Dear Debian Med team, We have now committed several fixes to the cmake files and increased the interface numbers in all libs (excepted the bpp-qt one, which did not change since the last version, only compatibility updates).
Everything is on the master branch, but I have not tagged the new versions... would there be a way to check that everything is in order before doing so? It seems to me that making a new version number and tag after each bug fix is rather ineffective... or maybe I should make a temporary tag only for testing purpose (sthg like v2.3.1-pre1?) All the best, Julien. On Wed, Jun 7, 2017 at 3:53 PM, GINDRAUD FRANCOIS < [email protected]> wrote: > 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 <[email protected]> > 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~ > exp1/+build/12681398, which seems to have a log of your build of > bpp-core, these files are missing from the bpp-core-devel package. > > > > 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 <[email protected]<mailto:[email protected]>> > > Date: Sat, Jun 3, 2017 at 4:29 PM > > Subject: Re: Open issue with libbpp-core > > To: Julien Yann Dutheil <[email protected]<mailto: > [email protected]>> > > Cc: Debian Med Project List <[email protected]<mailto: > [email protected]>> > > > > > > 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 > -- 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
