Re: What is the relation ncbi-magicblast and magicblast
Hi again,
On Sat, Jun 20, 2020 at 09:49:02PM -0400, Aaron M. Ucko wrote:
Seems I stopped reading from here on. May be I was distracted ...
Sorry for repeating myself.
> > Is there any chance to skip the build of makeblastdb to save computing
> > power and time if we ignore the build result anyway?
>
> Yes. For a fully minimal build, you can add the target name
> magicblast.exe to the dh_auto_build command. (The .exe suffix is an
> legacy of Makefile.flat's generator's origin as a tool to generate MS
> Visual Studio project files, and has no effect on the actual build
> product's name.)
>
> Throwing in offline-friendly tests as discussed above is a little
> trickier, but it should work to add, instead,
>
> all_projects="magicblast.exe datatool.exe gene_info_unit_test.exe proteinkmer_unit_test.exe blastdiag_unit_test.exe misc/jsonwrapp/test/"
>
> (Due to some additional build-system quirks, the trailing slash is
> mandatory and supplying multiple target names via all_projects rather
> than directly should save a little time.)
I'll try that.
> > E: ncbi-magicblast: custom-library-search-path usr/bin/magicblast /lib/x86_64-linux-gnu
>
> Please try running configure.orig ... --without-runpath ...
Trying ...
> > 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
>
> AFAICT, these are false positives -- upstream just bundles two rapidson
> versions' headers, which fall under the Expat license. (Per #840333 and
> the top of .../rapidjson11/license.txt, the only part of the full
> rapidjson tree that falls under the problematic JSON license is a
> jsonchecker subtree already omitted here.) It would of course be better
> practice to arrange to use packaged rapidjson, but there's at least no
> DFSG violation here.
OK, I will check this before uploading. If rapidjson was accepted once
may be we are lucky with magicblast as well.
> > If I'm not misleaded the JS errors can be overridden - its just a false
> > positive.
>
> Right, these aren't minified, just poorly formatted in spots. Lintian
> should perhaps consider average rather than maximum line length.
I'll do an override.
I'll report about my further progress.
Thanks a lot for your help
Andreas.
--
http://fam-tille.de
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