Build log

refmac-5.5.0109:20100505-073405.log (text/plain), 14.87 KB, created by Diego Elio Pettenò (RETIRED) on 2010-05-05 11:26:14 UTC

 * CPV:  sci-chemistry/refmac-5.5.0109
 * REPO: gentoo
 * USE:  elibc_glibc kernel_linux test userland_GNU x86
 * You need one of these Fortran Compilers: gfortran g77
 * Installed are:  gfortran
>>> Unpacking source...
>>> Unpacking refmac_5.5.0109.tar.gz to /var/tmp/portage/sci-chemistry/refmac-5.5.0109/work
>>> Unpacking test-framework.tar.gz to /var/tmp/portage/sci-chemistry/refmac-5.5.0109/work
>>> Source unpacked in /var/tmp/portage/sci-chemistry/refmac-5.5.0109/work
>>> Preparing source in /var/tmp/portage/sci-chemistry/refmac-5.5.0109/work ...
 * Applying 5.5-allow-dynamic-linking.patch ...
  [ ok ]
 * Applying 5.5-test.log.patch ...
  [ ok ]
>>> Source prepared.
>>> Configuring source in /var/tmp/portage/sci-chemistry/refmac-5.5.0109/work ...
>>> Source configured.
>>> Compiling source in /var/tmp/portage/sci-chemistry/refmac-5.5.0109/work ...
make -j14 FC=i686-pc-linux-gnu-gfortran CC=i686-pc-linux-gnu-gcc CXX=i686-pc-linux-gnu-g++ 'COPTIM=-O2 -pipe' 'FOPTIM=-O2 -pipe' VERSION= XFFLAGS=-fno-second-underscore 'LLIBCCP=-lccp4f -lccp4c -lccif -lmmdb -lstdc++' 'LLIBLAPACK=-llapack -lblas' 
i686-pc-linux-gnu-gfortran -O2 -pipe -fno-second-underscore   -c -o refmac_xml.o refmac_xml.f
i686-pc-linux-gnu-gfortran -O2 -pipe -fno-second-underscore   -c -o solvent_contr_mask.o solvent_contr_mask.f
i686-pc-linux-gnu-gfortran -O2 -pipe -fno-second-underscore   -c -o hkon_secder_tch.o hkon_secder_tch.f
i686-pc-linux-gnu-gfortran -O2 -pipe -fno-second-underscore   -c -o fast_hessian_tabulation.o fast_hessian_tabulation.f
i686-pc-linux-gnu-gfortran -O2 -pipe -fno-second-underscore   -c -o subvag.o subvag.f
i686-pc-linux-gnu-gfortran -O2 -pipe -fno-second-underscore   -c -o lsq_symm_symm.o lsq_symm_symm.f
i686-pc-linux-gnu-gfortran -O2 -pipe -fno-second-underscore   -c -o oppro_allocate.o oppro_allocate.f
i686-pc-linux-gnu-gfortran -O2 -pipe -fno-second-underscore   -c -o rcard_tor1.o rcard_tor1.f
i686-pc-linux-gnu-gfortran -O2 -pipe -fno-second-underscore   -c -o subcf_scale1.o subcf_scale1.f
i686-pc-linux-gnu-gfortran -O2 -pipe -fno-second-underscore   -c -o subag_scale_hessian.o subag_scale_hessian.f
i686-pc-linux-gnu-gfortran -O2 -pipe -fno-second-underscore   -c -o extra_eigen.o extra_eigen.f
i686-pc-linux-gnu-gfortran -O2 -pipe -fno-second-underscore   -c -o rigid_allocate.o rigid_allocate.f
i686-pc-linux-gnu-gfortran -O2 -pipe -fno-second-underscore   -c -o aniso_ref_eigen.o aniso_ref_eigen.f
i686-pc-linux-gnu-gfortran -O2 -pipe -fno-second-underscore   -c -o linalgebra.o linalgebra.f
i686-pc-linux-gnu-gfortran -O2 -pipe -fno-second-underscore   -c -o make_CIF.o make_CIF.f
i686-pc-linux-gnu-gfortran -O2 -pipe -fno-second-underscore   -c -o make_subr.o make_subr.f
i686-pc-linux-gnu-gfortran -O2 -pipe -fno-second-underscore   -c -o make_subr_refmac.o make_subr_refmac.f
i686-pc-linux-gnu-gfortran -O2 -pipe -fno-second-underscore   -c -o tls_allocate.o tls_allocate.f
i686-pc-linux-gnu-gfortran -O2 -pipe -fno-second-underscore   -c -o vdw_and_contacts.o vdw_and_contacts.f
i686-pc-linux-gnu-gfortran -O2 -pipe -fno-second-underscore   -c -o vdw_flexible.o vdw_flexible.f
i686-pc-linux-gnu-gfortran -O2 -pipe -fno-second-underscore   -c -o make_lib11.o make_lib11.f
i686-pc-linux-gnu-gfortran -O2 -pipe -fno-second-underscore   -c -o make_lib12.o make_lib12.f
i686-pc-linux-gnu-gfortran -O2 -pipe -fno-second-underscore   -c -o make_lib2.o make_lib2.f
i686-pc-linux-gnu-gfortran -O2 -pipe -fno-second-underscore   -c -o make_crd1.o make_crd1.f
i686-pc-linux-gnu-gfortran -O2 -pipe -fno-second-underscore   -c -o make_crd2.o make_crd2.f
i686-pc-linux-gnu-gfortran -O2 -pipe -fno-second-underscore   -c -o make_new1.o make_new1.f
i686-pc-linux-gnu-gfortran -O2 -pipe -fno-second-underscore   -c -o make_new2.o make_new2.f
i686-pc-linux-gnu-gfortran -O2 -pipe -fno-second-underscore   -c -o set_num.o set_num.f
i686-pc-linux-gnu-gfortran -O2 -pipe -fno-second-underscore   -c -o make_rst1.o make_rst1.f
i686-pc-linux-gnu-gfortran -O2 -pipe -fno-second-underscore   -c -o make_rst2.o make_rst2.f
i686-pc-linux-gnu-gfortran -O2 -pipe -fno-second-underscore   -c -o make_PDB.o make_PDB.f
i686-pc-linux-gnu-gfortran -O2 -pipe -fno-second-underscore   -c -o makecif.o makecif.f
i686-pc-linux-gnu-gfortran -O2 -pipe -fno-second-underscore   -c -o make_refmac_dummy.o make_refmac_dummy.f
i686-pc-linux-gnu-gfortran -O2 -pipe -fno-second-underscore   -c -o ls_scaling_double.o ls_scaling_double.f
i686-pc-linux-gnu-gfortran -O2 -pipe -fno-second-underscore   -c -o interpolate_mod.o interpolate_mod.f
i686-pc-linux-gnu-gfortran -O2 -pipe -fno-second-underscore   -c -o rharvest.o rharvest.f
i686-pc-linux-gnu-gfortran -O2 -pipe -fno-second-underscore   -c -o newentry_idealise.o newentry_idealise.f
i686-pc-linux-gnu-gfortran -O2 -pipe -fno-second-underscore   -c -o ml_scaling_double.o ml_scaling_double.f
i686-pc-linux-gnu-gfortran -O2 -pipe -fno-second-underscore   -c -o gaussian_int.o gaussian_int.f
i686-pc-linux-gnu-gfortran -O2 -pipe -fno-second-underscore   -c -o subnumrec.o subnumrec.f
i686-pc-linux-gnu-gfortran -O2 -pipe -fno-second-underscore   -c -o math_refmac.o math_refmac.f
i686-pc-linux-gnu-gfortran -O2 -pipe -fno-second-underscore   -c -o read_extra_restraints.o read_extra_restraints.f
i686-pc-linux-gnu-gfortran -O2 -pipe -fno-second-underscore   -c -o inout_routines.o inout_routines.f
i686-pc-linux-gnu-gfortran -O2 -pipe -fno-second-underscore   -c -o errwrt.o errwrt.f
i686-pc-linux-gnu-gfortran -O2 -pipe -fno-second-underscore   -c -o xml_writer.o xml_writer.f
i686-pc-linux-gnu-gfortran -O2 -pipe -fno-second-underscore   -c -o ncs_rest.o ncs_rest.f
i686-pc-linux-gnu-gfortran -O2 -pipe -fno-second-underscore   -c -o occupancy_only_refine.o occupancy_only_refine.f
i686-pc-linux-gnu-gfortran -O2 -pipe -fno-second-underscore   -c -o cell_symm_subrs.o cell_symm_subrs.f
i686-pc-linux-gnu-gfortran -O2 -pipe -fno-second-underscore   -c -o iheap_sort.o iheap_sort.f
i686-pc-linux-gnu-gfortran -O2 -pipe -fno-second-underscore   -c -o enm_restraints.o enm_restraints.f
i686-pc-linux-gnu-gfortran -O2 -pipe -fno-second-underscore   -c -o wave2f2prime.o wave2f2prime.f
i686-pc-linux-gnu-gfortran -O2 -pipe -fno-second-underscore   -c -o lnumrec.o lnumrec.f
i686-pc-linux-gnu-gfortran -O2 -pipe -fno-second-underscore   -c -o refpre_twin.o refpre_twin.f
i686-pc-linux-gnu-gfortran -O2 -pipe -fno-second-underscore   -c -o refall_twin.o refall_twin.f
i686-pc-linux-gnu-gfortran -O2 -pipe -fno-second-underscore   -c -o ls_scaling_twin_save.o ls_scaling_twin_save.f
i686-pc-linux-gnu-gfortran -O2 -pipe -fno-second-underscore   -c -o max_with_ints.o max_with_ints.f
i686-pc-linux-gnu-gfortran -O2 -pipe -fno-second-underscore   -c -o ml_params_refine.o ml_params_refine.f
i686-pc-linux-gnu-gfortran -O2 -pipe -fno-second-underscore   -c -o block_organization.o block_organization.f
i686-pc-linux-gnu-gfortran -O2 -pipe -fno-second-underscore   -c -o merohedr_twin.o merohedr_twin.f
i686-pc-linux-gnu-gfortran -O2 -pipe -fno-second-underscore   -c -o decide_twin_opers_0.o decide_twin_opers_0.f
i686-pc-linux-gnu-gfortran -O2 -pipe -fno-second-underscore   -c -o read_data.o read_data.f
i686-pc-linux-gnu-gfortran -O2 -pipe -fno-second-underscore   -c -o asym_list.o asym_list.f
i686-pc-linux-gnu-gfortran -O2 -pipe -fno-second-underscore   -c -o calc_stats_twin.o calc_stats_twin.f
i686-pc-linux-gnu-gfortran -O2 -pipe -fno-second-underscore   -c -o mtz_write_twin.o mtz_write_twin.f
i686-pc-linux-gnu-gfortran -O2 -pipe -fno-second-underscore   -c -o libT.o libT.f
i686-pc-linux-gnu-gfortran -O2 -pipe -fno-second-underscore   -c -o messy_pdb.o messy_pdb.f
i686-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -DGFORTRAN -DPROTOTYPE  -c -o bridge.o bridge.cpp
i686-pc-linux-gnu-gcc -O2 -pipe -DGFORTRAN -DPROTOTYPE -O2 -pipe -DGFORTRAN -DPROTOTYPE  -c -o i0.o i0.c
i686-pc-linux-gnu-gcc -O2 -pipe -DGFORTRAN -DPROTOTYPE -O2 -pipe -DGFORTRAN -DPROTOTYPE  -c -o i1.o i1.c
i686-pc-linux-gnu-gcc -O2 -pipe -DGFORTRAN -DPROTOTYPE -O2 -pipe -DGFORTRAN -DPROTOTYPE  -c -o chbevl.o chbevl.c
i686-pc-linux-gnu-gfortran -O2 -pipe -fno-second-underscore   -c -o main_libcheck.o main_libcheck.f
i686-pc-linux-gnu-gfortran -O2 -pipe -fno-second-underscore   -c -o make_subr_2.o make_subr_2.f
i686-pc-linux-gnu-gfortran -O2 -pipe -fno-second-underscore   -c -o libcheck.o libcheck.f
i686-pc-linux-gnu-gfortran -O2 -pipe -fno-second-underscore   -c -o make_unix_ccp4.o make_unix_ccp4.f
i686-pc-linux-gnu-gfortran -O2 -pipe -fno-second-underscore   -c -o emin.o emin.f
i686-pc-linux-gnu-gfortran -O2 -pipe -fno-second-underscore   -c -o libcheck_min.o libcheck_min.f
i686-pc-linux-gnu-gfortran -O2 -pipe -fno-second-underscore   -c -o mol2_file.o mol2_file.f
i686-pc-linux-gnu-gfortran -O2 -pipe -fno-second-underscore   -c -o sdf_files.o sdf_files.f
i686-pc-linux-gnu-gfortran -O2 -pipe -fno-second-underscore   -c -o main_makecif.o main_makecif.f
i686-pc-linux-gnu-gfortran -O2 -pipe -fno-second-underscore   -c -o make_vdw.o make_vdw.f
In file included from bridge.cpp:2:0:
covmat.h: In member function ‘void covar_matrix<realnum>::Alloc(int) [with realnum = double]’:
covmat.h:838:3:   instantiated from ‘covar_matrix<realnum>::covar_matrix(likelihood<realnum>*, int, int, int, std::string, int, int) [with realnum = double, std::string = std::basic_string<char>]’
llhood.h:885:57:   instantiated from ‘likelihood<realnum>::likelihood(int, int, int, int, std::string, int, int, int, int, int, Gauss_structure<realnum>*) [with realnum = double, std::string = std::basic_string<char>]’
bridge.cpp:95:116:   instantiated from here
covmat.h:133:56: warning: deprecated conversion from string constant to ‘char*’
covmat.h:134:60: warning: deprecated conversion from string constant to ‘char*’
covmat.h:141:41: warning: deprecated conversion from string constant to ‘char*’
covmat.h:143:51: warning: deprecated conversion from string constant to ‘char*’
covmat.h:145:60: warning: deprecated conversion from string constant to ‘char*’
covmat.h:148:59: warning: deprecated conversion from string constant to ‘char*’
covmat.h:152:49: warning: deprecated conversion from string constant to ‘char*’
covmat.h:153:48: warning: deprecated conversion from string constant to ‘char*’
covmat.h:156:54: warning: deprecated conversion from string constant to ‘char*’
covmat.h:157:53: warning: deprecated conversion from string constant to ‘char*’
covmat.h:180:56: warning: deprecated conversion from string constant to ‘char*’
covmat.h:180:72: warning: deprecated conversion from string constant to ‘char*’
i686-pc-linux-gnu-gfortran -O2 -pipe -fno-second-underscore  -Wl,-O1 -o refmac   refmac_xml.o solvent_contr_mask.o hkon_secder_tch.o fast_hessian_tabulation.o subvag.o lsq_symm_symm.o oppro_allocate.o rcard_tor1.o subcf_scale1.o subag_scale_hessian.o extra_eigen.o rigid_allocate.o aniso_ref_eigen.o linalgebra.o make_CIF.o make_subr.o make_subr_refmac.o tls_allocate.o vdw_and_contacts.o vdw_flexible.o make_lib11.o make_lib12.o make_lib2.o make_crd1.o make_crd2.o make_new1.o make_new2.o set_num.o make_rst1.o make_rst2.o make_PDB.o makecif.o make_refmac_dummy.o ls_scaling_double.o interpolate_mod.o rharvest.o newentry_idealise.o ml_scaling_double.o gaussian_int.o subnumrec.o math_refmac.o read_extra_restraints.o inout_routines.o errwrt.o xml_writer.o ncs_rest.o occupancy_only_refine.o cell_symm_subrs.o iheap_sort.o enm_restraints.o wave2f2prime.o lnumrec.o refpre_twin.o refall_twin.o ls_scaling_twin_save.o max_with_ints.o ml_params_refine.o block_organization.o merohedr_twin.o decide_twin_opers_0.o read_data.o asym_list.o calc_stats_twin.o mtz_write_twin.o libT.o messy_pdb.o bridge.o i0.o i1.o chbevl.o                     -lgfortran -lgfortranbegin -lstdc++  -lccp4f -lccp4c -lccif -lmmdb -lstdc++  -llapack -lblas
i686-pc-linux-gnu-gfortran -O2 -pipe -fno-second-underscore  -Wl,-O1 -o libcheck main_libcheck.o make_subr_2.o make_subr.o make_lib11.o make_lib12.o make_lib2.o make_crd1.o make_crd2.o libcheck.o make_PDB.o make_CIF.o make_new1.o make_new2.o set_num.o make_unix_ccp4.o emin.o libcheck_min.o mol2_file.o sdf_files.o                  -lccp4f -lccp4c -lccif -lmmdb -lstdc++
i686-pc-linux-gnu-gfortran -O2 -pipe -fno-second-underscore  -Wl,-O1 -o makecif main_makecif.o make_CIF.o make_subr.o make_subr_2.o make_lib11.o make_lib12.o make_lib2.o make_crd1.o make_crd2.o make_new1.o make_new2.o set_num.o make_rst1.o make_rst2.o make_PDB.o makecif.o make_unix_ccp4.o make_vdw.o                   -lccp4f -lccp4c -lccif -lmmdb -lstdc++ 
>>> Source compiled.
 * Starting tests ...
[REFMAC5] TLS refinement with 4 molecules (1VK8 INFL example.) ... FAIL
[REFMAC5] sad refinement (2ISB INFL example.) ... FAIL
[REFMAC5] twinned refinement (1VR7 example.) ... FAIL

======================================================================
FAIL: [REFMAC5] TLS refinement with 4 molecules (1VK8 INFL example.)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/var/tmp/portage/sci-chemistry/refmac-5.5.0109/work/test-framework/refmac5/test_refmac5.py", line 154, in test_4_domain_tls
    self.assertEqual(status, 0)
AssertionError: 1 != 0

======================================================================
FAIL: [REFMAC5] sad refinement (2ISB INFL example.)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/var/tmp/portage/sci-chemistry/refmac-5.5.0109/work/test-framework/refmac5/test_refmac5.py", line 199, in test_sad_refinement
    self.assertEqual(status, 0)
AssertionError: 1 != 0

======================================================================
FAIL: [REFMAC5] twinned refinement (1VR7 example.)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/var/tmp/portage/sci-chemistry/refmac-5.5.0109/work/test-framework/refmac5/test_refmac5.py", line 105, in test_twinned_refinement
    self.assertEqual(status, 0)
AssertionError: 1 != 0

----------------------------------------------------------------------
Ran 3 tests in 0.078s

FAILED (failures=3)
 * ERROR: sci-chemistry/refmac-5.5.0109 failed:
 *   (no error message)
 * 
 * Call stack:
 *     ebuild.sh, line  54:  Called src_test
 *   environment, line 3503:  Called die
 * The specific snippet of code:
 *       ccp4-run-thorough-tests -v test_refmac5 || die
 * 
 * If you need support, post the output of 'emerge --info =sci-chemistry/refmac-5.5.0109',
 * the complete build log and the output of 'emerge -pqv =sci-chemistry/refmac-5.5.0109'.
 * The complete build log is located at '/var/log/portage/build/sci-chemistry/refmac-5.5.0109:20100505-073405.log'.
 * The ebuild environment file is located at '/var/tmp/portage/sci-chemistry/refmac-5.5.0109/temp/environment'.
 * S: '/var/tmp/portage/sci-chemistry/refmac-5.5.0109/work'

>>> Install refmac-5.5.0109 into /var/tmp/portage/sci-chemistry/refmac-5.5.0109/image/ category sci-chemistry
>>> Completed installing refmac-5.5.0109 into /var/tmp/portage/sci-chemistry/refmac-5.5.0109/image/

strip: i686-pc-linux-gnu-strip --strip-unneeded -R .comment
   usr/bin/refmac
   usr/bin/makecif
   usr/bin/libcheck