Hi,
It seems the problem of debian arch-specific lib install paths is solved by using the CMake GNUInstallDirs package (https://wiki.debian.org/Multiarch/Implementation#CMake ).
I will update the CMake repositories to use it, which should solve the problem.
Julien: please wait until I've updated the CMakes before tagging the release.
--
François Gindraud
Ingénieur développement bioinformatique
LBBE, équipe BPGE, projet Grasp, Labex Ecofect
Bureau 116, Bâtiment Mendel 1er étage, UCBL
________________________________________
De : Andreas Tille <andreas@an3as.eu>
Envoyé : mardi 6 juin 2017 11:23
À : GINDRAUD FRANCOIS
Cc : Julien Yann Dutheil; Debian Med Project List
Objet : Re: Open issue with libbpp-core
Hi,
On Mon, Jun 05, 2017 at 12:14:13PM +0000, GINDRAUD FRANCOIS wrote:
> I'm the one responsible for the CMake upgrade in the Bio++ libraries.
>
> Since this version, Bio++ uses CMake package files to represent internal module dependencies, and allow users to use find_package(bpp-<module>).
>
> To support this, CMake generates a few files in <prefix>/lib/cmake/bpp-<module>/*.cmake, which are required to enable find_package to work.
>
> In your case it seems bpp-seq is unable to find the cmake package files of core (especially, bpp-core-config.cmake).
>
> According to https://launchpad.net/ubuntu/+source/libbpp-core/2.3.0-1~ , which seems to have a log of your build of bpp-core, these files are missing from the bpp-core-devel package.exp1/+build/12681398
>
> This explains why they cannot be found by bpp-seq.
>
> To fix the error you must ensure these files are included in the devel package.
You are right. I just commited a change which installs the missing files.
However, I have remaining problems wo build libbpp-seq:
...
dh_auto_configure
<------>cmake .. -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_BUILD_TYPE=None -DCMAKE_INSTALL_SYSCONFDIR=/etc -DCMAKE_INSTALL_LOCALSTATEDIR= /var
-- The CXX compiler identification is GNU 6.3.0
-- Check for working CXX compiler: /usr/bin/c++
-- Check for working CXX compiler: /usr/bin/c++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Detecting CXX compile features
-- Detecting CXX compile features - done
CMake Error at /usr/lib/cmake/bpp-core/bpp-core-targets.cmake:90 (message):
The imported target "bpp-core-static" references the file
"/usr/lib/libbpp-core.a"
but this file does not exist. Possible reasons include:
* The file was deleted, renamed, or moved to another location.
* An install or uninstall procedure did not complete successfully.
* The installation package was faulty and contained
"/usr/lib/cmake/bpp-core/bpp-core-targets.cmake"
but not all the files it references.
Cmake is correct that the said file does not exist since it is rather
in the multiarch dir - for amd64 architecture for instance
/usr/lib/x86_64-linux-gnu/libbpp-core.a
Do you have any idea how to fix the cmake files to respect multiarch?
Kind regards
Andreas.
> ---------- Forwarded message ----------
> From: Andreas Tille <tille@debian.org<mailto:tille@debian.org >>
> Date: Sat, Jun 3, 2017 at 4:29 PM
> Subject: Re: Open issue with libbpp-core
> To: Julien Yann Dutheil <dutheil@evolbio.mpg.de<mailto:dutheil@evolbio.mpg.de> >
> Cc: Debian Med Project List <debian-med@lists.debian.org<mailto:debian-med@lists. debian.org >>
>
>
> Hi Julien,
>
> On Sat, May 27, 2017 at 09:23:45PM +0200, Julien Yann Dutheil wrote:
> > We finally managed to update our Bio++ libraries and programs and released
> > a new version. We did a lot of cleaning in the CMake files, removed the
> > .all include files and moved the code to C++11. Everything is now on github
> > and has been tagged as suggested. Here is the list (repos + tag):
> > ...
> >
> > We hope this will make the packaging as smooth as possible. Please let me
> > know if there is more we can do.
>
> Thanks for the heads up. Since we are in "frozen policy" uploads are
> currently only possible to experimental. So I started uploading
> libbpp-core (2.3.0-1~exp1) but I had some issue to build
> libbpp-seq-2.3.0 against this. I was running into:
>
>
> ...
> -- Detecting CXX compile features - done
> CMake Error at CMakeLists.txt:55 (find_package):
> By not providing "Findbpp-core.cmake" in CMAKE_MODULE_PATH this project has
> asked CMake to find a package configuration file provided by "bpp-core",
> but CMake did not find one.
>
> Could not find a package configuration file provided by "bpp-core"
> (requested version 2.0.4) with any of the following names:
>
> bpp-coreConfig.cmake
> bpp-core-config.cmake
>
> Add the installation prefix of "bpp-core" to CMAKE_PREFIX_PATH or set
> "bpp-core_DIR" to a directory containing one of the above files. If
> "bpp-core" provides a separate development package or SDK, be sure it has
> been installed.
>
>
> -- Configuring incomplete, errors occurred!
> See also "/build/libbpp-seq-2.3.0/obj-x86_64-linux-gnu/CMakeFiles/ CMakeOutput.log".
> <------>"tail -v -n +0 CMakeCache.txt"
> ==> CMakeCache.txt <==
> ...
>
> despite libbpp-core was in the Build-Depends. Any hint from a cmake expert
> how to solve this?
>
> Kind regards
>
> Andreas.
>
> --
> http://fam-tille.de
>
>
>
> --
> Julien Y. Dutheil, Ph-D
> 0 (+49) 4522 763 298
>
> § Max Planck Institute for Evolutionary Biology
> Molecular Systems Evolution
> Department of Evolutionary Genetics
> Plön -- GERMANY
>
> § Institute of Evolutionary Sciences - Montpellier
> University of Montpellier 2 -- FRANCE
--
http://fam-tille.de