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

[Bui Quang Minh]

Dear Andreas,

> On Dec 14, 2015, at 9:30 AM, Andreas Tille <andreas at an3as.eu> wrote:
> 
> 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].  

I see, that explains

> 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

I overlooked, please, take the files from example (without s)

> 
> 
> 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This manual is outdated and we updated a series of extensive online documentation which I find much more convenient: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?

> 
> 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...

> 
> 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

Cheers, Minh

PS: Please feel free to change and then create a pull request, I will then merge it into the master branch

Minh

> 
> 
> -- 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