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

[Andreas Tille]

Hi Minh,

I forgot to include some license statements in the debian/copyright file
and thus ftmaster rejected the once uploaded version 1.3.8[1].  While I
fixed this by adding the according paragraphs to debian/copyright in the
packaging Git, I decided to not to upload the old version again but
switch to 1.3.11 for the next upload to new (which should went faster
now after the first cycle).

I have some comments to the new download:

1. Are you sure that you want to provide example.phy twice?

$ ls example*
example:
example.nex  example.phy  models.nex

examples:
example.phy


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).

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.

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.


-- 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