error installing metis

[mfadams@…]

I get this error when I try to install Octave. I have OSX 10.8.5 and XCode 5.0.2. Any ideas? Thanks, Mark

12:56  ~$  sudo port install octave +atlas+docs 
Warning: No port clang found in the index.
--->  Computing dependencies for octave
--->  Dependencies to be installed: SuiteSparse metis arpack atlas clang-3.3 clang_select ld64 llvm-3.3 llvm_select gcc48 cctools cctools-headers cloog isl gcc_select libgcc epstool fftw-3-single gnuplot aquaterm pdflib wxWidgets-3.0 wxWidgets_select grep hdf5-18 less pstoedit ImageMagick djvulibre urw-fonts plotutils qhull qrupdate
--->  Configuring metis
Error: org.macports.configure for port metis returned: configure failure: command execution failed
Error: Failed to install metis
Please see the log file for port metis for details:
    /opt/local/var/macports/logs/_Users_markadams_Codes_scienceports_math_metis/metis/main.log
Error: The following dependencies were not installed: SuiteSparse metis arpack atlas clang-3.3 clang_select ld64 llvm-3.3 llvm_select gcc48 cctools cctools-headers cloog isl gcc_select libgcc epstool fftw-3-single gnuplot aquaterm pdflib wxWidgets-3.0 wxWidgets_select grep hdf5-18 less pstoedit ImageMagick djvulibre urw-fonts plotutils qhull qrupdate
To report a bug, follow the instructions in the guide:
    http://guide.macports.org/#project.tickets
Error: Processing of port octave failed
12:56 1  ~$ cat  /opt/local/var/macports/logs/_Users_markadams_Codes_scienceports_math_metis/metis/main.log
version:1
:debug:main changing euid/egid - current euid: 0 - current egid: 0
:debug:main egid changed to: 501
:debug:main euid changed to: 503
:debug:main Executing org.macports.main (metis)
:debug:main Privilege de-escalation not attempted as not running as root.
:debug:main Skipping completed org.macports.archivefetch (metis)
:debug:main Privilege de-escalation not attempted as not running as root.
:debug:main Skipping completed org.macports.fetch (metis)
:debug:main Privilege de-escalation not attempted as not running as root.
:debug:main Skipping completed org.macports.checksum (metis)
:debug:main Privilege de-escalation not attempted as not running as root.
:debug:main Skipping completed org.macports.extract (metis)
:debug:main Privilege de-escalation not attempted as not running as root.
:debug:main Skipping completed org.macports.patch (metis)
:debug:main Privilege de-escalation not attempted as not running as root.
:debug:configure configure phase started at Mon Dec 23 12:56:39 EST 2013
:notice:configure --->  Configuring metis
:debug:configure Using compiler 'Xcode Clang'
:debug:configure Executing proc-pre-org.macports.configure-configure-0
:debug:configure Executing org.macports.configure (metis)
:debug:configure Environment: CPATH='/opt/local/include' CFLAGS='-pipe -Os -mtune=native' CPPFLAGS='-I/opt/local/include -mtune=native' CXXFLAGS='-pipe -Os -mtune=native' LIBRARY_PATH='/opt/local/lib' MACOSX_DEPLOYMENT_TARGET='10.8' CXX='clang++' CC_PRINT_OPTIONS_FILE='/opt/local/var/macports/build/_Users_markadams_Codes_scienceports_math_metis/metis/work/.CC_PRINT_OPTIONS' F90FLAGS='-pipe -Os -mtune=native' LDFLAGS='-L/opt/local/lib -Wl,-headerpad_max_install_names' __CFPREFERENCES_AVOID_DAEMON='1' FCFLAGS='-pipe -Os -mtune=native' OBJC='clang' OBJCXX='/usr/bin/clang++' INSTALL='/usr/bin/install -c' OBJCFLAGS='-pipe -Os' OBJCXXFLAGS='-pipe -Os' FFLAGS='-pipe -Os -mtune=native' CC_PRINT_OPTIONS='YES' CC='clang'
:debug:configure Assembled command: 'cd "/opt/local/var/macports/build/_Users_markadams_Codes_scienceports_math_metis/metis/work/metis-5.0.2" && cmake -DCMAKE_INSTALL_PREFIX=/opt/local -DGKLIB_PATH=/opt/local/var/macports/build/_Users_markadams_Codes_scienceports_math_metis/metis/work/metis-5.0.2/GKlib -DSHARED=1 -DMETIS_USE_DOUBLEPRECISION=1 -DCMAKE_OSX_ARCHITECTURES="" -DCMAKE_OSX_SYSROOT=/'
:debug:configure Executing command line:  cd "/opt/local/var/macports/build/_Users_markadams_Codes_scienceports_math_metis/metis/work/metis-5.0.2" && cmake -DCMAKE_INSTALL_PREFIX=/opt/local -DGKLIB_PATH=/opt/local/var/macports/build/_Users_markadams_Codes_scienceports_math_metis/metis/work/metis-5.0.2/GKlib -DSHARED=1 -DMETIS_USE_DOUBLEPRECISION=1 -DCMAKE_OSX_ARCHITECTURES="" -DCMAKE_OSX_SYSROOT=/ 
:info:configure -- The C compiler identification is Clang 4.0.0
:info:configure -- The CXX compiler identification is Clang 4.0.0
:info:configure CMake Error at /opt/local/share/cmake-2.8/Modules/Platform/Darwin.cmake:211 (message):
:info:configure   CMAKE_OSX_DEPLOYMENT_TARGET is '10.8' but CMAKE_OSX_SYSROOT:
:info:configure 
:info:configure    "/"
:info:configure 
:info:configure   is not set to a MacOSX SDK with a recognized version.  Either set
:info:configure   CMAKE_OSX_SYSROOT to a valid SDK or set CMAKE_OSX_DEPLOYMENT_TARGET to
:info:configure   empty.
:info:configure Call Stack (most recent call first):
:info:configure   /opt/local/share/cmake-2.8/Modules/CMakeSystemSpecificInformation.cmake:36 (include)
:info:configure   CMakeLists.txt:2 (project)
:info:configure 
:info:configure 
:info:configure -- Configuring incomplete, errors occurred!
:info:configure See also "/opt/local/var/macports/build/_Users_markadams_Codes_scienceports_math_metis/metis/work/metis-5.0.2/CMakeFiles/CMakeOutput.log".
:info:configure Command failed:  cd "/opt/local/var/macports/build/_Users_markadams_Codes_scienceports_math_metis/metis/work/metis-5.0.2" && cmake -DCMAKE_INSTALL_PREFIX=/opt/local -DGKLIB_PATH=/opt/local/var/macports/build/_Users_markadams_Codes_scienceports_math_metis/metis/work/metis-5.0.2/GKlib -DSHARED=1 -DMETIS_USE_DOUBLEPRECISION=1 -DCMAKE_OSX_ARCHITECTURES="" -DCMAKE_OSX_SYSROOT=/ 
:info:configure Exit code: 1
:error:configure org.macports.configure for port metis 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 metis: org.macports.activate org.macports.configure org.macports.build org.macports.destroot org.macports.install
:error:configure Failed to install metis
: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 $dir tclIndex]"
:notice:configure Please see the log file for port metis for details:
    /opt/local/var/macports/logs/_Users_markadams_Codes_scienceports_math_metis/metis/main.log
12:56  ~$ 

[mf2k (Frank Schima)]

In the future, please use WikiFormatting, and fill in the Port field of the failed port. Also, attach the complete main.log after cleaning the port instead of pasting it inline.

[ryandesign (Ryan Carsten Schmidt)]

It may not be related to this issue, but if you have Xcode 5.0.2, you should have a newer version of clang than 4.0.0. This suggests you did not update the command line tools after upgrading Xcode. Open Xcode and visit its Preferences window. Go to the Downloads section and there should be an option to update or install the command line tools.

[ryandesign (Ryan Carsten Schmidt)]

Did updating the command line tools change the error at all, or make it go away?

[mfadams@…]

Replying to ryandesign@…:

Did updating the command line tools change the error at all, or make it go away?

I have the command line tools installed. I do not see a way to update them. I installed them recently, within the past year for another ports issues as I recall. I'm I missing something? I have Xcode Version 5.0.2 (5A3005).

Thanks,
Mark

[larryv (Lawrence Velázquez)]

Replying to mfadams@…:

I have the command line tools installed. I do not see a way to update them.

Run xcode-select --install. If you receive an error about not being able to contact the update server or something like that, it means you’re up to date. (I know, it’s weird.)

[mfadams@…]

Replying to larryv@…:

Replying to mfadams@…:

I have the command line tools installed. I do not see a way to update them.

Run xcode-select --install. If you receive an error about not being able to contact the update server or something like that, it means you’re up to date. (I know, it’s weird.)

My xcode does not seem take the options that I see on the web (eg, --install):

17:02 master ~/Codes/hpgmg$ xcode-select --install
xcode-select: Error: unknown command option '--install'.

xcode-select: Report or change the path to the active
              Xcode installation for this machine.

Usage: xcode-select --print-path
           Prints the path of the active Xcode folder
   or: xcode-select --switch <xcode_path>
           Sets the path for the active Xcode folder
   or: xcode-select --version
           Prints the version of xcode-select

17:02 1 master ~/Codes/hpgmg$  xcode-select --print-path
/Applications/Xcode.app/Contents/Developer

[larryv (Lawrence Velázquez)]

Replying to mfadams@…:

My xcode does not seem take the options that I see on the web (eg, --install):

Sorry, I missed the part where you said you were on Mountain Lion. What I said only applies to Mavericks. On Mountain Lion, open Xcode and check Xcode > Preferences > Downloads.

[mfadams@…]

Replying to larryv@…:

Replying to mfadams@…:

My xcode does not seem take the options that I see on the web (eg, --install):

Sorry, I missed the part where you said you were on Mountain Lion. What I said only applies to Mavericks. On Mountain Lion, open Xcode and check Xcode > Preferences > Downloads.

This shows that Command Line Tools are installed (checked).

[ryandesign (Ryan Carsten Schmidt)]

The version of clang you should have with Xcode 5.0.2 is "Apple LLVM version 5.0 (clang-500.2.79) (based on LLVM 3.3svn)" If anything less than that is printed when you run "clang -v" your command line tools are out of date and you should update them. If the Xcode preferences window isn't letting you do so, then manually download the latest command line tools installer for Mountain Lion from ​Apple Developer Downloads and run it; the latest version I see there now is October 22, 2013.

[mfadams@…]

I seem to be uptodate:

17:11 master ~/Codes/hpgmg/impls$ clang -v
Apple LLVM version 5.0 (clang-500.2.79) (based on LLVM 3.3svn)
Target: x86_64-apple-darwin12.5.0
Thread model: posix

I have 5.0.2 and I see a Nov 11 2013 release. This is newer than what i have now. I will try updating.

[mfadams@…]

I updated xcode and the output to sudo port install octave changed a bit. But still have a clang warning and failed on metis. I attached the new log file.

[seanfarley (Sean Farley)]

This is probably my fault since Mark is using a local copy of my SciencePorts. Mark, could you delete that directory entirely and remove the entry from /opt/local/etc/macports/macports.conf? I've integrated the SciencePorts stuff into MacPorts now so hopefully this issue should be fixed. If not, let's try figuring it out in a new ticket.