build.log

build.log (text/plain), 7.50 KB, created by Juergen Rose on 2016-03-19 22:36:41 UTC

[32;01m * [39;49;00mPackage:    sci-libs/msms-1.5.6
[32;01m * [39;49;00mRepository: science
[32;01m * [39;49;00mMaintainer: [e-mail]
[32;01m * [39;49;00mUSE:        abi_x86_64 amd64 elibc_glibc kernel_linux python_targets_python2_7 userland_GNU
[32;01m * [39;49;00mFEATURES:   preserve-libs sandbox userpriv usersandbox
>>> Unpacking source...
>>> Source unpacked in /var/tmp/portage/sci-libs/msms-1.5.6/work
>>> Preparing source in /var/tmp/portage/sci-libs/msms-1.5.6/work/mslib-1.5.6 ...
 [32;01m*[0m Applying build-with-linux-3.0.patch ...
[A[155C [34;01m[ [32;01mok[34;01m ][0m
>>> Source prepared.
>>> Configuring source in /var/tmp/portage/sci-libs/msms-1.5.6/work/mslib-1.5.6 ...
>>> Source configured.
>>> Compiling source in /var/tmp/portage/sci-libs/msms-1.5.6/work/mslib-1.5.6 ...
 [32;01m*[0m python2_7: running distutils-r1_run_phase distutils-r1_python_compile
/usr/bin/python2.7 setup.py build
running build
running build_ext
building '_msms' extension
swigging mslib/msms.i to mslib/msms_wrap.c
swig -python -o mslib/msms_wrap.c mslib/msms.i
mslib/msms.i:181: Warning 121: %name is deprecated.  Use %rename instead.
mslib/msms.i:269: Warning 121: %name is deprecated.  Use %rename instead.
mslib/msms.i:327: Warning 121: %name is deprecated.  Use %rename instead.
mslib/msms.i:387: Warning 121: %name is deprecated.  Use %rename instead.
mslib/msms.i:441: Warning 121: %name is deprecated.  Use %rename instead.
mslib/msms.i:479: Warning 121: %name is deprecated.  Use %rename instead.
mslib/msms.i:510: Warning 121: %name is deprecated.  Use %rename instead.
mslib/msms.i:526: Warning 121: %name is deprecated.  Use %rename instead.
mslib/msms.i:563: Warning 121: %name is deprecated.  Use %rename instead.
mslib/msms.i:614: Warning 121: %name is deprecated.  Use %rename instead.
mslib/msms.i:676: Warning 121: %name is deprecated.  Use %rename instead.
mslib/msms.i:759: Warning 121: %name is deprecated.  Use %rename instead.
creating /var/tmp/portage/sci-libs/msms-1.5.6/work/mslib-1.5.6-python2_7/temp.linux-x86_64-2.7
creating /var/tmp/portage/sci-libs/msms-1.5.6/work/mslib-1.5.6-python2_7/temp.linux-x86_64-2.7/mslib
x86_64-pc-linux-gnu-gcc -march=amdfam10 -O2 -pipe -fPIC -DLONGJMP_EXIT -I./include -I/usr/lib64/python2.7/site-packages/numpy/core/include -I/usr/include/python2.7 -c mslib/msms_wrap.c -o /var/tmp/portage/sci-libs/msms-1.5.6/work/mslib-1.5.6-python2_7/temp.linux-x86_64-2.7/mslib/msms_wrap.o
In file included from /usr/lib64/python2.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1781:0,
                 from /usr/lib64/python2.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:18,
                 from /usr/lib64/python2.7/site-packages/numpy/core/include/numpy/arrayobject.h:4,
                 from mslib/msms_wrap.c:3056:
/usr/lib64/python2.7/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:15:2: warning: #warning "Using deprecated NumPy API, disable it by " "#defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
 #warning "Using deprecated NumPy API, disable it by " \
  ^
mslib/msms_wrap.c: In function ‘contiguous_typed_array’:
mslib/msms_wrap.c:3101:31: warning: format ‘%d’ expects argument of type ‘int’, but argument 4 has type ‘npy_intp {aka long int}’ [-Wformat=]
                   sprintf(buf,"The extent of dimension %d is %d while %d was expected\n",
                               ^
mslib/msms_wrap.c: In function ‘MOLSRF_findBuriedVertices’:
mslib/msms_wrap.c:3878:22: warning: return makes integer from pointer without a cast [-Wint-conversion]
       if (!c) return NULL;
                      ^
mslib/msms_wrap.c:3884:11: warning: return makes integer from pointer without a cast [-Wint-conversion]
    return NULL;
           ^
mslib/msms_wrap.c: In function ‘MS_readxyzr’:
mslib/msms_wrap.c:3912:57: warning: passing argument 5 of ‘MS_read_xyzr’ from incompatible pointer type [-Wincompatible-pointer-types]
   stat = MS_read_xyzr( filename, &nat, &coords, &names, &surfflags, &hdflags);
                                                         ^
In file included from mslib/msms_wrap.c:3141:0:
./include/msmsAllProto.h:161:16: note: expected ‘int **’ but argument is of type ‘float **’
 extern int     MS_read_xyzr(char *file, int *nat, 
                ^
mslib/msms_wrap.c:3959:37: warning: passing argument 4 of ‘MS_free_coord’ from incompatible pointer type [-Wincompatible-pointer-types]
   MS_free_coord(coords, nat, names, surfflags, hdflags);
                                     ^
In file included from mslib/msms_wrap.c:3141:0:
./include/msmsAllProto.h:159:16: note: expected ‘int *’ but argument is of type ‘float *’
 extern void    MS_free_coord(float **Coord,int nbat, char *names[], int *surf,
                ^
mslib/msms_wrap.c: In function ‘_wrap_MS_addSpheres’:
mslib/msms_wrap.c:14407:17: warning: implicit declaration of function ‘MS_addSpheres’ [-Wimplicit-function-declaration]
   result = (int)MS_addSpheres(arg1,arg2,arg3,arg4);
                 ^
creating /var/tmp/portage/sci-libs/msms-1.5.6/work/mslib-1.5.6-python2_7/lib/mslib
x86_64-pc-linux-gnu-gcc -shared -Wl,-O1 -Wl,--as-needed -march=amdfam10 -O2 -pipe /var/tmp/portage/sci-libs/msms-1.5.6/work/mslib-1.5.6-python2_7/temp.linux-x86_64-2.7/mslib/msms_wrap.o -L./lib/x86_64Linux4 -L/usr/lib64 -lmsms1.4.4 -lpython2.7 -o /var/tmp/portage/sci-libs/msms-1.5.6/work/mslib-1.5.6-python2_7/lib/mslib/_msms.so
/usr/lib/gcc/x86_64-pc-linux-gnu/5.3.0/../../../../x86_64-pc-linux-gnu/bin/ld: cannot find -lmsms1.4.4
collect2: error: ld returned 1 exit status
error: command 'x86_64-pc-linux-gnu-gcc' failed with exit status 1
 [31;01m*[0m ERROR: sci-libs/msms-1.5.6::science failed (compile phase):
 [31;01m*[0m   (no error message)
 [31;01m*[0m 
 [31;01m*[0m Call stack:
 [31;01m*[0m     ebuild.sh, line  133:  Called src_compile
 [31;01m*[0m   environment, line 3674:  Called distutils-r1_src_compile
 [31;01m*[0m   environment, line  984:  Called _distutils-r1_run_foreach_impl 'distutils-r1_python_compile'
 [31;01m*[0m   environment, line  400:  Called python_foreach_impl 'distutils-r1_run_phase' 'distutils-r1_python_compile'
 [31;01m*[0m   environment, line 3208:  Called multibuild_foreach_variant '_python_multibuild_wrapper' 'distutils-r1_run_phase' 'distutils-r1_python_compile'
 [31;01m*[0m   environment, line 2317:  Called _multibuild_run '_python_multibuild_wrapper' 'distutils-r1_run_phase' 'distutils-r1_python_compile'
 [31;01m*[0m   environment, line 2315:  Called _python_multibuild_wrapper 'distutils-r1_run_phase' 'distutils-r1_python_compile'
 [31;01m*[0m   environment, line  667:  Called distutils-r1_run_phase 'distutils-r1_python_compile'
 [31;01m*[0m   environment, line  975:  Called distutils-r1_python_compile
 [31;01m*[0m   environment, line  847:  Called esetup.py 'build'
 [31;01m*[0m   environment, line 1475:  Called die
 [31;01m*[0m The specific snippet of code:
 [31;01m*[0m       "${@}" || die "${die_args[@]}" || return ${?}
 [31;01m*[0m 
 [31;01m*[0m If you need support, post the output of `emerge --info '=sci-libs/msms-1.5.6::science'`,
 [31;01m*[0m the complete build log and the output of `emerge -pqv '=sci-libs/msms-1.5.6::science'`.
 [31;01m*[0m The complete build log is located at '/var/tmp/portage/sci-libs/msms-1.5.6/temp/build.log'.
 [31;01m*[0m The ebuild environment file is located at '/var/tmp/portage/sci-libs/msms-1.5.6/temp/environment'.
 [31;01m*[0m Working directory: '/var/tmp/portage/sci-libs/msms-1.5.6/work/mslib-1.5.6'
 [31;01m*[0m S: '/var/tmp/portage/sci-libs/msms-1.5.6/work/mslib-1.5.6'