I see you're on a PowerPC running Mac OS X 10.4, which could be relevant.
Interesting parts of the log are:
:info:build Timeout waiting for file /opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_ports_math_atlas/work/atlas-3.9.37/build/include/atlas_pthreads.h!!
:info:build
:info:build /opt/local/bin/gcc-mp-4.4 -o ATL_ptflushcache.o -c -DL2SIZE=4194304 -I/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_ports_math_atlas/work/atlas-3.9.37/build/include -I/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_ports_math_atlas/work/atlas-3.9.37/build/..//include -I/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_ports_math_atlas/work/atlas-3.9.37/build/..//include/contrib -DAdd_ -DF77_INTEGER=int -DStringSunStyle -DATL_OS_OSX -DATL_ARCH_PPCG4 -DATL_CPUMHZ=466 -DATL_AltiVec -DATL_GAS_PPC -DATL_AVgcc -DWALL -DATL_FULL_LAPACK -O3 -maltivec -mabi=altivec -mcpu=7400 -mtune=7400 -fPIC -m32 -m32 /opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_ports_math_atlas/work/atlas-3.9.37/build/..//src/auxil/ATL_ptflushcache.c
:info:build In file included from /opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_ports_math_atlas/work/atlas-3.9.37/build/..//src/auxil/ATL_ptflushcache.c:33:
:info:build /opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_ports_math_atlas/work/atlas-3.9.37/build/..//include/atlas_threads.h:13:78: error: atlas_pthreads.h: No such file or directory
:info:build /opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_ports_math_atlas/work/atlas-3.9.37/build/..//src/auxil/ATL_ptflushcache.c: In function 'ATL_ptflushcache':
:info:build /opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_ports_math_atlas/work/atlas-3.9.37/build/..//src/auxil/ATL_ptflushcache.c:71: error: 'ATL_NTHREADS' undeclared (first use in this function)
:info:build /opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_ports_math_atlas/work/atlas-3.9.37/build/..//src/auxil/ATL_ptflushcache.c:71: error: (Each undeclared identifier is reported only once
:info:build /opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_ports_math_atlas/work/atlas-3.9.37/build/..//src/auxil/ATL_ptflushcache.c:71: error: for each function it appears in.)
:info:build /opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_ports_math_atlas/work/atlas-3.9.37/build/..//src/auxil/ATL_ptflushcache.c: In function 'ATL_ptFlushAreasByCL':
:info:build /opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_ports_math_atlas/work/atlas-3.9.37/build/..//src/auxil/ATL_ptflushcache.c:123: error: 'ATL_NTHREADS' undeclared (first use in this function)
:info:build make[3]: *** [ATL_ptflushcache.o] Error 1
:info:build make[2]: *** [IBuildPtlibs0] Error 2
and:
:debug:build Executing proc-post-org.macports.build-build-0
:info:build /usr/bin/ld: warning -L: directory name (/opt/local/lib/gcc44/ppc) does not exist
:info:build /usr/bin/ld: Undefined symbols:
:info:build rest_world
:info:build save_world
The latter makes this look like a duplicate of #28996.
