py27-numpy @1.8.0_2 +atlas +gcc48 compile error - build failure

[freezingmariner@…]

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.

[michaelld (Michael Dickens)]

Did you maybe update the OS to 10.9 without ​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.

[kaplan@…]

Replying to michaelld@…:

Did you maybe update the OS to 10.9 without ​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]"

[seanfarley (Sean Farley)]

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.

[Veence (Vincent)]

The compiler failing to locate <stdio.h> is certainly no Atlas failure. Something is obviously amiss in the compiler installation/environment!

[mf2k (Frank Schima)]

dh has retired. See #51239.

[reneeotten (Renee Otten)]

the py27-subport is currently at version 1.16.6 and I see in the Portfile that gcc48 (and gcc49 for that matter) are excluded as possible compilers. There is no way/reason to fix this ticket; please update and see if there still is a problem and, if so, you could consider opening a new ticket if you're still interested.