jsonwrapp/rapidjson10/license.txt
E: ncbi-magicblast source: license-problem-json-evil c++/include/misc/jsonwrapp/rapidjson11/license.txt
E: ncbi-magicblast source: source-is-missing c++/src/html/ncbi_menu.js line length is 357 characters (>256)
E: ncbi-magicblast source: source-is-missing c++/src/html/ncbi_menu_dnd.js line length is 333 characters (>256)
E: ncbi-magicblast source: source-is-missing c++/src/html/ncbi_menu_dyn.js line length is 333 characters (>256)
If I'm not misleaded the JS errors can be overridden - its just a false
positive. However, I'm worried about the evil json library and need
help for the custom-library-search-path one.
Kind regards
Andreas.
--
http://fam-tille.de
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