[MacPorts] #43393: installation of `atlas' fails in configure phase

17 Apr 2014


      #43393: installation of `atlas' fails in configure phase
--------------------------+--------------------------------
 Reporter:  veedeehjay@…  |      Owner:  macports-tickets@…
     Type:  defect        |     Status:  new
 Priority:  Normal        |  Milestone:
Component:  ports         |    Version:  2.2.1
 Keywords:                |       Port:  atlas
--------------------------+--------------------------------
 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
  }}}
-- 
Ticket URL: <https://trac.macports.org/ticket/43393>
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