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  1. Data Management
  2. DM-3200

Base package fails to build under OS X El Capitan

    Details

    • Type: Bug
    • Status: Done
    • Resolution: Done
    • Fix Version/s: None
    • Component/s: base
    • Labels:
      None
    • Templates:
    • Team:
      Architecture

      Description

      I tried to build the stack on a Mac running El Capitan Public beta 2, and it gave three errors in base.

       % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                       Dload  Upload   Total   Spent    Left  Speed
      100 12671  100 12671    0     0  18798      0 --:--:-- --:--:-- --:--:-- 18799
       
      LSST Software Stack Builder
      =======================================================================
       
      Detected git version 2.3.2 (Apple Git-55). OK.
       
       
      In addition to Python 2.7, some LSST packages depend on recent versions of numpy,
      matplotlib, and scipy. If you don't have all of these, the installation may fail.
      Using the Anaconda Python distribution will ensure all these are set up.
       
      Anaconda Python installed by this installer will be managed by LSST's EUPS
      package manager, and will not replace or modify your system python.
       
      Would you like us to install Anaconda Python distribution (if unsure, say yes)? yes
       
      Installing EUPS (v1.5.9)...  done.
      Installing Anaconda Python Distribution ... 
        [  1/1  ]  anaconda 2.2.0                                             done. 
      Installing the basic environment ... 
        [  1/5  ]  doxygen 1.8.5                                              done. 
        [  2/5  ]  python 0.0.3 ...
                   Using externally provided Python 2.7.9 :: Anaconda 2.2.0 (x86_64).
        [  2/5  ]  python 0.0.3                                               done. 
        [  3/5  ]  scons 2.3.4                                                done. 
        [  4/5  ]  sconsUtils 10.1-4-gce72cec+1                               done. 
        [  5/5  ]  lsst 10.1-1-g84e9557+13                                    done. 
      Creating startup scripts (bash) ... done.
      Creating startup scripts (ksh) ... done.
      Creating startup scripts (csh) ... done.
      Creating startup scripts (zsh) ... done.
       
      Bootstrap complete. To continue installing (and to use) the LSST stack
      type one of:
       
      source "/Users/srp/stack/lsst/loadLSST.bash"  # for bash
      source "/Users/srp/stack/lsst/loadLSST.csh"   # for csh
      source "/Users/srp/stack/lsst/loadLSST.ksh"   # for ksh
      source "/Users/srp/stack/lsst/loadLSST.zsh"   # for zsh
       
      Individual LSST packages may now be installed with the usual `eups
      distrib install' command.  For example, to install the science pipeline
      elements of the LSST stack, use:
       
      eups distrib install lsst_apps
       
      Next, read the documentation at:
       
          https://confluence.lsstcorp.org/display/LSWUG/LSST+Software+User+Guide
       
      and feel free to ask any questions via our mailing list at:
       
          https://lists.lsst.org/mailman/listinfo/dm-users
       
                                             Thanks!
                                                      -- The LSST Software Teams
                                                             http://dm.lsst.org/
       
      srps-Mac-Pro:stack srp$ pwd
      /Users/srp/stack
      srps-Mac-Pro:stack srp$ ls
      install.sh	lsst
      srps-Mac-Pro:stack srp$ cd lsst
      srps-Mac-Pro:lsst srp$ ls
      DarwinX86	eups		loadLSST.csh	newinstall.sh
      EupsBuildDir	eupsbuild.log	loadLSST.ksh	site
      _build		loadLSST.bash	loadLSST.zsh	ups_db
      srps-Mac-Pro:lsst srp$ source loadLSST.bash
      srps-Mac-Pro:lsst srp$ eups distrib install lsst_apps
        [  1/51 ]  cfitsio 3360.lsst1                                         done. 
        [  2/51 ]  doxygen 1.8.5 (already installed)                          done. 
        [  3/51 ]  eigen 3.2.0                                                done. 
        [  4/51 ]  fftw 3.3.3                                                 done. 
        [  5/51 ]  gsl 1.16.lsst1                                             done. 
        [  6/51 ]  minuit2 5.28.00                                            done. 
        [  7/51 ]  mysqlclient 5.1.73.lsst1-1-gb8bcc43                        done. 
        [  8/51 ]  python 0.0.3 (already installed)                           done. 
        [  9/51 ]  swig 3.0.2.lsst1                                           done. 
        [ 10/51 ]  xpa 2.1.15.lsst2                                           done. 
        [ 11/51 ]  boost 1.55.0.1.lsst2+3                                     done. 
        [ 12/51 ]  mysqlpython 1.2.3+17                                       done. 
        [ 13/51 ]  numpy 0.0.1+5 ...
                   Using externally provided numpy v1.9.2.
        [ 13/51 ]  numpy 0.0.1+5                                              done. 
        [ 14/51 ]  scons 2.3.4 (already installed)                            done. 
        [ 15/51 ]  wcslib 4.14+7                                              done. 
        [ 16/51 ]  astrometry_net 0.50.1+6                                    done. 
        [ 17/51 ]  matplotlib 0.0.1+5 ...
                   Using externally provided matplotlib v1.4.3.
        [ 17/51 ]  matplotlib 0.0.1+5                                         done. 
        [ 18/51 ]  pyfits 3.2.4.lsst1+3                                       done. 
        [ 19/51 ]  sconsUtils 10.1-4-gce72cec+1 (already installed)           done. 
        [ 20/51 ]  astrometry_net_data 10.0+23                                done. 
        [ 21/51 ]  base 10.1-1-g8080078+14 ...
       
      ***** error: from /Users/srp/stack/lsst/EupsBuildDir/DarwinX86/base-10.1-1-g8080078+14/build.log:
      c++ -o lib/libbase.dylib -dynamiclib -Wl,-install_name -Wl,libbase.dylib src/ModuleImporter.os -Llib -L/Users/srp/stack/lsst/DarwinX86/boost/1.55.0.1.lsst2+3/lib -L/Users/srp/stack/lsst/DarwinX86/anaconda/2.2.0/lib/python2.7/config -lpthread
      swig -o tests/testModuleImporterLib_wrap.cc -Iinclude -I/Users/srp/stack/lsst/DarwinX86/boost/1.55.0.1.lsst2+3/include -I/Users/srp/stack/lsst/DarwinX86/anaconda/2.2.0/include/python2.7 -c++ -python tests/testModuleImporterLib.i
      c++ -o python/lsstcppimport_wrap.os -c -std=c++11 -g -DLSST_HAVE_TR1=0 -DLSST_LITTLE_ENDIAN=1 -O3 -Wall -Wno-unused-function -fPIC -Iinclude -I/Users/srp/stack/lsst/DarwinX86/boost/1.55.0.1.lsst2+3/include -I/Users/srp/stack/lsst/DarwinX86/anaconda/2.2.0/include/python2.7 python/lsstcppimport_wrap.cc
      c++ -o tests/ptr tests/ptr.o -Llib -L/Users/srp/stack/lsst/DarwinX86/boost/1.55.0.1.lsst2+3/lib -L/Users/srp/stack/lsst/DarwinX86/anaconda/2.2.0/lib/python2.7/config -lbase -lpthread
      running tests/ptr... c++ -o tests/testModuleImporter1 tests/testModuleImporter1.o -Llib -L/Users/srp/stack/lsst/DarwinX86/boost/1.55.0.1.lsst2+3/lib -L/Users/srp/stack/lsst/DarwinX86/anaconda/2.2.0/lib/python2.7/config -lbase -lpthread
      c++ -o tests/testModuleImporterLib_wrap.os -c -std=c++11 -g -DLSST_HAVE_TR1=0 -DLSST_LITTLE_ENDIAN=1 -O3 -Wall -Wno-unused-function -fPIC -Iinclude -I/Users/srp/stack/lsst/DarwinX86/boost/1.55.0.1.lsst2+3/include -I/Users/srp/stack/lsst/DarwinX86/anaconda/2.2.0/include/python2.7 tests/testModuleImporterLib_wrap.cc
      sh: line 1: 70182 Trace/BPT trap: 5       "tests/ptr" >> "tests/.tests/ptr" 2>&1
      failed
      buildConfig(["doc/doxygen.conf"], ["doc/doxygen.conf.in"])
      running tests/testModuleImporter1... sh: line 1: 70192 Trace/BPT trap: 5       "tests/testModuleImporter1" >> "tests/.tests/testModuleImporter1" 2>&1
      failed
      doxygen /Users/srp/stack/lsst/EupsBuildDir/DarwinX86/base-10.1-1-g8080078+14/base-10.1-1-g8080078+14/doc/doxygen.conf
      /Users/srp/stack/lsst/EupsBuildDir/DarwinX86/base-10.1-1-g8080078+14/base-10.1-1-g8080078+14/doc/mainpage.dox:61: warning: unable to resolve link to `lsst.pipe.base.cmdLineTask.CmdLineTask' for \link command
      c++ -o python/_lsstcppimport.so -bundle -F/ -undefined suppress -flat_namespace python/lsstcppimport_wrap.os -Llib -L/Users/srp/stack/lsst/DarwinX86/boost/1.55.0.1.lsst2+3/lib -L/Users/srp/stack/lsst/DarwinX86/anaconda/2.2.0/lib/python2.7/config -lbase -lpthread -ldl -lpython2.7
      c++ -o tests/_testModuleImporterLib.so -bundle -F/ -undefined suppress -flat_namespace tests/testModuleImporterLib_wrap.os -Llib -L/Users/srp/stack/lsst/DarwinX86/boost/1.55.0.1.lsst2+3/lib -L/Users/srp/stack/lsst/DarwinX86/anaconda/2.2.0/lib/python2.7/config -lbase -lpthread -ldl -lpython2.7
      running tests/testModuleImporter2.py... failed
      3 tests failed
      scons: *** [checkTestStatus] Error 1
      scons: building terminated because of errors.
      + exit -4
      eups distrib: Failed to build base-10.1-1-g8080078+14.eupspkg: Command:
      	source /Users/srp/stack/lsst/eups/bin/setups.sh; export EUPS_PATH=/Users/srp/stack/lsst; (/Users/srp/stack/lsst/EupsBuildDir/DarwinX86/base-10.1-1-g8080078+14/build.sh) >> /Users/srp/stack/lsst/EupsBuildDir/DarwinX86/base-10.1-1-g8080078+14/build.log 2>&1 4>/Users/srp/stack/lsst/EupsBuildDir/DarwinX86/base-10.1-1-g8080078+14/build.msg 
      exited with code 252
       
      srps-Mac-Pro:lsst srp$ 
      

      In the file /Users/srp/stack/lsst/EupsBuildDir/DarwinX86/base-10.1-1-g8080078+14/build.log, near the end, we have:

      Checking whether the C++ compiler works... yes
      C++11 supported with '-std=c++11'
      Checking for C++ header file tr1/unordered_map... no
      Setting up environment to build package 'base'.
      Checking whether int64_t is long ... no
      Determining RTLD values...ok
      scons: done reading SConscript files.
      scons: Building targets ...
      c++ -o src/ModuleImporter.os -c -std=c++11 -g -DLSST_HAVE_TR1=0 -DLSST_LITTLE_ENDIAN=1 -O3 -Wall -Wno-unused-function -fPIC -Iinclude -I/Users/srp/stack/lsst/DarwinX86/boost/1.55.0.1.lsst2+3/include -I/Users/srp/stack/lsst/DarwinX86/anaconda/2.2.0/include/python2.7 src/ModuleImporter.cc
      Cannot guess fingerprint without .git directory; will be set to '0x0'.
      swig -o python/lsstcppimport_wrap.cc -Iinclude -I/Users/srp/stack/lsst/DarwinX86/boost/1.55.0.1.lsst2+3/include -I/Users/srp/stack/lsst/DarwinX86/anaconda/2.2.0/include/python2.7 -c++ -python python/lsstcppimport.i
      c++ -o tests/ptr.o -c -std=c++11 -g -DLSST_HAVE_TR1=0 -DLSST_LITTLE_ENDIAN=1 -O3 -Wall -Wno-unused-function -Iinclude -I/Users/srp/stack/lsst/DarwinX86/boost/1.55.0.1.lsst2+3/include -I/Users/srp/stack/lsst/DarwinX86/anaconda/2.2.0/include/python2.7 tests/ptr.cc
      cd python && m4 -Dm4_RTLD_GLOBAL=8 -Dm4_RTLD_NOW=2 < lsst64defs.py.m4 > /Users/srp/stack/lsst/EupsBuildDir/DarwinX86/base-10.1-1-g8080078+14/base-10.1-1-g8080078+14/python/lsst64defs.py
      c++ -o tests/testModuleImporter1.o -c -std=c++11 -g -DLSST_HAVE_TR1=0 -DLSST_LITTLE_ENDIAN=1 -O3 -Wall -Wno-unused-function -Iinclude -I/Users/srp/stack/lsst/DarwinX86/boost/1.55.0.1.lsst2+3/include -I/Users/srp/stack/lsst/DarwinX86/anaconda/2.2.0/include/python2.7 tests/testModuleImporter1.cc
      c++ -o lib/libbase.dylib -dynamiclib -Wl,-install_name -Wl,libbase.dylib src/ModuleImporter.os -Llib -L/Users/srp/stack/lsst/DarwinX86/boost/1.55.0.1.lsst2+3/lib -L/Users/srp/stack/lsst/DarwinX86/anaconda/2.2.0/lib/python2.7/config -lpthread
      swig -o tests/testModuleImporterLib_wrap.cc -Iinclude -I/Users/srp/stack/lsst/DarwinX86/boost/1.55.0.1.lsst2+3/include -I/Users/srp/stack/lsst/DarwinX86/anaconda/2.2.0/include/python2.7 -c++ -python tests/testModuleImporterLib.i
      c++ -o python/lsstcppimport_wrap.os -c -std=c++11 -g -DLSST_HAVE_TR1=0 -DLSST_LITTLE_ENDIAN=1 -O3 -Wall -Wno-unused-function -fPIC -Iinclude -I/Users/srp/stack/lsst/DarwinX86/boost/1.55.0.1.lsst2+3/include -I/Users/srp/stack/lsst/DarwinX86/anaconda/2.2.0/include/python2.7 python/lsstcppimport_wrap.cc
      c++ -o tests/ptr tests/ptr.o -Llib -L/Users/srp/stack/lsst/DarwinX86/boost/1.55.0.1.lsst2+3/lib -L/Users/srp/stack/lsst/DarwinX86/anaconda/2.2.0/lib/python2.7/config -lbase -lpthread
      running tests/ptr... c++ -o tests/testModuleImporter1 tests/testModuleImporter1.o -Llib -L/Users/srp/stack/lsst/DarwinX86/boost/1.55.0.1.lsst2+3/lib -L/Users/srp/stack/lsst/DarwinX86/anaconda/2.2.0/lib/python2.7/config -lbase -lpthread
      c++ -o tests/testModuleImporterLib_wrap.os -c -std=c++11 -g -DLSST_HAVE_TR1=0 -DLSST_LITTLE_ENDIAN=1 -O3 -Wall -Wno-unused-function -fPIC -Iinclude -I/Users/srp/stack/lsst/DarwinX86/boost/1.55.0.1.lsst2+3/include -I/Users/srp/stack/lsst/DarwinX86/anaconda/2.2.0/include/python2.7 tests/testModuleImporterLib_wrap.cc
      sh: line 1: 70182 Trace/BPT trap: 5       "tests/ptr" >> "tests/.tests/ptr" 2>&1
      failed
      buildConfig(["doc/doxygen.conf"], ["doc/doxygen.conf.in"])
      running tests/testModuleImporter1... sh: line 1: 70192 Trace/BPT trap: 5       "tests/testModuleImporter1" >> "tests/.tests/testModuleImporter1" 2>&1
      failed
      doxygen /Users/srp/stack/lsst/EupsBuildDir/DarwinX86/base-10.1-1-g8080078+14/base-10.1-1-g8080078+14/doc/doxygen.conf
      /Users/srp/stack/lsst/EupsBuildDir/DarwinX86/base-10.1-1-g8080078+14/base-10.1-1-g8080078+14/doc/mainpage.dox:61: warning: unable to resolve link to `lsst.pipe.base.cmdLineTask.CmdLineTask' for \link command
      c++ -o python/_lsstcppimport.so -bundle -F/ -undefined suppress -flat_namespace python/lsstcppimport_wrap.os -Llib -L/Users/srp/stack/lsst/DarwinX86/boost/1.55.0.1.lsst2+3/lib -L/Users/srp/stack/lsst/DarwinX86/anaconda/2.2.0/lib/python2.7/config -lbase -lpthread -ldl -lpython2.7
      c++ -o tests/_testModuleImporterLib.so -bundle -F/ -undefined suppress -flat_namespace tests/testModuleImporterLib_wrap.os -Llib -L/Users/srp/stack/lsst/DarwinX86/boost/1.55.0.1.lsst2+3/lib -L/Users/srp/stack/lsst/DarwinX86/anaconda/2.2.0/lib/python2.7/config -lbase -lpthread -ldl -lpython2.7
      running tests/testModuleImporter2.py... failed
      3 tests failed
      scons: *** [checkTestStatus] Error 1
      scons: building terminated because of errors.
      + exit -4
      

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                • Assignee:
                  tjenness Tim Jenness
                  Reporter:
                  spietrowicz Steve Pietrowicz
                  Reviewers:
                  Russell Owen
                  Watchers:
                  Chris Walter, David Shupe, Frossie Economou, Jim Bosch, John Swinbank, Paul Price, Russell Owen, Steve Pietrowicz, Tim Jenness
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                  0 Vote for this issue
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                  9 Start watching this issue

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                  • Created:
                    Updated:
                    Resolved:

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