Packaging iqtree for Debian
[authors of iqtree in Bcc to hide address from spammers]
Hi,
I'm writing you on behalf of the Debian Med team that has the objective
to package all free software that is relevant in the fields of Biology
and Medicine for official Debian. We have assembled a fair amount of
biological software[1] and since I've got a user request to also package
iqtree I started to package your program. When doing so some question
were raised which I like to discuss here:
1. zlib and eigen
Per Debian policy we do not use code copies of third party libraries due
to the potential security risks that might occure if one code might be
fixed but other copies remain untouched (and there are other good
reasons for this). So I used a patch that links iqtree against the
Debian packaged zlib and eigen lib. You can download this patch here[2].
I recommend to use some detection algorithm to check whether the needed
libraries do exist on a given system and use these instead of the code
copies.
2. sprng
While libsprng also packaged for Debian I was not able to use this since
you have changed its interface by adding a parameter to init_sprng. I
documented this here[3] and deactivated this patch. I do not think that
it is a good idea to patch a third party library without any
documentation. Could you please give reasons for the change or could
your even consider using the originally released libsprng?
3. Nexus Class Library and PLL
I might consider packaging these two libraries separately for Debian
since they might be useful in other projects than iqtree. Could you
please confirm that you are using the plain upstream source or are there
possibly also some changes applied in the copy inside the iqtree source
tree?
4. Location of file models.nex
The file models.nex is installed into the very same directory as the
executable iqtree. This is invalild according to FHS since iqtree will
be installed to /usr/bin/iqtree since it is an executable binary but
models.nex is just a non-executable data file and should rather go to
/usr/share/iqtree/models.nex. I would have provided a patch but I
admit I'm not fully sure where this file is used at all. I did not
found this verbose string inside the code. Could you please give any
hint where this file is loaded?
5. File example.phy is missing in download
While the CMakeLists.txt tries to install a file
examples/example.phy
this is missing in your download tarball. This is an error and any
user will stumble upon it. Could you please add this file to the
download tarball.
BTW, if there would be some publicly readable Git repository this
would be helpful to download this kind of missing files.
6. Missing source for Documents/iqtree-manual-1.0.pdf
In Debian PDF files without the according source (LaTeX, or something
like this) are considered as "binary without source". As a consequence
I would need to remove this documentation which would not be in the
interest of the iqtree users. Could you be so kind to provide the
according source in your download tarball (or anywhere else if this
seems more convenient to you)?
Kind regards and thanks for providing iqtree as Free Software
Andreas.
[1] http://blends.debian.org/med/tasks/bio
[2] https://anonscm.debian.org/cgit/debian-med/iqtree.git/tree/debian/patches/use_debian_packaged_libs.patch
[3] https://anonscm.debian.org/cgit/debian-med/iqtree.git/tree/debian/patches/debian_packaged_sprng.patch
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