[Debian-med-packaging] IQ-TREE version 1.3.11

[Andreas Tille]

Dear Minh,

On Mon, Dec 14, 2015 at 09:57:18AM +0100, Bui Quang Minh wrote:
> > 1. Are you sure that you want to provide example.phy twice?
> > 
> > $ ls example*
> > example:
> > example.nex  example.phy  models.nex
> > 
> > examples:
> > example.phy
> 
> I overlooked, please, take the files from example (without s)

Yes, that's what I'm coding now in the packaging - just wanted to
let you know ...
 
> > 2. Would you consider providing the LaTeX source of the manual right
> >   inside the download tarball (which would enable me droping it from
> >   the debian/ dir).
> 
> This manual is outdated and we updated a series of extensive online documentation which I find much more convenient:
> 
> http://www.cibiv.at/software/iqtree/doc
> 
> If you however still prefer pdf, I can add the latex code again…what do you think?

I will provide what you consider most convinient for the users.  As long
as the download tarball contains the pdf without LaTeX source per Debian
policy I have two options:

   1. Provide the LaTeX source in addition to the PDF
   2. Remove the PDF

If you think the latter is the better solution I'll do so and will remove
the PDF.
 
> > 3. In end of August we talked about your code copy of libsprng which
> >   you changed from the original.  I wonder whether you would consider
> >   to migrate to the original version.
> 
> Sure I will consider this, just did not have time yet. Will let you know once I find how to change...

OK.
 
> > 4. Finally I was running into a build problem:
> > 
> > ...
> > -- Looking for strndup - found
> > CMake Error at CMakeLists.txt:337 (add_subdirectory):
> >  add_subdirectory given source "pllrepo/src" which is not an existing
> >  directory.
> 
> that’s right, pllrepo is a submodule pointing to the PLL repository at assembla.com, please see here:
> 
> http://www.cibiv.at/software/iqtree/doc/Compilation-Guide/
> 
> This should resolve this problem

Sorry, but the link above does not contain any strings "pll" or
"assembla" - I have no idea how to solve the issue. :-(
 
Kind regards

       Andreas.


> > -- Found Eigen3: /usr/include/eigen3 (Required is at least version "2.91.0") 
> > -- Found ZLIB: /usr/lib/x86_64-linux-gnu/libz.so (found version "1.2.8") 
> > Using system zlib
> > CMake Error at CMakeLists.txt:436 (set_target_properties):
> >  set_target_properties Can not find target to add properties to: pll
> > 
> > 
> > CMake Error at CMakeLists.txt:438 (set_target_properties):
> >  set_target_properties Can not find target to add properties to: pllavx
> > 
> > 
> > -- Configuring incomplete, errors occurred!
> > See also "/build/iqtree-1.3.11+dfsg/obj-x86_64-linux-gnu/CMakeFiles/CMakeOutput.log".
> > ...
> > 
> > 
> > Any hints how to solve this?
> > 
> > 
> > Kind regards
> > 
> >        Andreas.
> > 
> > 
> > 
> > [1] https://lists.alioth.debian.org/pipermail/debian-med-packaging/2015-December/037265.html
> > 
> > 
> > On Sun, Dec 13, 2015 at 03:42:14PM +0100, Bui Quang Minh wrote:
> >> Dear Andreas, 
> >> 
> >> thanks for the info. Please let me know once it is accepted. I will then also post a link in the IQ-TREE website. Please note that iqtree is now available via github:
> >> 
> >> https://github.com/Cibiv/IQ-TREE 
> >> 
> >> If you have any further suggestions, let me know and I am happy to include them into the iqtree repository.
> >> 
> >> Cheers, Minh
> >> 
> >>> On Dec 10, 2015, at 7:04 PM, Andreas Tille <tille at debian.org> wrote:
> >>> 
> >>> Hi Minh,
> >>> 
> >>> thanks for the information.  Unfortunately iqtree is in the Debian New
> >>> queue (https://ftp-master.debian.org/new/iqtree_1.3.8+dfsg-1.html) since
> >>> three monthes.  Not all packages are that long in the queue but I hope
> >>> it will be accepted soon since not many packages are waiting in front of
> >>> it.
> >>> 
> >>> I'll upgrade the version immediately once it is in Debian.
> >>> 
> >>> Thanks a lot for keeping me informed
> >>> 
> >>>     Andreas.
> >>> 
> >>> On Thu, Dec 10, 2015 at 04:39:40PM +0100, Bui Quang Minh wrote:
> >>>> Dear Andreas,
> >>>> 
> >>>> We have just released version 1.3.11 and about to announce in Debian mailling list. However, I am not sure if iqtree debian package is already officially available? If so, can you send me the link?
> >>>> 
> >>>> Thanks, Minh
> >>> 
> >>> -- 
> >>> http://fam-tille.de
> >> 
> >> --
> >> Bui Quang Minh
> >> Center for Integrative Bioinformatics Vienna (CIBIV)
> >> Campus Vienna Biocenter 5, VBC5, Ebene 1
> >> A-1030 Vienna, Austria
> >> Phone: ++43 1 4277 74326
> >> Email: minh.bui (AT) univie.ac.at
> >> 
> >> 
> >> 
> >> 
> >> 
> >> 
> >> 
> >> 
> > 
> > -- 
> > http://fam-tille.de
> 
> --
> Bui Quang Minh
> Center for Integrative Bioinformatics Vienna (CIBIV)
> Campus Vienna Biocenter 5, VBC5, Ebene 1
> A-1030 Vienna, Austria
> Phone: ++43 1 4277 74326
> Email: minh.bui (AT) univie.ac.at
> 
> 
> 
> 
> 
> 
> 
> 

-- 
http://fam-tille.de