[DM-3200] Base package fails to build under OS X El Capitan - Jira

Details

Type: Bug
Status: Done
Resolution: Done
Fix Version/s: None
Component/s: base
Labels:
None

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

Attachments

Issue Links

is triggering

DM-4310 Missing Doxygen documentation

Done

DM-4327 ActiveMQCPP does not build on OS X El Capitan

Done

DM-4334 libevent does not build on OS X El Capitan

Done

DM-4360 obs_subaru fails to compile after DM-3200

Done

DM-4396 ctrl_execute test fails to find test binary

Done

DM-4609 Partition package should use the standard package layout

Done

DM-4378 Improve SConscript product discovery in AFW and coadd_utils

Done

DM-4513 Quoting of paths in doxygen configuration files breaks makeDocs

Done

relates to

DM-5030 Tests fail on Qserv on OS X El Capitan because of SIP

Done

RFC-215 Disallow executable tests due to "#!/usr/bin/env python" problems on OSX

Adopted

DM-4359 lsstsw deploy on OS X El Capitan fails with git / openssl

Done

DM-4345 OSX CI/jenkins build slaves

Done

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(3 is triggering, 4 relates to, 1 mentioned in)

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Base package fails to build under OS X El Capitan

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