openbabel @2.3.1 missing dependency on wxwidgets-(devel,3.0)

[ba306@…]

Hi, Trying to install python bindings for openbabel. Mac lion. Have been working on this for 4 days now! most recent error:

version:1
:debug:main Executing org.macports.main (openbabel)
:debug:main changing euid/egid - current euid: 0 - current egid: 0
:debug:main egid changed to: 501
:debug:main euid changed to: 502
:debug:main Skipping completed org.macports.archivefetch (openbabel)
:debug:main Privilege de-escalation not attempted as not running as root.
:debug:main Skipping completed org.macports.fetch (openbabel)
:debug:main Privilege de-escalation not attempted as not running as root.
:debug:main Skipping completed org.macports.checksum (openbabel)
:debug:main Privilege de-escalation not attempted as not running as root.
:debug:main Skipping completed org.macports.extract (openbabel)
:debug:main Privilege de-escalation not attempted as not running as root.
:debug:main Skipping completed org.macports.patch (openbabel)
:debug:main Privilege de-escalation not attempted as not running as root.
:debug:configure configure phase started at Wed Jul 17 12:14:16 BST 2013
:notice:configure --->  Configuring openbabel
:debug:configure Using compiler 'Mac OS X clang'
:debug:configure Executing proc-pre-org.macports.configure-configure-0
:debug:configure Executing org.macports.configure (openbabel)
:debug:configure Environment: CPATH='/opt/local/include' CFLAGS='-pipe -O2 -arch x86_64' CPPFLAGS='-I/opt/local/include' CXXFLAGS='-pipe -O2 -arch x86_64' LIBRARY_PATH='/opt/local/lib' MACOSX_DEPLOYMENT_TARGET='10.7' CXX='/usr/bin/clang++' CC_PRINT_OPTIONS_FILE='/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_science_openbabel/openbabel/work/.CC_PRINT_OPTIONS' F90FLAGS='-pipe -O2 -m64' LDFLAGS='-L/opt/local/lib -arch x86_64' OBJC='/usr/bin/clang' FCFLAGS='-pipe -O2 -m64' INSTALL='/usr/bin/install -c' OBJCFLAGS='-pipe -O2 -arch x86_64' FFLAGS='-pipe -O2 -m64' CC_PRINT_OPTIONS='YES' CC='/usr/bin/clang'
:debug:configure Assembled command: 'cd "/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_science_openbabel/openbabel/work/openbabel-2.3.1" && /opt/local/bin/cmake -DCMAKE_INSTALL_PREFIX=/opt/local -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_COLOR_MAKEFILE=ON -DCMAKE_BUILD_TYPE=Release -DCMAKE_BUILD_WITH_INSTALL_RPATH=ON -DCMAKE_INSTALL_NAME_DIR=/opt/local/lib -DCMAKE_SYSTEM_PREFIX_PATH="/opt/local;/usr" -DCMAKE_MODULE_PATH=/opt/local/share/cmake/modules -DCMAKE_FIND_FRAMEWORK=LAST -Wno-dev -DBUILD_GUI=OFF -DBUILD_TESTING=OFF -DPYTHON_BINDINGS=OFF -DCMAKE_OSX_ARCHITECTURES="x86_64" -DCMAKE_OSX_SYSROOT=/ -DCMAKE_OSX_DEPLOYMENT_TARGET=""'
:debug:configure Executing command line:  cd "/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_science_openbabel/openbabel/work/openbabel-2.3.1" && /opt/local/bin/cmake -DCMAKE_INSTALL_PREFIX=/opt/local -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_COLOR_MAKEFILE=ON -DCMAKE_BUILD_TYPE=Release -DCMAKE_BUILD_WITH_INSTALL_RPATH=ON -DCMAKE_INSTALL_NAME_DIR=/opt/local/lib -DCMAKE_SYSTEM_PREFIX_PATH="/opt/local;/usr" -DCMAKE_MODULE_PATH=/opt/local/share/cmake/modules -DCMAKE_FIND_FRAMEWORK=LAST -Wno-dev -DBUILD_GUI=OFF -DBUILD_TESTING=OFF -DPYTHON_BINDINGS=OFF -DCMAKE_OSX_ARCHITECTURES="x86_64" -DCMAKE_OSX_SYSROOT=/ -DCMAKE_OSX_DEPLOYMENT_TARGET="" 
:info:configure -- Using included inchi library.
:info:configure -- Could NOT find wxWidgets (missing:  wxWidgets_FOUND) 
:info:configure CMake Error at /opt/local/share/cmake-2.8/Modules/FindPackageHandleStandardArgs.cmake:97 (message):
:info:configure   Could NOT find PkgConfig (missing: PKG_CONFIG_EXECUTABLE)
:info:configure Call Stack (most recent call first):
:info:configure   /opt/local/share/cmake-2.8/Modules/FindPackageHandleStandardArgs.cmake:291 (_FPHSA_FAILURE_MESSAGE)
:info:configure   /opt/local/share/cmake-2.8/Modules/FindPkgConfig.cmake:102 (find_package_handle_standard_args)
:info:configure   cmake/modules/FindCairo.cmake:23 (find_package)
:info:configure   CMakeLists.txt:404 (find_package)
:info:configure 
:info:configure 
:info:configure -- Configuring incomplete, errors occurred!
:info:configure Command failed:  cd "/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_science_openbabel/openbabel/work/openbabel-2.3.1" && /opt/local/bin/cmake -DCMAKE_INSTALL_PREFIX=/opt/local -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_COLOR_MAKEFILE=ON -DCMAKE_BUILD_TYPE=Release -DCMAKE_BUILD_WITH_INSTALL_RPATH=ON -DCMAKE_INSTALL_NAME_DIR=/opt/local/lib -DCMAKE_SYSTEM_PREFIX_PATH="/opt/local;/usr" -DCMAKE_MODULE_PATH=/opt/local/share/cmake/modules -DCMAKE_FIND_FRAMEWORK=LAST -Wno-dev -DBUILD_GUI=OFF -DBUILD_TESTING=OFF -DPYTHON_BINDINGS=OFF -DCMAKE_OSX_ARCHITECTURES="x86_64" -DCMAKE_OSX_SYSROOT=/ -DCMAKE_OSX_DEPLOYMENT_TARGET="" 
:info:configure Exit code: 1
:error:configure org.macports.configure for port openbabel returned: configure failure: command execution failed
:debug:configure Error code: NONE
:debug:configure Backtrace: configure failure: command execution failed
    while executing
"$procedure $targetname"
:info:configure Warning: targets not executed for openbabel: org.macports.activate org.macports.configure org.macports.build org.macports.destroot org.macports.install
:error:configure Failed to install openbabel
:debug:configure couldn't open "/System/Library/Frameworks/Tcl.framework/Versions/8.5/Resources/tclIndex": no such file or directory
    while executing
"open [file join $dir tclIndex]"
:notice:configure Please see the log file for port openbabel for details:
    /opt/local/var/macports/logs/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_science_openbabel/openbabel/main.log

[ci42]

This was not a clean attempt. Please try again:

$ sudo port selfupdate
$ sudo port install py-openbabel

and attach the log file if it fails.

In the future please remember to use WikiFormatting and fill in the port field.

[mf2k (Frank Schima)]

openbabel is the port that failed. So the modified commands to run are as follows:

sudo port selfupdate
sudo port clean openbabel
sudo port install openbabel

[ba306@…]

Thanks but that lead to the issues in the attached file

[ci42]

Replying to ba306@…:

Thanks but that lead to the issues in the attached file

It looks like openbabel is missing a dependency on pkgconfig:

Could NOT find PkgConfig

It works on my machine when pkgconfig is installed. It fails when pkgconfig is not installed albeit with a different error message.

What's the output of?

$ port installed pkgconfig

If it says:

None of the specified ports are installed.

Try:

$ sudo port install pkgconfig
$ sudo port clean openbabel
$ sudo port install openbabel

If it succeeds try:

$ sudo port clean py-openbabel
$ sudo port install py-openbabel

Otherwise attach the log file.

[ba306@…]

The log file indicated that wxWidgets could not be found before it complained about pkgconfig. Installing wxWidgets installed pkgconfig, but then complained that it did not support OS X 10.7 (Lion). It recommended installed wxWidgets-devel instead, which was successful.

Once that was completed, I was able to install openbabel and then py-openbabel with MacPorts.

Thanks for all of your help!

[ci42]

Pkgconfig is a rdep of wxwidgets, but probably openbabel should declare an explicit dependency on it.

[ci42]

Cc Me!

[c.herbig@…]

OpenBabel does not require wxWidgets unless the cmake -DBUILD_GUI=ON is set. See ​compiling open babel. In the current portfile it is specifically set to off. Meanwhile the only reference the portfile (or the eigen dependency) has to pkgconfig is in this line:

depends_lib         path:lib/pkgconfig/cairo.pc:cairo port:libiconv port:libxml2 port:zlib

Perhaps that's where the issue comes from?

[ci42]

Replying to c.herbig@…:

OpenBabel does not require wxWidgets unless the cmake -DBUILD_GUI=ON is set. See ​compiling open babel. In the current portfile it is specifically set to off. Meanwhile the only reference the portfile (or the eigen dependency) has to pkgconfig is in this line:

depends_lib         path:lib/pkgconfig/cairo.pc:cairo port:libiconv port:libxml2 port:zlib

Perhaps that's where the issue comes from?

The problem is that OpenBabel uses pkgconfig to find cairo. Have a look at ​http://sourceforge.net/p/openbabel/code/5041/tree/openbabel/tags/openbabel-2-3-2/cmake/modules/FindCairo.cmake. Therefore OpenBabel must declare a dependency on pkgconfig like this:

depends_build port:pkgconfig

[ci42]

Fixed in r108435.