I am using MacOSX Yosemite 10.10.5
I have just update my Xcode to Version 7.2.1 (7C1002),
I had never installed the stack before.
I had python 2.7 installed with anaconda.
after a source
source loadLSST.bash
I failed in installing the stack in doxygen.1.8.5 as follow
eups distrib install -t v11_0 lsst_apps
(pyastrophys)/Users/dagoret-campagnesylvie/MacOsX/LSST/softs/LSSTStack>eups distrib install -t v11_0 lsst_apps
[ 1/53 ] cfitsio 3360.lsst3 (already installed) done.
[ 2/53 ] doxygen 1.8.5 ...
***** error: from /Users/dagoret-campagnesylvie/MacOsX/LSST/softs/LSSTStack/EupsBuildDir/DarwinX86/doxygen-1.8.5/build.log:
../qtools/qglobal.h:99:6: warning: "This version of Mac OS X is unsupported" [-W#warnings]
# warning "This version of Mac OS X is unsupported"
^
1 warning and 2 errors generated.
Makefile.libdoxygen:643: recipe for target '../objects/commentscan.o' failed
gmake[2]: *** [../objects/commentscan.o] Error 1
gmake[2]: *** Waiting for unfinished jobs....
2 warnings generated.
2 warnings generated.
5 warnings generated.
2 warnings generated.
2 warnings generated.
2 warnings generated.
1 warning generated.
gmake[2]: Leaving directory '/Users/dagoret-campagnesylvie/MacOsX/LSST/softs/LSSTStack/EupsBuildDir/DarwinX86/doxygen-1.8.5/doxygen-1.8.5/src'
Makefile:38: recipe for target 'all' failed
gmake[1]: *** [all] Error 2
gmake[1]: Leaving directory '/Users/dagoret-campagnesylvie/MacOsX/LSST/softs/LSSTStack/EupsBuildDir/DarwinX86/doxygen-1.8.5/doxygen-1.8.5/src'
make: *** [all] Error 2
+ exit -4
eups distrib: Failed to build doxygen-1.8.5.eupspkg: Command:
source /Users/dagoret-campagnesylvie/MacOsX/LSST/softs/LSSTStack/eups/bin/setups.sh; export EUPS_PATH=/Users/dagoret-campagnesylvie/MacOsX/LSST/softs/LSSTStack; (/Users/dagoret-campagnesylvie/MacOsX/LSST/softs/LSSTStack/EupsBuildDir/DarwinX86/doxygen-1.8.5/build.sh) >> /Users/dagoret-campagnesylvie/MacOsX/LSST/softs/LSSTStack/EupsBuildDir/DarwinX86/doxygen-1.8.5/build.log 2>&1 4>/Users/dagoret-campagnesylvie/MacOsX/LSST/softs/LSSTStack/EupsBuildDir/DarwinX86/doxygen-1.8.5/build.msg
exited with code 252
Here is the compile error I get
In file included from commentscan.l:26:
In file included from ../qtools/qarray.h:42:
In file included from ../qtools/qgarray.h:42:
In file included from ../qtools/qshared.h:42:
../qtools/qglobal.h:99:6: warning: "This version of Mac OS X is unsupported" [-W#warnings]
# warning "This version of Mac OS X is unsupported"
^
commentscan.l:1064:55: error: use of undeclared identifier 'yy_current_buffer'
inputPosition=prevPosition + (int)(yy_bp - yy_current_buffer->yy_ch_buf);
^
commentscan.l:1126:58: error: use of undeclared identifier 'yy_current_buffer'
inputPosition=prevPosition + (int)(yy_bp - yy_current_buffer->yy_ch_buf) + strlen(commentScanYYtext);
^
In file included from scanner.l:28:
In file included from ../qtools/qarray.h:42:
In file included from ../qtools/qgarray.h:42:
In file included from ../qtools/qshared.h:42:
../qtools/qglobal.h:99:6: warning: "This version of Mac OS X is unsupported" [-W#warnings]
# warning "This version of Mac OS X is unsupported"
^
I’m at the end of a very poor network connection at the moment and so can’t check for sure, but:
I’m pretty sure this is because you have a recent (2.6.0 or later) version of flex installed. That’s (much) newer than ships with OSX 10.10.5 (but it might have been pulled in by Homebrew or Macports or something).
You’ll need to either revert to an older version of flex, or install a newer version of the stack. To do the latter, replace v11_0 in your eups distrib line with the name of a nightly build (w_2016_19 is the latest at time of writing). Note that the nightlies are unofficial pre-release versions of the stack, and there are a number of other changes in w_2016_19 relative to v11_0.
There is a ready-to-use binary distribution of the stack which is known to work on Yosemite. You can find the details at https://github.com/airnandez/lsst-cvmfs. The latest version available via this channel is v11.0.
Please post the contents of /Users/dagoret-campagnesylvie/MacOsX/LSST/softs/LSSTStack/EupsBuildDir/DarwinX86/meas_algorithms-2016_01.0-11-ge027a04+1/build.log. Thanks!
It’s been pointed out to me that g++ and c++ are slightly different on OS X. They both are clang++ but g++ adds extra include paths for GCC compatibility that are probably breaking your build. Are you setting an override environment variable to select a different C++ compiler?
Yes, don’t use that one. See the extra include search path? You must use either clang++ or c++. c++ is the default so you must be asking it to to use g++ (maybe with some environment variable override). I assume c++ exists on your system.
It seems I was forwarding misinformation. I just checked my build (El Capitan) and it’s using g++ if I build a package independently. I have not tried building the relevant package manually though to see if it works fine (Xcode 7.3.1). If you look at the difference between c++ —version, clang++ —version and g++ —version you’ll see a difference in the last one.
Doing the builds from EUPS is somewhat different though in that it does use the $CC environment variable to do the building so will override the default of g++. This may explain why things work for me but fail for you. Do you have $CC=gcc ?
As for reinstalling, eups should not bother rebuilding things that have already been built. It will check them though and there will be a pause as it builds the dependency graph.