Opened 11 years ago
Closed 11 years ago
#39774 closed defect (fixed)
openbabel @2.3.1 missing dependency on wxwidgets-(devel,3.0)
Reported by: | ba306@… | Owned by: | mlund (Mikael Lund) |
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Priority: | Normal | Milestone: | |
Component: | ports | Version: | 2.1.3 |
Keywords: | Cc: | ci42 | |
Port: | openbabel |
Description (last modified by ci42)
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
Attachments (1)
Change History (11)
comment:1 Changed 11 years ago by ci42
Description: | modified (diff) |
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Keywords: | python removed |
Port: | py-openbabel added |
Summary: | py-openbabel lion install cd failure → py-openbabel install failure |
comment:2 follow-up: 3 Changed 11 years ago by mf2k (Frank Schima)
Owner: | changed from macports-tickets@… to mlund@… |
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Port: | openbabel added; py-openbabel removed |
Summary: | py-openbabel install failure → openbabel configure failure |
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
comment:3 follow-up: 4 Changed 11 years ago by ba306@…
Thanks but that lead to the issues in the attached file
Changed 11 years ago by ba306@…
comment:4 Changed 11 years ago by 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.
comment:5 Changed 11 years ago by 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!
comment:6 Changed 11 years ago by ci42
Summary: | openbabel configure failure → openbabel @2.3.1 missing dependency on wxwidgets-(devel,3.0) |
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comment:8 follow-up: 9 Changed 11 years ago by 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?
comment:9 Changed 11 years ago by 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:zlibPerhaps 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
This was not a clean attempt. Please try again:
and attach the log file if it fails.
In the future please remember to use WikiFormatting and fill in the port field.