installation of `atlas' fails in configure phase

[veedeehjay@…]

this happens under 10.9.2. atlas' is a dependency of several packages, specifically octave', all of which don't install, accordingly. here is the logfile:

version:1
:debug:main changing euid/egid - current euid: 0 - current egid: 0
:debug:main egid changed to: 501
:debug:main euid changed to: 502
:debug:main Executing org.macports.main (atlas)
:debug:main Privilege de-escalation not attempted as not running as root.
:debug:main Skipping completed org.macports.archivefetch (atlas)
:debug:main Privilege de-escalation not attempted as not running as root.
:debug:main Skipping completed org.macports.fetch (atlas)
:debug:main Privilege de-escalation not attempted as not running as root.
:debug:main Skipping completed org.macports.checksum (atlas)
:debug:main Privilege de-escalation not attempted as not running as root.
:debug:main Skipping completed org.macports.extract (atlas)
:debug:main Privilege de-escalation not attempted as not running as root.
:debug:main Skipping completed org.macports.patch (atlas)
:debug:main Privilege de-escalation not attempted as not running as root.
:debug:configure configure phase started at Thu Apr 17 15:07:35 CEST 2014
:notice:configure --->  Configuring atlas
:debug:configure Using compiler 'MacPorts Clang 3.3'
:debug:configure Executing proc-pre-org.macports.configure-configure-0
:msg:configure Selected C compiler: /opt/local/bin/clang-mp-3.3
:msg:configure Selected F77 compiler: gfortran48
:debug:configure Executing reinplace: /usr/bin/sed -E {s|GOODGCC =.*|GOODGCC = /opt/local/bin/clang-mp-3.3");|} < /opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_math_atlas/atlas/work/ATLAS/CONFIG/src/SpewMakeInc.c >@ file12
:debug:configure euid/egid changed to: 0/0
:debug:configure chowned /opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_math_atlas/atlas/work/ATLAS/CONFIG/src/SpewMakeInc.c to macports
:debug:configure euid/egid changed to: 502/501
: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/work/ATLAS/CONFIG/src/SpewMakeInc.c
:debug:configure euid/egid changed to: 502/501
:debug:configure Executing reinplace: /usr/bin/sed s|cc=gcc|cc=/opt/local/bin/clang-mp-3.3|g < /opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_math_atlas/atlas/work/ATLAS/configure >@ file12
:debug:configure euid/egid changed to: 0/0
:debug:configure chowned /opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_math_atlas/atlas/work/ATLAS/configure to macports
:debug:configure euid/egid changed to: 502/501
: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/work/ATLAS/configure
:debug:configure euid/egid changed to: 502/501
:debug:configure Executing reinplace: /usr/bin/sed s|-no-cpp-precomp||g < /opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_math_atlas/atlas/work/ATLAS/CONFIG/src/atlcomp.txt >@ file12
:debug:configure euid/egid changed to: 0/0
:debug:configure chowned /opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_math_atlas/atlas/work/ATLAS/CONFIG/src/atlcomp.txt to macports
:debug:configure euid/egid changed to: 502/501
: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/work/ATLAS/CONFIG/src/atlcomp.txt
:debug:configure euid/egid changed to: 502/501
:debug:configure Executing org.macports.configure (atlas)
:debug:configure Environment: CPATH='/opt/local/include' CFLAGS='-pipe -Os -arch x86_64' CPPFLAGS='-I/opt/local/include' CXXFLAGS='-pipe -Os -arch x86_64' LIBRARY_PATH='/opt/local/lib' MACOSX_DEPLOYMENT_TARGET='10.9' CXX='/opt/local/bin/clang++-mp-3.3' CC_PRINT_OPTIONS_FILE='/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_math_atlas/atlas/work/.CC_PRINT_OPTIONS' F90FLAGS='-pipe -Os -m64' LDFLAGS='-L/opt/local/lib -Wl,-headerpad_max_install_names -arch x86_64' FCFLAGS='-pipe -Os -m64' OBJC='/opt/local/bin/clang-mp-3.3' OBJCXX='/opt/local/bin/clang++-mp-3.3' INSTALL='/usr/bin/install -c' FFLAGS='-pipe -Os -m64' OBJCFLAGS='-pipe -Os -arch x86_64' OBJCXXFLAGS='-pipe -Os -arch x86_64' F77='/opt/local/bin/gfortran-mp-4.8' CC_PRINT_OPTIONS='YES' CC='/opt/local/bin/clang-mp-3.3'
:debug:configure Assembled command: 'cd "/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_math_atlas/atlas/work/ATLAS/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 -C acg /opt/local/bin/clang-mp-3.3 -F acg '-O3 -fomit-frame-pointer -fPIC -march=native -mavx' -C if /opt/local/bin/gfortran-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=3000'
:debug:configure Executing command line:  cd "/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_math_atlas/atlas/work/ATLAS/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 -C acg /opt/local/bin/clang-mp-3.3 -F acg '-O3 -fomit-frame-pointer -fPIC -march=native -mavx' -C if /opt/local/bin/gfortran-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=3000 
:info:configure /opt/local/bin/clang-mp-3.3 -I/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_math_atlas/atlas/work/ATLAS/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_atlas/atlas/work/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/ATLAS/build/..//CONFIG/src/atlconf_misc.c:30:
:info:configure /opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_math_atlas/atlas/work/ATLAS/build/..//CONFIG/include/atlconf.h:4:10: fatal error: 'stdio.h' file not found
:info:configure #include <stdio.h>
:info:configure          ^
:info:configure 1 error generated.
: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/build/../ -d 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 -v 5 -D c -DATL_DYLIBS -Si omp 0 -C acg /opt/local/bin/clang-mp-3.3 -F acg '-O3 -fomit-frame-pointer -fPIC -march=native -mavx' -C if /opt/local/bin/gfortran-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=3000
: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/ATLAS/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 -C acg /opt/local/bin/clang-mp-3.3 -F acg '-O3 -fomit-frame-pointer -fPIC -march=native -mavx' -C if /opt/local/bin/gfortran-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=3000 
: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]"
:notice:configure 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

[mf2k (Frank Schima)]

In the future, please Cc the port maintainers (port info --maintainers atlas).

Error is:

fatal error: 'stdio.h' file not found

The only way this could happen is if you did not ​install the Xcode command line tools.

[veedeehjay@…]

oops! you are right, indeed I forgot about that after the upgrade to 10.9. sorry for the noise. it seems to build now (still running). thanks a lot. will also try to remember to Cc the maintainer in the future.