[MacPorts] #41766: py27-numpy @1.8.0_2 +atlas +gcc48 compile error - build failure
#41766: py27-numpy @1.8.0_2 +atlas +gcc48 compile error - build failure -------------------------------+-------------------------------- Reporter: freezingmariner@… | Owner: macports-tickets@… Type: defect | Status: new Priority: Normal | Milestone: Component: ports | Version: 2.2.1 Keywords: | Port: -------------------------------+-------------------------------- Here is the error that I'm encountering during build: {{{ :info:build building library "npysort" sources :info:build building extension "numpy.core._dummy" sources :info:build Generating build/src.macosx-10.9-x86_64-2.7/numpy/core/include/numpy/config.h :info:build C compiler: /opt/local/bin/gcc-mp-4.8 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -m64 :info:build :info:build compile options: '-Inumpy/core/src/private -Inumpy/core/src -Inumpy/core -Inumpy/core/src/npymath -Inumpy/core/src/multiarray -Inumpy/core/src/umath -Inumpy/core/src/npysort -Inumpy/core/include -I/opt/local/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c' :info:build gcc-mp-4.8: _configtest.c :info:build In file included from /opt/local/lib/gcc48/gcc/x86_64-apple- darwin13/4.8.2/include-fixed/syslimits.h:7:0, :info:build from /opt/local/lib/gcc48/gcc/x86_64-apple- darwin13/4.8.2/include-fixed/limits.h:34, :info:build from /opt/local/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7/Python.h:19, :info:build from _configtest.c:1: :info:build /opt/local/lib/gcc48/gcc/x86_64-apple-darwin13/4.8.2/include- fixed/limits.h:168:61: fatal error: limits.h: No such file or directory :info:build #include_next <limits.h> /* recurse down to the real one */ :info:build ^ :info:build compilation terminated. :info:build In file included from /opt/local/lib/gcc48/gcc/x86_64-apple- darwin13/4.8.2/include-fixed/syslimits.h:7:0, :info:build from /opt/local/lib/gcc48/gcc/x86_64-apple- darwin13/4.8.2/include-fixed/limits.h:34, :info:build from /opt/local/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7/Python.h:19, :info:build from _configtest.c:1: :info:build /opt/local/lib/gcc48/gcc/x86_64-apple-darwin13/4.8.2/include- fixed/limits.h:168:61: fatal error: limits.h: No such file or directory :info:build #include_next <limits.h> /* recurse down to the real one */ :info:build ^ :info:build compilation terminated. :info:build failure. }}} -- Ticket URL: <https://trac.macports.org/ticket/41766> MacPorts <http://www.macports.org/> Ports system for OS X
#41766: py27-numpy @1.8.0_2 +atlas +gcc48 compile error - build failure --------------------------------+------------------- Reporter: freezingmariner@… | Owner: dh@… Type: defect | Status: new Priority: Normal | Milestone: Component: ports | Version: 2.2.1 Resolution: | Keywords: Port: py-numpy | --------------------------------+------------------- Changes (by ryandesign@…): * cc: michaelld@… (added) * owner: macports-tickets@… => dh@… * port: => py-numpy -- Ticket URL: <https://trac.macports.org/ticket/41766#comment:1> MacPorts <http://www.macports.org/> Ports system for OS X
#41766: py27-numpy @1.8.0_2 +atlas +gcc48 compile error - build failure --------------------------------+------------------- Reporter: freezingmariner@… | Owner: dh@… Type: defect | Status: new Priority: Normal | Milestone: Component: ports | Version: 2.2.1 Resolution: | Keywords: Port: py-numpy | --------------------------------+------------------- Comment (by michaelld@…): Did you maybe update the OS to 10.9 without [http://trac.macports.org/wiki/Migration migrating MacPorts]? If you did not yet do the migration, then I highly recommend you do what that page says. If you did, then I'd recommend the following: {{{ sudo port -f uninstall gcc48 sudo port clean py27-numpy gcc48 sudo port installed gcc48 sudo port install py27-numpy +atlas +gcc48 }}} and see if that works. -- Ticket URL: <https://trac.macports.org/ticket/41766#comment:2> MacPorts <http://www.macports.org/> Ports system for OS X
#41766: py27-numpy @1.8.0_2 +atlas +gcc48 compile error - build failure --------------------------------+------------------- Reporter: freezingmariner@… | Owner: dh@… Type: defect | Status: new Priority: Normal | Milestone: Component: ports | Version: 2.2.1 Resolution: | Keywords: Port: py-numpy | --------------------------------+------------------- Comment (by kaplan@…): Replying to [comment:2 michaelld@…]:
Did you maybe update the OS to 10.9 without [http://trac.macports.org/wiki/Migration migrating MacPorts]? If you did not yet do the migration, then I highly recommend you do what that page says.
If you did, then I'd recommend the following: {{{ sudo port -f uninstall gcc48 sudo port clean py27-numpy gcc48 sudo port installed gcc48 sudo port install py27-numpy +atlas +gcc48 }}} and see if that works.
It does not work : apcmc143[140]:~> sudo port install py27-numpy +atlas +gcc48 Password: ---> Computing dependencies for py27-numpy ---> Dependencies to be installed: atlas ---> Configuring atlas Selected C compiler: /opt/local/bin/gcc-mp-4.8 Selected F77 compiler: gfortran48 Warning: GCC compilers on MacOS do not support AVX: downgrading. Error: org.macports.configure for port atlas returned: configure failure: command execution failed Error: Failed to install atlas Please see the log file for port atlas for details: /opt/local/var/macports/logs/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_math_atlas/atlas/main.log Error: The following dependencies were not installed: atlas bellow : the last part of the log file :debug:configure euid/egid changed to: 501/20 :debug:configure euid/egid changed to: 0/0 :debug:configure setting attributes on /opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_math_atlas/atlas/workFIG/src/atlcomp.txt :debug:configure euid/egid changed to: 501/20 :warn:configure GCC compilers on MacOS do not support AVX: downgrading. :debug:configure Executing org.macports.configure (atlas) :debug:configure Environment: CPATH='/opt/local/include' CFLAGS='-pipe -Os -m64' CPPFLAGS='-I/opt/local/include' CXXFLAGS='-pipe -Os -m64' LIBRARY_PATH='/opt/local/X_DEPLOYMENT_TARGET='10.9' CXX='/opt/local/bin/g++-mp-4.8' CC_PRINT_OPTIONS_FILE='/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_rballs_ports_math_atlas/atlas/work/.CC_PRINT_OPTIONS' F90FLAGS='-pipe -Os -m64' LDFLAGS='-L/opt/local/lib -Wl,-headerpad_max_install_names' FCFLAGS='-pipe -Os -m64' /local/bin/gcc- mp-4.8' OBJCXX='/opt/local/bin/g++-mp-4.8' INSTALL='/usr/bin/install -c' F90='/opt/local/bin/gfortran-mp-4.8' FC='/opt/local/bin/gfortran-mp-4.8' FFL -Os -m64' OBJCXXFLAGS='-pipe -Os -m64' OBJCFLAGS='-pipe -Os -m64' F77='/opt/local/bin/gfortran-mp-4.8' CC_PRINT_OPTIONS='YES' CC='/opt/local/bin/gcc-mp-4.8' :debug:configure Assembled command: 'cd "/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_math_atlas/atlas/wouild" && ../configure --prefix=/opt/local --with-netlib-lapack- tarfile=/opt/local/var/macports/distfiles/atlas/lapack-3.4.2.tgz -O 12 -v 5 --dylibs -Si omp 0 -C acgl/bin/gcc-mp-4.8 -A 25 -F acg '-fomit-frame- pointer -mfpmath=sse -O3 -fno-schedule-insns2 -fPIC -msse4.2' -C if /opt/local/bin/gfortran-mp-4.8 -F if '-fomit-frame-ppmath=sse -O3 -fno- schedule-insns2 -fPIC -msse4.2' -Ss f77lib /opt/local/lib/gcc48/libgfortran.dylib -b 64 -D c -DPentiumCPS=2400' :debug:configure Executing command line: cd "/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_math_atlas/atlLAS/build" && ../configure --prefix=/opt/local --with-netlib-lapack- tarfile=/opt/local/var/macports/distfiles/atlas/lapack-3.4.2.tgz -O 12 -v 5 --dylibs -Si omp 0 -/local/bin/gcc-mp-4.8 -A 25 -F acg '-fomit-frame- pointer -mfpmath=sse -O3 -fno-schedule-insns2 -fPIC -msse4.2' -C if /opt/local/bin/gfortran-mp-4.8 -F if '-fomit-frr -mfpmath=sse -O3 -fno- schedule-insns2 -fPIC -msse4.2' -Ss f77lib /opt/local/lib/gcc48/libgfortran.dylib -b 64 -D c -DPentiumCPS=2400 :info:configure /opt/local/bin/gcc-mp-4.8 -I/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_math_atlas/atlasS/build/..//CONFIG/include -g -w -DATL_DYLIBS -c /opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_math_atlask/ATLAS/build/..//CONFIG/src/atlconf_misc.c :info:configure In file included from /opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_math_atlas/atlas/work/d/..//CONFIG/src/atlconf_misc.c:30:0: :info:configure /opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_math_atlas/atlas/work/ATLAS/build/..//CONFIGtlconf.h:4:19: fatal error: stdio.h: No such file or directory :info:configure #include <stdio.h> :info:configure ^ :info:configure compilation terminated. :info:configure make: *** [atlconf_misc.o] Error 1 :info:configure ./xconfig -d s /opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_math_atlas/atlas/work/ATLAS/bd b /opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_math_atlas/atlas/work/ATLAS/build -Si lapackref 1 -O 12 -DATL_DYLIBS -Si omp 0 -C acg /opt/local/bin/gcc- mp-4.8 -A 25 -F acg '-fomit-frame-pointer -mfpmath=sse -O3 -fno-schedule- insns2 -fPIC -msse4.2' -C if /opt/local/bn-mp-4.8 -F if '-fomit-frame- pointer -mfpmath=sse -O3 -fno-schedule-insns2 -fPIC -msse4.2' -Ss f77lib /opt/local/lib/gcc48/libgfortran.dylib -b 64 -D c -DPentiumCPS :info:configure /bin/sh: line 1: ./xconfig: No such file or directory :info:configure xconfig exited with 127 :info:configure Command failed: cd "/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_math_atlas/atlas/work/A" && ../configure --prefix=/opt/local --with-netlib-lapack- tarfile=/opt/local/var/macports/distfiles/atlas/lapack-3.4.2.tgz -O 12 -v 5 --dylibs -Si omp 0 -C acg /opn/gcc-mp-4.8 -A 25 -F acg '-fomit-frame- pointer -mfpmath=sse -O3 -fno-schedule-insns2 -fPIC -msse4.2' -C if /opt/local/bin/gfortran-mp-4.8 -F if '-fomit-frame-pointh=sse -O3 -fno- schedule-insns2 -fPIC -msse4.2' -Ss f77lib /opt/local/lib/gcc48/libgfortran.dylib -b 64 -D c -DPentiumCPS=2400 :info:configure Exit code: 127 :error:configure org.macports.configure for port atlas 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 atlas: org.macports.activate org.macports.configure org.macports.build org.macports.destroot org.macports.install :error:configure Failed to install atlas :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]" -- Ticket URL: <https://trac.macports.org/ticket/41766#comment:3> MacPorts <http://www.macports.org/> Ports system for OS X
#41766: py27-numpy @1.8.0_2 +atlas +gcc48 compile error - build failure --------------------------------+------------------- Reporter: freezingmariner@… | Owner: dh@… Type: defect | Status: new Priority: Normal | Milestone: Component: ports | Version: 2.2.1 Resolution: | Keywords: Port: py-numpy | --------------------------------+------------------- Comment (by sean@…): A few things I noticed about this ticket: * This is a build error in ATLAS, not py27-numpy * Because you're using +gcc48, you won't be compiling the fancy AVX stuff in ATLAS * ATLAS and whatnot is only really good for doing dense linear algebra, is that what you need? If you don't have a specific need for ATLAS, I would just recommend using the default install of py27-numpy: {{{ $ port clean atlas py27-numpy $ port install py27-numpy }}} This will get you a working numpy which you can optimize later. -- Ticket URL: <https://trac.macports.org/ticket/41766#comment:4> MacPorts <http://www.macports.org/> Ports system for OS X
#41766: py27-numpy @1.8.0_2 +atlas +gcc48 compile error - build failure --------------------------------+------------------- Reporter: freezingmariner@… | Owner: dh@… Type: defect | Status: new Priority: Normal | Milestone: Component: ports | Version: 2.2.1 Resolution: | Keywords: Port: py-numpy | --------------------------------+------------------- Comment (by vince@…): The compiler failing to locate <studio.h> is certainly no Atlas failure. Something is obviously amiss in the compiler installation/ environment! -- Ticket URL: <https://trac.macports.org/ticket/41766#comment:5> MacPorts <http://www.macports.org/> Ports system for OS X
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