Hi. We are attempting to set up a Galaxy instance on our local TORQUE cluster, but the Documentation instructions to scramble as such:
LIBTORQUE_DIR=/path/to/libtorque python scripts/scramble.py -e pbs_python
Gives the following barrage of output:
(galaxy_env)[root@galaxy galaxy-dist]# LIBTORQUE_DIR=/rc/tools/free/redhat_6_x86_64/torque-4.2.2/lib/ python scripts/scramble.py -e pbs_python --config=universe_wsgi.ini fetch_one(): Using existing source, remove to download again: /rc/galaxy/galaxy-dist/scripts/scramble/archives/pbs_python-4.1.0.tar.gz unpack_source(): Removing old build directory at:
/rc/galaxy/galaxy-dist/scripts/scramble/build/py2.6-linux-x86_64-ucs4/pbs_python unpack_source(): Unpacked to:
/rc/galaxy/galaxy-dist/scripts/scramble/build/py2.6-linux-x86_64-ucs4/pbs_python copy_build_script(): Using build script /rc/galaxy/galaxy-dist/scripts/scramble/scripts/pbs_python.py run_scramble_script(): Beginning build run_scramble_script(): Executing in /rc/galaxy/galaxy-dist/scripts/scramble/build/py2.6-linux-x86_64-ucs4/pbs_python: /rc/galaxy/tools/galaxy_env/bin/python scramble.py checking for pbs-config... /rc/tools/free/redhat_6_x86_64/torque-4.2.2/lib//../bin/pbs-config Found torque version: 4.2.2 checking for python... /rc/galaxy/tools/galaxy_env/bin/python checking for python version... 2.6 checking for python platform... linux2 checking for python script directory... ${prefix}/lib/python2.6/site-packages checking for python extension module directory... ${exec_prefix}/lib64/python2.6/site-packages configure: creating ./config.status config.status: creating Makefile config.status: creating setup.py scramble(): Patching setup.py running egg_info creating src/pbs_python.egg-info writing src/pbs_python.egg-info/PKG-INFO writing top-level names to src/pbs_python.egg-info/top_level.txt writing dependency_links to src/pbs_python.egg-info/dependency_links.txt writing manifest file 'src/pbs_python.egg-info/SOURCES.txt' reading manifest file 'src/pbs_python.egg-info/SOURCES.txt' writing manifest file 'src/pbs_python.egg-info/SOURCES.txt' running bdist_egg installing library code to build/bdist.linux-x86_64/egg running install_lib running build_py creating build creating build/lib.linux-x86_64-2.6 copying src/pbs.py -> build/lib.linux-x86_64-2.6 copying src/PBSQuery.py -> build/lib.linux-x86_64-2.6 running build_ext building '_pbs' extension creating build/temp.linux-x86_64-2.6 creating build/temp.linux-x86_64-2.6/src gcc -pthread -fno-strict-aliasing -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fwrapv -DNDEBUG -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fwrapv -fPIC -DTORQUE_OLD -I/usr/include/python2.6 -c src/pbs_wrap.c -o build/temp.linux-x86_64-2.6/src/pbs_wrap.o src/pbs_wrap.c:124:20: error: Python.h: No such file or directory src/pbs_wrap.c:730: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token src/pbs_wrap.c:785: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token src/pbs_wrap.c:806: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token src/pbs_wrap.c: In function ‘SWIG_Python_AddErrorMsg’: src/pbs_wrap.c:853: error: ‘PyObject’ undeclared (first use in this function) src/pbs_wrap.c:853: error: (Each undeclared identifier is reported only once src/pbs_wrap.c:853: error: for each function it appears in.) src/pbs_wrap.c:853: error: ‘type’ undeclared (first use in this function) src/pbs_wrap.c:854: error: ‘value’ undeclared (first use in this function) src/pbs_wrap.c:855: error: ‘traceback’ undeclared (first use in this function) src/pbs_wrap.c:857: warning: implicit declaration of function ‘PyErr_Occurred’ src/pbs_wrap.c:857: warning: implicit declaration of function ‘PyErr_Fetch’ src/pbs_wrap.c:859: error: ‘old_str’ undeclared (first use in this function) src/pbs_wrap.c:859: warning: implicit declaration of function ‘PyObject_Str’ src/pbs_wrap.c:860: warning: implicit declaration of function ‘PyErr_Clear’ src/pbs_wrap.c:861: warning: implicit declaration of function ‘Py_XINCREF’ src/pbs_wrap.c:862: warning: implicit declaration of function ‘PyErr_Format’ src/pbs_wrap.c:862: warning: implicit declaration of function ‘PyString_AsString’ src/pbs_wrap.c:863: warning: implicit declaration of function ‘Py_DECREF’ src/pbs_wrap.c:866: warning: implicit declaration of function ‘PyErr_SetString’ src/pbs_wrap.c:866: error: ‘PyExc_RuntimeError’ undeclared (first use in this function) src/pbs_wrap.c: At top level: src/pbs_wrap.c:1034: error: expected ‘)’ before ‘*’ token src/pbs_wrap.c:1042: error: expected ‘)’ before ‘*’ token src/pbs_wrap.c:1053: error: expected ‘)’ before ‘*’ token src/pbs_wrap.c:1060: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token src/pbs_wrap.c:1106: error: expected ‘)’ before ‘*’ token src/pbs_wrap.c:1208: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token src/pbs_wrap.c:1219: error: expected specifier-qualifier-list before ‘PyObject’ src/pbs_wrap.c: In function ‘SWIG_Python_CheckImplicit’: src/pbs_wrap.c:1231: error: ‘PySwigClientData’ has no member named ‘implicitconv’ src/pbs_wrap.c: At top level: src/pbs_wrap.c:1234: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token src/pbs_wrap.c:1243: error: expected ‘)’ before ‘*’ token src/pbs_wrap.c: In function ‘PySwigClientData_Del’: src/pbs_wrap.c:1298: warning: implicit declaration of function ‘Py_XDECREF’ src/pbs_wrap.c:1298: error: ‘PySwigClientData’ has no member named ‘newraw’ src/pbs_wrap.c:1299: error: ‘PySwigClientData’ has no member named ‘newargs’ src/pbs_wrap.c:1300: error: ‘PySwigClientData’ has no member named ‘destroy’ src/pbs_wrap.c: At top level: src/pbs_wrap.c:1306: error: expected specifier-qualifier-list before ‘PyObject_HEAD’ src/pbs_wrap.c:1313: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token src/pbs_wrap.c:1319: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token src/pbs_wrap.c:1337: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token src/pbs_wrap.c:1343: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token src/pbs_wrap.c:1349: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token src/pbs_wrap.c:1372: error: expected declaration specifiers or ‘...’ before ‘FILE’ src/pbs_wrap.c: In function ‘PySwigObject_print’: src/pbs_wrap.c:1377: error: ‘PyObject’ undeclared (first use in this function) src/pbs_wrap.c:1377: error: ‘repr’ undeclared (first use in this function) src/pbs_wrap.c:1377: warning: implicit declaration of function ‘PySwigObject_repr’ src/pbs_wrap.c:1380: warning: implicit declaration of function ‘fputs’ src/pbs_wrap.c:1380: error: ‘fp’ undeclared (first use in this function) src/pbs_wrap.c: At top level: src/pbs_wrap.c:1388: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token src/pbs_wrap.c: In function ‘PySwigObject_compare’: src/pbs_wrap.c:1399: error: ‘PySwigObject’ has no member named ‘ptr’ src/pbs_wrap.c:1400: error: ‘PySwigObject’ has no member named ‘ptr’ src/pbs_wrap.c: At top level: src/pbs_wrap.c:1404: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token src/pbs_wrap.c:1406: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token src/pbs_wrap.c:1413: error: expected ‘)’ before ‘*’ token src/pbs_wrap.c:1418: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token src/pbs_wrap.c:1422: error: expected ‘)’ before ‘*’ token src/pbs_wrap.c:1456: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token src/pbs_wrap.c:1473: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token src/pbs_wrap.c:1489: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token src/pbs_wrap.c:1501: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token src/pbs_wrap.c:1513: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token src/pbs_wrap.c:1561: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘swigobject_methods’ src/pbs_wrap.c:1573: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token src/pbs_wrap.c:1580: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token src/pbs_wrap.c:1688: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token src/pbs_wrap.c:1706: error: expected specifier-qualifier-list before ‘PyObject_HEAD’ src/pbs_wrap.c:1713: error: expected declaration specifiers or ‘...’ before ‘FILE’ src/pbs_wrap.c: In function ‘PySwigPacked_print’: src/pbs_wrap.c:1716: error: ‘fp’ undeclared (first use in this function) src/pbs_wrap.c:1717: error: ‘PySwigPacked’ has no member named ‘pack’ src/pbs_wrap.c:1717: error: ‘PySwigPacked’ has no member named ‘size’ src/pbs_wrap.c:1721: error: ‘PySwigPacked’ has no member named ‘ty’ src/pbs_wrap.c: At top level: src/pbs_wrap.c:1726: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token src/pbs_wrap.c:1737: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token src/pbs_wrap.c: In function ‘PySwigPacked_compare’: src/pbs_wrap.c:1751: error: ‘PySwigPacked’ has no member named ‘size’ src/pbs_wrap.c:1752: error: ‘PySwigPacked’ has no member named ‘size’ src/pbs_wrap.c:1754: error: ‘PySwigPacked’ has no member named ‘size’ src/pbs_wrap.c:1754: error: ‘PySwigPacked’ has no member named ‘pack’ src/pbs_wrap.c:1754: error: ‘PySwigPacked’ has no member named ‘pack’ src/pbs_wrap.c:1754: error: ‘PySwigPacked’ has no member named ‘size’ src/pbs_wrap.c:1754: error: ‘PySwigPacked’ has no member named ‘pack’ src/pbs_wrap.c:1754: error: ‘PySwigPacked’ has no member named ‘pack’ src/pbs_wrap.c:1754: error: ‘PySwigPacked’ has no member named ‘size’ src/pbs_wrap.c:1754: error: ‘PySwigPacked’ has no member named ‘pack’ src/pbs_wrap.c:1754: error: ‘PySwigPacked’ has no member named ‘pack’ src/pbs_wrap.c:1754: error: ‘PySwigPacked’ has no member named ‘pack’ src/pbs_wrap.c:1754: error: ‘PySwigPacked’ has no member named ‘pack’ src/pbs_wrap.c:1754: warning: left-hand operand of comma expression has no effect src/pbs_wrap.c:1754: error: ‘PySwigPacked’ has no member named ‘pack’ src/pbs_wrap.c:1754: error: ‘PySwigPacked’ has no member named ‘pack’ src/pbs_wrap.c:1754: error: ‘PySwigPacked’ has no member named ‘pack’ src/pbs_wrap.c:1754: error: ‘PySwigPacked’ has no member named ‘pack’ src/pbs_wrap.c:1754: warning: left-hand operand of comma expression has no effect src/pbs_wrap.c:1754: error: ‘PySwigPacked’ has no member named ‘pack’ src/pbs_wrap.c:1754: error: ‘PySwigPacked’ has no member named ‘pack’ src/pbs_wrap.c:1754: error: ‘PySwigPacked’ has no member named ‘pack’ src/pbs_wrap.c:1754: error: ‘PySwigPacked’ has no member named ‘pack’ src/pbs_wrap.c:1754: error: ‘PySwigPacked’ has no member named ‘pack’ src/pbs_wrap.c:1754: error: ‘PySwigPacked’ has no member named ‘pack’ src/pbs_wrap.c:1754: warning: left-hand operand of comma expression has no effect src/pbs_wrap.c:1754: error: ‘PySwigPacked’ has no member named ‘pack’ src/pbs_wrap.c:1754: error: ‘PySwigPacked’ has no member named ‘pack’ src/pbs_wrap.c:1754: error: ‘PySwigPacked’ has no member named ‘pack’ src/pbs_wrap.c:1754: error: ‘PySwigPacked’ has no member named ‘pack’ src/pbs_wrap.c:1754: error: ‘PySwigPacked’ has no member named ‘pack’ src/pbs_wrap.c:1754: error: ‘PySwigPacked’ has no member named ‘pack’ src/pbs_wrap.c:1754: error: ‘PySwigPacked’ has no member named ‘pack’ src/pbs_wrap.c:1754: error: ‘PySwigPacked’ has no member named ‘pack’ src/pbs_wrap.c:1754: error: ‘PySwigPacked’ has no member named ‘pack’ src/pbs_wrap.c:1754: error: ‘PySwigPacked’ has no member named ‘pack’ src/pbs_wrap.c:1754: error: ‘PySwigPacked’ has no member named ‘pack’ src/pbs_wrap.c:1754: error: ‘PySwigPacked’ has no member named ‘pack’ src/pbs_wrap.c:1754: error: ‘PySwigPacked’ has no member named ‘pack’ src/pbs_wrap.c:1754: error: ‘PySwigPacked’ has no member named ‘pack’ src/pbs_wrap.c:1754: warning: left-hand operand of comma expression has no effect src/pbs_wrap.c:1754: error: ‘PySwigPacked’ has no member named ‘pack’ src/pbs_wrap.c:1754: error: ‘PySwigPacked’ has no member named ‘pack’ src/pbs_wrap.c:1754: error: ‘PySwigPacked’ has no member named ‘pack’ src/pbs_wrap.c:1754: error: ‘PySwigPacked’ has no member named ‘pack’ src/pbs_wrap.c:1754: error: ‘PySwigPacked’ has no member named ‘pack’ src/pbs_wrap.c:1754: error: ‘PySwigPacked’ has no member named ‘pack’ src/pbs_wrap.c:1754: error: ‘PySwigPacked’ has no member named ‘pack’ src/pbs_wrap.c:1754: error: ‘PySwigPacked’ has no member named ‘pack’ src/pbs_wrap.c:1754: error: ‘PySwigPacked’ has no member named ‘pack’ src/pbs_wrap.c:1754: error: ‘PySwigPacked’ has no member named ‘pack’ src/pbs_wrap.c:1754: error: ‘PySwigPacked’ has no member named ‘pack’ src/pbs_wrap.c:1754: error: ‘PySwigPacked’ has no member named ‘pack’ src/pbs_wrap.c:1754: error: ‘PySwigPacked’ has no member named ‘pack’ src/pbs_wrap.c:1754: error: ‘PySwigPacked’ has no member named ‘pack’ src/pbs_wrap.c:1754: error: ‘PySwigPacked’ has no member named ‘size’ src/pbs_wrap.c: At top level: src/pbs_wrap.c:1757: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token src/pbs_wrap.c:1759: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token src/pbs_wrap.c:1766: error: expected ‘)’ before ‘*’ token src/pbs_wrap.c:1772: error: expected ‘)’ before ‘*’ token src/pbs_wrap.c:1781: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token src/pbs_wrap.c:1851: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token src/pbs_wrap.c:1871: error: expected ‘)’ before ‘*’ token src/pbs_wrap.c:1887: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token src/pbs_wrap.c:1893: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token src/pbs_wrap.c:1903: error: expected ‘)’ before ‘*’ token src/pbs_wrap.c:1954: error: expected ‘)’ before ‘*’ token src/pbs_wrap.c:1969: error: expected ‘)’ before ‘*’ token src/pbs_wrap.c:2060: error: expected ‘)’ before ‘*’ token src/pbs_wrap.c:2092: error: expected ‘)’ before ‘*’ token src/pbs_wrap.c:2114: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token src/pbs_wrap.c:2178: error: expected ‘)’ before ‘*’ token src/pbs_wrap.c:2199: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token src/pbs_wrap.c:2217: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token src/pbs_wrap.c:2238: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token src/pbs_wrap.c: In function ‘SWIG_Python_GetModule’: src/pbs_wrap.c:2259: warning: implicit declaration of function ‘PyCObject_Import’ src/pbs_wrap.c:2260: warning: assignment makes pointer from integer without a cast src/pbs_wrap.c: At top level: src/pbs_wrap.c:2274: error: expected ‘)’ before ‘*’ token src/pbs_wrap.c: In function ‘SWIG_Python_DestroyModule’: src/pbs_wrap.c:2315: warning: implicit declaration of function ‘SWIG_This’ src/pbs_wrap.c: In function ‘SWIG_Python_SetModule’: src/pbs_wrap.c:2320: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘swig_empty_runtime_method_table’ src/pbs_wrap.c:2320: error: ‘swig_empty_runtime_method_table’ undeclared (first use in this function) src/pbs_wrap.c:2320: error: expected expression before ‘]’ token src/pbs_wrap.c:2322: error: ‘PyObject’ undeclared (first use in this function) src/pbs_wrap.c:2322: error: ‘module’ undeclared (first use in this function) src/pbs_wrap.c:2322: warning: implicit declaration of function ‘Py_InitModule’ src/pbs_wrap.c:2324: error: ‘pointer’ undeclared (first use in this function) src/pbs_wrap.c:2324: warning: implicit declaration of function ‘PyCObject_FromVoidPtr’ src/pbs_wrap.c:2326: warning: implicit declaration of function ‘PyModule_AddObject’ src/pbs_wrap.c: At top level: src/pbs_wrap.c:2333: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token src/pbs_wrap.c: In function ‘SWIG_Python_TypeQuery’: src/pbs_wrap.c:2342: error: ‘PyObject’ undeclared (first use in this function) src/pbs_wrap.c:2342: error: ‘cache’ undeclared (first use in this function) src/pbs_wrap.c:2342: warning: implicit declaration of function ‘SWIG_Python_TypeCache’ src/pbs_wrap.c:2343: error: ‘key’ undeclared (first use in this function) src/pbs_wrap.c:2343: warning: implicit declaration of function ‘PyString_FromString’ src/pbs_wrap.c:2344: error: ‘obj’ undeclared (first use in this function) src/pbs_wrap.c:2344: warning: implicit declaration of function ‘PyDict_GetItem’ src/pbs_wrap.c:2347: warning: implicit declaration of function ‘PyCObject_AsVoidPtr’ src/pbs_wrap.c:2353: warning: implicit declaration of function ‘PyDict_SetItem’ src/pbs_wrap.c: In function ‘SWIG_Python_AddErrMesg’: src/pbs_wrap.c:2372: error: ‘PyObject’ undeclared (first use in this function) src/pbs_wrap.c:2372: error: ‘type’ undeclared (first use in this function) src/pbs_wrap.c:2373: error: ‘value’ undeclared (first use in this function) src/pbs_wrap.c:2374: error: ‘traceback’ undeclared (first use in this function) src/pbs_wrap.c:2377: error: ‘old_str’ undeclared (first use in this function) src/pbs_wrap.c: In function ‘SWIG_Python_ArgFail’: src/pbs_wrap.c:2399: warning: implicit declaration of function ‘snprintf’ src/pbs_wrap.c:2399: warning: incompatible implicit declaration of built-in function ‘snprintf’ src/pbs_wrap.c: At top level: src/pbs_wrap.c:2407: error: expected ‘)’ before ‘*’ token src/pbs_wrap.c:2415: error: expected declaration specifiers or ‘...’ before ‘PyObject’ src/pbs_wrap.c: In function ‘SWIG_Python_TypeError’: src/pbs_wrap.c:2429: error: ‘obj’ undeclared (first use in this function) src/pbs_wrap.c:2431: error: ‘PyObject’ undeclared (first use in this function) src/pbs_wrap.c:2431: error: ‘str’ undeclared (first use in this function) src/pbs_wrap.c:2434: error: ‘PyExc_TypeError’ undeclared (first use in this function) src/pbs_wrap.c: At top level: src/pbs_wrap.c:2453: error: expected ‘)’ before ‘*’ token src/pbs_wrap.c:2499:4: error: #error "This python version requires swig to be run with the '-classic' option" src/pbs_wrap.c:2530: error: expected ‘)’ before ‘*’ token src/pbs_wrap.c: In function ‘get_error’: src/pbs_wrap.c:2636: warning: implicit declaration of function ‘printf’ src/pbs_wrap.c:2636: warning: incompatible implicit declaration of built-in function ‘printf’ src/pbs_wrap.c: At top level: src/pbs_wrap.c:2656: error: expected ‘)’ before ‘*’ token src/pbs_wrap.c: In function ‘SWIG_CanCastAsInteger’: src/pbs_wrap.c:2712: error: ‘errno’ undeclared (first use in this function) src/pbs_wrap.c:2712: error: ‘EDOM’ undeclared (first use in this function) src/pbs_wrap.c:2712: error: ‘ERANGE’ undeclared (first use in this function) src/pbs_wrap.c: At top level: src/pbs_wrap.c:2736: error: expected ‘)’ before ‘*’ token src/pbs_wrap.c:2775: error: expected ‘)’ before ‘*’ token src/pbs_wrap.c:2793: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token src/pbs_wrap.c:2813: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token src/pbs_wrap.c:2830: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token src/pbs_wrap.c:2838: error: expected ‘)’ before ‘*’ token src/pbs_wrap.c: In function ‘attrl___str__’: src/pbs_wrap.c:2893: warning: incompatible implicit declaration of built-in function ‘snprintf’ src/pbs_wrap.c: In function ‘delete_attrl’: src/pbs_wrap.c:2900: warning: incompatible implicit declaration of built-in function ‘printf’ src/pbs_wrap.c: In function ‘attropl___str__’: src/pbs_wrap.c:2908: warning: incompatible implicit declaration of built-in function ‘snprintf’ src/pbs_wrap.c: In function ‘delete_attropl’: src/pbs_wrap.c:2915: warning: incompatible implicit declaration of built-in function ‘printf’ src/pbs_wrap.c: At top level: src/pbs_wrap.c:2923: error: expected ‘)’ before ‘*’ token src/pbs_wrap.c:2967: error: expected ‘)’ before ‘*’ token src/pbs_wrap.c:2983: error: expected ‘)’ before ‘*’ token src/pbs_wrap.c:3008: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token src/pbs_wrap.c:3055: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token src/pbs_wrap.c:3100: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token src/pbs_wrap.c:3146: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token src/pbs_wrap.c:3159: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token src/pbs_wrap.c:3189: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token src/pbs_wrap.c:3236: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token src/pbs_wrap.c:3275: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token src/pbs_wrap.c:3297: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token src/pbs_wrap.c:3336: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token src/pbs_wrap.c:3358: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token src/pbs_wrap.c:3397: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token src/pbs_wrap.c:3419: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token src/pbs_wrap.c:3449: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token src/pbs_wrap.c:3471: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token src/pbs_wrap.c:3493: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token src/pbs_wrap.c:3514: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token src/pbs_wrap.c:3521: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token src/pbs_wrap.c:3551: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token src/pbs_wrap.c:3596: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token src/pbs_wrap.c:3635: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token src/pbs_wrap.c:3657: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token src/pbs_wrap.c:3696: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token src/pbs_wrap.c:3718: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token src/pbs_wrap.c:3757: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token src/pbs_wrap.c:3779: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token src/pbs_wrap.c:3809: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token src/pbs_wrap.c:3831: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token src/pbs_wrap.c:3853: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token src/pbs_wrap.c:3874: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token src/pbs_wrap.c:3881: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token src/pbs_wrap.c:3911: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token src/pbs_wrap.c:3966: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token src/pbs_wrap.c:4005: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token src/pbs_wrap.c:4027: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token src/pbs_wrap.c:4057: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token src/pbs_wrap.c:4104: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token src/pbs_wrap.c:4143: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token src/pbs_wrap.c:4165: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token src/pbs_wrap.c:4172: error: expected ‘)’ before ‘*’ token src/pbs_wrap.c:4187: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token src/pbs_wrap.c:4195: error: expected ‘)’ before ‘*’ token src/pbs_wrap.c:4215: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token src/pbs_wrap.c:4223: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token src/pbs_wrap.c:4257: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token src/pbs_wrap.c:4315: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token src/pbs_wrap.c:4413: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token src/pbs_wrap.c:4438: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token src/pbs_wrap.c:4451: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token src/pbs_wrap.c:4464: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token src/pbs_wrap.c:4510: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token src/pbs_wrap.c:4532: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token src/pbs_wrap.c:4554: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token src/pbs_wrap.c:4612: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token src/pbs_wrap.c:4658: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token src/pbs_wrap.c:4774: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token src/pbs_wrap.c:4832: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token src/pbs_wrap.c:4899: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token src/pbs_wrap.c:4957: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token src/pbs_wrap.c:5066: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token src/pbs_wrap.c:5148: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token src/pbs_wrap.c:5179: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token src/pbs_wrap.c:5225: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token src/pbs_wrap.c:5283: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token src/pbs_wrap.c:5341: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token src/pbs_wrap.c:5454: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token src/pbs_wrap.c:5512: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token src/pbs_wrap.c:5578: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token src/pbs_wrap.c:5709: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token src/pbs_wrap.c:5828: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token src/pbs_wrap.c:5959: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token src/pbs_wrap.c:6078: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token src/pbs_wrap.c:6209: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token src/pbs_wrap.c:6319: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token src/pbs_wrap.c:6362: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token src/pbs_wrap.c:6393: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token src/pbs_wrap.c:6424: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token src/pbs_wrap.c:6458: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token src/pbs_wrap.c:6480: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token src/pbs_wrap.c:6502: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token src/pbs_wrap.c:6536: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token src/pbs_wrap.c:6570: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token src/pbs_wrap.c:6595: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token src/pbs_wrap.c:6617: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token src/pbs_wrap.c:6630: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token src/pbs_wrap.c:6643: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token src/pbs_wrap.c:6664: error: expected ‘)’ before ‘*’ token src/pbs_wrap.c:6679: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token src/pbs_wrap.c:6687: error: expected ‘)’ before ‘*’ token src/pbs_wrap.c:6702: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token src/pbs_wrap.c:6710: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token src/pbs_wrap.c:6731: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token src/pbs_wrap.c:6776: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token src/pbs_wrap.c:6830: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token src/pbs_wrap.c:6867: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token src/pbs_wrap.c:6921: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token src/pbs_wrap.c:6942: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token src/pbs_wrap.c:6955: error: expected ‘)’ before ‘*’ token src/pbs_wrap.c:6968: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token src/pbs_wrap.c:6980: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token src/pbs_wrap.c:7053: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token src/pbs_wrap.c:7078: error: expected ‘)’ before ‘*’ token src/pbs_wrap.c:7098: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token src/pbs_wrap.c:7106: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘SwigMethods’ src/pbs_wrap.c:7503: error: expected specifier-qualifier-list before ‘PyObject’ src/pbs_wrap.c:7509: error: expected specifier-qualifier-list before ‘PyObject_HEAD’ src/pbs_wrap.c:7513: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token src/pbs_wrap.c:7518: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token src/pbs_wrap.c:7531: error: expected declaration specifiers or ‘...’ before ‘FILE’ src/pbs_wrap.c: In function ‘swig_varlink_print’: src/pbs_wrap.c:7532: error: ‘PyObject’ undeclared (first use in this function) src/pbs_wrap.c:7532: error: ‘str’ undeclared (first use in this function) src/pbs_wrap.c:7532: warning: implicit declaration of function ‘swig_varlink_str’ src/pbs_wrap.c:7533: warning: implicit declaration of function ‘fprintf’ src/pbs_wrap.c:7533: warning: incompatible implicit declaration of built-in function ‘fprintf’ src/pbs_wrap.c:7533: error: ‘fp’ undeclared (first use in this function) src/pbs_wrap.c: In function ‘swig_varlink_dealloc’: src/pbs_wrap.c:7541: error: ‘swig_varlinkobject’ has no member named ‘vars’ src/pbs_wrap.c:7543: error: ‘swig_globalvar’ has no member named ‘next’ src/pbs_wrap.c:7544: warning: implicit declaration of function ‘free’ src/pbs_wrap.c:7544: warning: incompatible implicit declaration of built-in function ‘free’ src/pbs_wrap.c: At top level: src/pbs_wrap.c:7550: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token src/pbs_wrap.c:7568: error: expected declaration specifiers or ‘...’ before ‘PyObject’ src/pbs_wrap.c: In function ‘swig_varlink_setattr’: src/pbs_wrap.c:7570: error: ‘swig_varlinkobject’ has no member named ‘vars’ src/pbs_wrap.c:7573: error: ‘swig_globalvar’ has no member named ‘set_attr’ src/pbs_wrap.c:7573: error: ‘p’ undeclared (first use in this function) src/pbs_wrap.c:7576: error: ‘swig_globalvar’ has no member named ‘next’ src/pbs_wrap.c:7579: error: ‘PyExc_NameError’ undeclared (first use in this function) src/pbs_wrap.c: At top level: src/pbs_wrap.c:7584: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token src/pbs_wrap.c:7636: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token src/pbs_wrap.c:7646: error: expected ‘)’ before ‘*’ token src/pbs_wrap.c:7662: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token src/pbs_wrap.c:7675: error: expected ‘)’ before ‘*’ token src/pbs_wrap.c:7702: error: expected ‘)’ before ‘*’ token src/pbs_wrap.c: In function ‘init_pbs’: src/pbs_wrap.c:7755: error: ‘PyObject’ undeclared (first use in this function) src/pbs_wrap.c:7755: error: ‘m’ undeclared (first use in this function) src/pbs_wrap.c:7755: error: ‘d’ undeclared (first use in this function) src/pbs_wrap.c:7755: warning: left-hand operand of comma expression has no effect src/pbs_wrap.c:7758: warning: implicit declaration of function ‘SWIG_Python_FixMethods’ src/pbs_wrap.c:7758: error: ‘SwigMethods’ undeclared (first use in this function) src/pbs_wrap.c:7761: warning: implicit declaration of function ‘PyModule_GetDict’ src/pbs_wrap.c:7764: warning: implicit declaration of function ‘SWIG_Python_InstallConstants’ src/pbs_wrap.c:7767: warning: implicit declaration of function ‘SWIG_Python_SetConstant’ src/pbs_wrap.c:7767: warning: implicit declaration of function ‘SWIG_FromCharPtr’ src/pbs_wrap.c:7966: warning: implicit declaration of function ‘SWIG_From_int’ src/pbs_wrap.c:8036: warning: implicit declaration of function ‘PyDict_SetItemString’ src/pbs_wrap.c:8036: warning: implicit declaration of function ‘SWIG_globals’ src/pbs_wrap.c:8037: warning: implicit declaration of function ‘SWIG_Python_addvarlink’ src/pbs_wrap.c:8037: error: ‘Swig_var_pbs_errno_get’ undeclared (first use in this function) src/pbs_wrap.c:8037: error: ‘Swig_var_pbs_errno_set’ undeclared (first use in this function) src/pbs_wrap.c:8038: error: ‘Swig_var_pbs_server_get’ undeclared (first use in this function) src/pbs_wrap.c:8038: error: ‘Swig_var_pbs_server_set’ undeclared (first use in this function) src/pbs_wrap.c:8048: error: ‘Swig_var_log_event_mask_get’ undeclared (first use in this function) src/pbs_wrap.c:8048: error: ‘Swig_var_log_event_mask_set’ undeclared (first use in this function) src/pbs_wrap.c:8049: error: ‘Swig_var_chk_file_sec_stderr_get’ undeclared (first use in this function) src/pbs_wrap.c:8049: error: ‘Swig_var_chk_file_sec_stderr_set’ undeclared (first use in this function) src/pbs_wrap.c:8050: error: ‘Swig_var_log_buffer_get’ undeclared (first use in this function) src/pbs_wrap.c:8050: error: ‘Swig_var_log_buffer_set’ undeclared (first use in this function) src/pbs_wrap.c:8073: error: ‘Swig_var_msg_daemonname_get’ undeclared (first use in this function) src/pbs_wrap.c:8073: error: ‘Swig_var_msg_daemonname_set’ undeclared (first use in this function) error: command 'gcc' failed with exit status 1 Traceback (most recent call last): File "scripts/scramble.py", line 50, in <module> egg.scramble() File "/rc/galaxy/galaxy-dist/lib/galaxy/eggs/scramble.py", line 57, in scramble self.run_scramble_script() File "/rc/galaxy/galaxy-dist/lib/galaxy/eggs/scramble.py", line 206, in run_scramble_script raise ScrambleFailure( self, "%s(): Egg build failed for %s %s" % ( sys._getframe().f_code.co_name, self.name, self.version ) ) galaxy.eggs.scramble.ScrambleFailure: run_scramble_script(): Egg build failed for pbs_python 4.1.0
Any tips or tricks for a fix would be much appreciated. If it's the only alternative, we could run jobs through DRMAA, though from what I have been reading plenty of issues arise with that as well.
Thanks,
Frost Mitchell Department of Research Computing Utah State University