Stack installation failed on doxygen.1.8.5

sylvielsstfr · May 10, 2016, 2:01pm

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"
     ^

May thanks for help and advices.

Best regards.

Sylvie

swinbank · May 10, 2016, 2:36pm

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.

FabioHernandez · May 10, 2016, 2:52pm

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.

sylvielsstfr · May 10, 2016, 3:49pm

Thanks for your advices,

proceeding with w_2016_19 allowed me to go further.

However its failed installing boost as follow:

 [ 50/61 ]  meas_algorithms 2016_01.0-11-ge027a04+1 ... 

***** error: from /Users/dagoret-campagnesylvie/MacOsX/LSST/softs/LSSTStack/EupsBuildDir/DarwinX86/meas_algorithms-2016_01.0-11-ge027a04+1/build.log:
/Users/dagoret-campagnesylvie/MacOsX/LSST/softs/LSSTStack/DarwinX86/boost/1.60/include/boost/gil/gil_concept.hpp:1877:59: warning: unused typedef 'transposed_t' [-Wunused-local-typedef]
        typedef typename transposed_type<View>::type      transposed_t;
                                                          ^
/Users/dagoret-campagnesylvie/MacOsX/LSST/softs/LSSTStack/DarwinX86/boost/1.60/include/boost/gil/gil_concept.hpp:1875:59: warning: unused typedef 'dynamic_x_step_t' [-Wunused-local-typedef]
        typedef typename dynamic_x_step_type<View>::type  dynamic_x_step_t;
                                                          ^
/Users/dagoret-campagnesylvie/MacOsX/LSST/softs/LSSTStack/DarwinX86/boost/1.60/include/boost/gil/gil_concept.hpp:1876:59: warning: unused typedef 'dynamic_y_step_t' [-Wunused-local-typedef]
        typedef typename dynamic_y_step_type<View>::type  dynamic_y_step_t;
                                                          ^
/Users/dagoret-campagnesylvie/MacOsX/LSST/softs/LSSTStack/DarwinX86/boost/1.60/include/boost/gil/gil_concept.hpp:1940:50: warning: unused typedef 'coord_t' [-Wunused-local-typedef]
        typedef typename View::coord_t           coord_t;      // 1D difference type (same for all dimensions)
                                                 ^
27 warnings generated.
27 warnings gen

Best regards.

Sylvie

sylvielsstfr · May 10, 2016, 3:56pm

Sorry Fabio,

The installation ran badly when I acceptted GoOSXFuse.
I have no idea about the problem.

Many thanks.

Sylvie

swinbank · May 10, 2016, 4:05pm

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!

sylvielsstfr · May 10, 2016, 4:53pm

Here are the errors in build.log

Best regards.

Sylvie

build.log (779.9 KB)

timj · May 10, 2016, 5:06pm

g++ -o src/Interp.os -c -std=c++11 -g -DLSST_LITTLE_ENDIAN=1 -O3 -Wall -Wno-unused-function -fPIC -Iinclude -I/Users/dagoret-campagnesylvie/MacOsX/LSST/softs/LSSTStack/DarwinX86/meas_base/2016_01.0-19-gf7ff187+1/include -I/Users/dagoret-cam
pagnesylvie/MacOsX/LSST/softs/LSSTStack/DarwinX86/afw/2.2016.10-14-g48615cd+2/include -I/Users/dagoret-campagnesylvie/MacOsX/LSST/softs/LSSTStack/DarwinX86/ndarray/2016_01.0-1-g4d828c7+4/include -I/Users/dagoret-campagnesylvie/MacOsX/LSST/s
ofts/LSSTStack/DarwinX86/pex_config/2016_01.0-1-g6fbf654+6/include -I/Users/dagoret-campagnesylvie/MacOsX/LSST/softs/LSSTStack/DarwinX86/daf_persistence/2016_01.0-9-ga3a0b07+2/include -I/Users/dagoret-campagnesylvie/MacOsX/LSST/softs/LSSTSt
ack/DarwinX86/pex_policy/2016_01.0-1-g9f41d6c+2/include -I/Users/dagoret-campagnesylvie/MacOsX/LSST/softs/LSSTStack/DarwinX86/pex_logging/2016_01.0-2-g2d05c3d+2/include -I/Users/dagoret-campagnesylvie/MacOsX/LSST/softs/LSSTStack/DarwinX86/d
af_base/2016_01.0-1-g30982e3+2/include -I/Users/dagoret-campagnesylvie/MacOsX/LSST/softs/LSSTStack/DarwinX86/utils/tickets.DM-5979-g76d91cf90e/include -I/Users/dagoret-campagnesylvie/MacOsX/LSST/softs/LSSTStack/DarwinX86/pex_exceptions/2016
_01.0-1-gfde6942/include -I/Users/dagoret-campagnesylvie/MacOsX/LSST/softs/LSSTStack/DarwinX86/base/2.2016.10-2-ge90c490/include -I/Users/dagoret-campagnesylvie/MacOsX/LSST/softs/LSSTStack/DarwinX86/wcslib/5.13.lsst1/include -I/Users/dagore
t-campagnesylvie/MacOsX/LSST/softs/LSSTStack/DarwinX86/cfitsio/3360.lsst4/include -I/Users/dagoret-campagnesylvie/MacOsX/LSST/softs/LSSTStack/DarwinX86/gsl/1.16.lsst3/include -I/Users/dagoret-campagnesylvie/MacOsX/LSST/softs/LSSTStack/Darwi
nX86/minuit2/5.34.14/include -I/Users/dagoret-campagnesylvie/MacOsX/LSST/softs/LSSTStack/DarwinX86/fftw/3.3.4.lsst2/include -I/Users/dagoret-campagnesylvie/MacOsX/LSST/softs/LSSTStack/DarwinX86/eigen/3.2.5.lsst1/include -I/Users/dagoret-cam
pagnesylvie/MacOsX/LSST/softs/LSSTStack/DarwinX86/mariadbclient/10.1.11.lsst2/include -I/Users/dagoret-campagnesylvie/MacOsX/LSST/softs/LSSTStack/DarwinX86/boost/1.60/include -I/Users/dagoret-campagnesylvie/anaconda/envs/pyastrophys/include
/python2.7 -I/Users/dagoret-campagnesylvie/anaconda/envs/pyastrophys/lib/python2.7/site-packages/numpy/core/include src/Interp.cc
In file included from src/BinnedWcs.cc:24:
In file included from include/lsst/meas/algorithms/BinnedWcs.h:28:
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/memory:4032:35: error: no viable overloaded '='
                __e->__weak_this_ = *this;
                ~~~~~~~~~~~~~~~~~ ^ ~~~~~
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/memory:4070:5: note: in instantiation of function template specialization 'std::__1::shared_ptr<lsst::afw::image::Wcs>::__enable_weak_t
his<lsst::meas::algorithms::BinnedWcs>' requested here
    __enable_weak_this(__p);
    ^
include/lsst/meas/algorithms/BinnedWcs.h:47:16: note: in instantiation of function template specialization 'std::__1::shared_ptr<lsst::afw::image::Wcs>::shared_ptr<lsst::meas::algorithms::BinnedWcs>' requested here
        return PTR(afw::image::Wcs)(new BinnedWcs(_parent, _xBin, _yBin, _xy0));
               ^
/Users/dagoret-campagnesylvie/MacOsX/LSST/softs/LSSTStack/DarwinX86/base/2.2016.10-2-ge90c490/include/lsst/base.h:41:18: note: expanded from macro 'PTR'
#define PTR(...) std::shared_ptr<__VA_ARGS__ LSST_WHITESPACE > LSST_WHITESPACE
                 ^
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/memory:4984:15: note: candidate function not viable: no known conversion from 'std::__1::shared_ptr<lsst::afw::image::Wcs>' to 'const s
td::__1::weak_ptr<lsst::meas::algorithms::BinnedWcs>' for 1st argument
    weak_ptr& operator=(weak_ptr const& __r) _NOEXCEPT;
              ^
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/memory:4995:15: note: candidate function not
 viable: no known conversion from 'std::__1::shared_ptr<lsst::afw::image::Wcs>' to 'std::__1::weak_ptr<lsst::meas::algorithms::BinnedWcs>' for 1st argument
    weak_ptr& operator=(weak_ptr&& __r) _NOEXCEPT;
              ^
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/memory:4991:9: note: candidate template ignored: could not match 'weak_ptr' against 'shared_ptr'
        operator=(weak_ptr<_Yp> const& __r) _NOEXCEPT;
        ^
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/memory:5002:9: note: candidate template ignored: could not match 'weak_ptr' against 'shared_ptr'
        operator=(weak_ptr<_Yp>&& __r) _NOEXCEPT;
        ^
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/memory:5009:13: note: candidate template ignored: disabled by 'enable_if' [with _Yp = lsst::afw::image::Wcs]
            is_convertible<_Yp*, element_type*>::value,
            ^
1 error generated.
scons: *** [src/BinnedWcs.os] Error 1

I haven’t seen this before. What’s the output of g++ —version ?

timj · May 10, 2016, 5:17pm

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?

sylvielsstfr · May 10, 2016, 7:05pm

here it is.

g++ --version
Configured with: --prefix=/Applications/Xcode.app/Contents/Developer/usr --with-gxx-include-dir=/usr/include/c++/4.2.1
Apple LLVM version 7.0.2 (clang-700.1.81)
Target: x86_64-apple-darwin14.5.0
Thread model: posix

Sylvie

timj · May 10, 2016, 7:18pm

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.

sylvielsstfr · May 10, 2016, 7:30pm

OK thanks, I will try to play with environnement variables.
On my system c++ and clang are the same:

lrwxr-xr-x 1 root wheel 7 Jan 29 2015 /usr/bin/c++ -> clang++

g++ and gcc may be differents.
-rwxr-xr-x 1 root wheel 14160 Sep 29 2014 /usr/bin/g++
-rwxr-xr-x 1 root wheel 14160 Sep 29 2014 /usr/bin/gcc

I will try to play with compilers configuration.

By the way, Is there a command with eups to build only meas_algorithms to avoid reinstallling the 50 previous packages ?

Sylvie

timj · May 10, 2016, 7:38pm

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.