Name Description Owner Revision Installation Status package_rpy_1_0_3<http://seachildrenslinuxvm.cloudapp.net:8080/admin_toolshed/manage_repository?id=2f94e8ae9edff68a> Contains a tool dependency definition that downloads and installs version 1.0.3 of the python R interface. devteam 82170c94ca7c Installed, missing both tool and repository dependencies package_r_2_11_0<http://seachildrenslinuxvm.cloudapp.net:8080/admin_toolshed/manage_repository?id=0c5ffef6d88a1e97> Contains a tool dependency definition that downloads and compiles version 2.11.0 of the R interpreter. devteam 5824d2b3bc8b Installed stalled tool shed repository 'package_rpy_1_0_3' Top of Form Tool shed:toolshed.g2.bx.psu.edu Name:package_rpy_1_0_3 Description: Revision:82170c94ca7c Owner:devteam Location:/apps/galaxy/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/package_rpy_1_0_3/82170c94ca7c/package_rpy_1_0_3 Deleted:False Bottom of Form Dependencies of this repository Missing repository dependencies - installation of these additional repositories is required<javascript:void(0);> Installed repository dependencies<javascript:void(0);> Name Revision Owner Installation status package_r_2_11_0<http://seachildrenslinuxvm.cloudapp.net:8080/admin_toolshed/manage_repository?id=0c5ffef6d88a1e97> 5824d2b3bc8b devteam Installed Installed tool dependencies - click the name to browse the dependency installation directory<javascript:void(0);> Name Version Type Installation status R<http://seachildrenslinuxvm.cloudapp.net:8080/admin_toolshed/browse_tool_dependency?id=f09437b8822035f7> 2.11.0 package Installed Missing tool dependencies - click the name to install the missing dependency<javascript:void(0);> Name Version Type Installation status rpy<http://seachildrenslinuxvm.cloudapp.net:8080/admin_toolshed/manage_repository_tool_dependencies?tool_dependency_ids=fb85969571388350> 1.0.3 package Error Tool shed repository 'package_rpy_1_0_3' tool dependencies Name Version Type Status Error R<http://seachildrenslinuxvm.cloudapp.net:8080/admin_toolshed/manage_repository_tool_dependencies?repository_id=2f94e8ae9edff68a&operation=browse&tool_dependency_ids=f09437b8822035f7> 2.11.0 package Installed rpy<http://seachildrenslinuxvm.cloudapp.net:8080/admin_toolshed/manage_repository_tool_dependencies?repository_id=2f94e8ae9edff68a&operation=browse&tool_dependency_ids=fb85969571388350> 1.0.3 package Error In file included from src/rpymodule2130.c:51: src/RPy.h:56:20: error: Python.h: No such file or directory In file included from /usr/lib64/python2.6/site-packages/numpy/core/include/numpy/ndarrayobject.h:68, from /usr/lib64/python2.6/site-packages/numpy/core/include/numpy/arrayobject.h:14, from src/RPy.h:89, from src/rpymodule2130.c:51: /usr/lib64/python2.6/site-packages/numpy/core/include/numpy/npy_common.h:79:2: error: #error Must use Python with unicode enabled. In file included from /usr/lib64/python2.6/site-packages/numpy/core/include/numpy/arrayobject.h:14, from src/RPy.h:89, from src/rpymodule2130.c:51: /usr/lib64/python2.6/site-packages/numpy/core/include/numpy/ndarrayobject.h:227: error: expected '=', ',', ';', 'asm' or '__attribute__' before 'npy_intp' /usr/lib64/python2.6/site-packages/numpy/core/include/numpy/ndarrayobject.h:228: error: expected '=', ',', ';', 'asm' or '__attribute__' before 'npy_uintp' /usr/lib64/python2.6/site-packages/numpy/core/include/numpy/ndarrayobject.h:330: error: expected '=', ',', ';', 'asm' or '__attribute__' before '*' token /usr/lib64/python2.6/site-packages/numpy/core/include/numpy/ndarrayobject.h:331: error: expected ')' before '*' token /usr/lib64/python2.6/site-packages/numpy/core/include/numpy/ndarrayobject.h:333: error: expected declaration specifiers or '...' before 'npy_intp' /usr/lib64/python2.6/site-packages/numpy/core/include/numpy/ndarrayobject.h:333: error: expected declaration specifiers or '...' before 'npy_intp' /usr/lib64/python2.6/site-packages/numpy/core/include/numpy/ndarrayobject.h:334: error: expected declaration specifiers or '...' before 'npy_intp' /usr/lib64/python2.6/site-packages/numpy/core/include/numpy/ndarrayobject.h:344: error: expected declaration specifiers or '...' before 'npy_intp' /usr/lib64/python2.6/site-packages/numpy/core/include/numpy/ndarrayobject.h:344: error: expected declaration specifiers or '...' before 'npy_intp' /usr/lib64/python2.6/site-packages/numpy/core/include/numpy/ndarrayobject.h:346: error: expected declaration specifiers or '...' before 'npy_intp' /usr/lib64/python2.6/site-packages/numpy/core/include/numpy/ndarrayobject.h:346: error: expected declaration specifiers or '...' before 'npy_intp' /usr/lib64/python2.6/site-packages/numpy/core/include/numpy/ndarrayobject.h:347: error: expected declaration specifiers or '...' before 'npy_intp' /usr/lib64/python2.6/site-packages/numpy/core/include/numpy/ndarrayobject.h:349: error: expected declaration specifiers or '...' before 'npy_intp' /usr/lib64/python2.6/site-packages/numpy/core/include/numpy/ndarrayobject.h:359: error: expected declaration specifiers or '...' before 'npy_intp' /usr/lib64/python2.6/site-packages/numpy/core/include/numpy/ndarrayobject.h:361: error: expected declaration specifiers or '...' before 'npy_intp' /usr/lib64/python2.6/site-packages/numpy/core/include/numpy/ndarrayobject.h:362: error: expected declaration specifiers or '...' before 'npy_intp' /usr/lib64/python2.6/site-packages/numpy/core/include/numpy/ndarrayobject.h:362: error: expected declaration specifiers or '...' before 'npy_intp' /usr/lib64/python2.6/site-packages/numpy/core/include/numpy/ndarrayobject.h:364: error: expected declaration specifiers or '...' before 'npy_intp' /usr/lib64/python2.6/site-packages/numpy/core/include/numpy/ndarrayobject.h:368: error: expected declaration specifiers or '...' before 'npy_intp' /usr/lib64/python2.6/site-packages/numpy/core/include/numpy/ndarrayobject.h:370: error: expected declaration specifiers or '...' before 'npy_intp' /usr/lib64/python2.6/site-packages/numpy/core/include/numpy/ndarrayobject.h:371: error: expected declaration specifiers or '...' before 'npy_intp' /usr/lib64/python2.6/site-packages/numpy/core/include/numpy/ndarrayobject.h:372: error: expected declaration specifiers or '...' before 'npy_intp' /usr/lib64/python2.6/site-packages/numpy/core/include/numpy/ndarrayobject.h:373: error: expected declaration specifiers or '...' before 'npy_intp' /usr/lib64/python2.6/site-packages/numpy/core/include/numpy/ndarrayobject.h:373: error: expected declaration specifiers or '...' before 'npy_intp' /usr/lib64/python2.6/site-packages/numpy/core/include/numpy/ndarrayobject.h:374: error: expected declaration specifiers or '...' before 'npy_intp' /usr/lib64/python2.6/site-packages/numpy/core/include/numpy/ndarrayobject.h:374: error: expected declaration specifiers or '...' before 'npy_intp' /usr/lib64/python2.6/site-packages/numpy/core/include/numpy/ndarrayobject.h:378: error: expected specifier-qualifier-list before 'npy_intp' /usr/lib64/python2.6/site-packages/numpy/core/include/numpy/ndarrayobject.h:391: error: expected specifier-qualifier-list before 'PyArray_GetItemFunc' /usr/lib64/python2.6/site-packages/numpy/core/include/numpy/ndarrayobject.h:492: error: expected specifier-qualifier-list before 'PyObject_HEAD' /usr/lib64/python2.6/site-packages/numpy/core/include/numpy/ndarrayobject.h:526: error: expected specifier-qualifier-list before 'PyObject' /usr/lib64/python2.6/site-packages/numpy/core/include/numpy/ndarrayobject.h:536: error: expected specifier-qualifier-list before 'PyObject_HEAD' /usr/lib64/python2.6/site-packages/numpy/core/include/numpy/ndarrayobject.h:561: error: expected specifier-qualifier-list before 'PyObject_HEAD' /usr/lib64/python2.6/site-packages/numpy/core/include/numpy/ndarrayobject.h:569: error: expected specifier-qualifier-list before 'PyObject_HEAD' In file included from /usr/lib64/python2.6/site-packages/numpy/core/include/numpy/arrayobject.h:14, from src/RPy.h:89, from src/rpymodule2130.c:51: /usr/lib64/python2.6/site-packages/numpy/core/include/numpy/ndarrayobject.h:578: error: expected declaration specifiers or '...' before 'PyObject' /usr/lib64/python2.6/site-packages/numpy/core/include/numpy/ndarrayobject.h:728: error: expected declaration specifiers or '...' before 'npy_intp' /usr/lib64/python2.6/site-packages/numpy/core/include/numpy/ndarrayobject.h:731: error: expected specifier-qualifier-list before 'PyObject_HEAD' /usr/lib64/python2.6/site-packages/numpy/core/include/numpy/ndarrayobject.h:883: error: expected specifier-qualifier-list before 'PyObject_HEAD' /usr/lib64/python2.6/site-packages/numpy/core/include/numpy/ndarrayobject.h:937: error: expected specifier-qualifier-list before 'PyObject_HEAD' /usr/lib64/python2.6/site-packages/numpy/core/include/numpy/ndarrayobject.h:980: error: expected specifier-qualifier-list before 'PyObject_HEAD' In file included from /usr/lib64/python2.6/site-packages/numpy/core/include/numpy/ndarrayobject.h:1036, from /usr/lib64/python2.6/site-packages/numpy/core/include/numpy/arrayobject.h:14, from src/RPy.h:89, from src/rpymodule2130.c:51: /usr/lib64/python2.6/site-packages/numpy/core/include/numpy/_neighborhood_iterator_imp.h: In function '_PyArrayNeighborhoodIter_IncrCoord': /usr/lib64/python2.6/site-packages/numpy/core/include/numpy/_neighborhood_iterator_imp.h:40: error: 'npy_intp' undeclared (first use in this function) /usr/lib64/python2.6/site-packages/numpy/core/include/numpy/_neighborhood_iterator_imp.h:40: error: (Each undeclared identifier is reported only once /usr/lib64/python2.6/site-packages/numpy/core/include/numpy/_neighborhood_iterator_imp.h:40: error: for each function it appears in.) /usr/lib64/python2.6/site-packages/numpy/core/include/numpy/_neighborhood_iterator_imp.h:40: error: expected ';' before 'i' /usr/lib64/python2.6/site-packages/numpy/core/include/numpy/_neighborhood_iterator_imp.h:42: error: 'i' undeclared (first use in this function) /usr/lib64/python2.6/site-packages/numpy/core/include/numpy/_neighborhood_iterator_imp.h:42: error: 'PyArrayNeighborhoodIterObject' has no member named 'nd' /usr/lib64/python2.6/site-packages/numpy/core/include/numpy/_neighborhood_iterator_imp.h:43: error: 'wb' undeclared (first use in this function) /usr/lib64/python2.6/site-packages/numpy/core/include/numpy/_neighborhood_iterator_imp.h:43: error: 'PyArrayNeighborhoodIterObject' has no member named 'coordinates' /usr/lib64/python2.6/site-packages/numpy/core/include/numpy/_neighborhood_iterator_imp.h:43: error: 'PyArrayNeighborhoodIterObject' has no member named 'bounds' /usr/lib64/python2.6/site-packages/numpy/core/include/numpy/_neighborhood_iterator_imp.h:43: error: 'PyArrayNeighborhoodIterObject' has no member named 'coordinates' /usr/lib64/python2.6/site-packages/numpy/core/include/numpy/_neighborhood_iterator_imp.h:43: error: 'PyArrayNeighborhoodIterObject' has no member named 'coordinates' /usr/lib64/python2.6/site-packages/numpy/core/include/numpy/_neighborhood_iterator_imp.h:43: error: 'PyArrayNeighborhoodIterObject' has no member named 'bounds' /usr/lib64/python2.6/site-packages/numpy/core/include/numpy/_neighborhood_iterator_imp.h: In function '_PyArrayNeighborhoodIter_IncrCoord2D': /usr/lib64/python2.6/site-packages/numpy/core/include/numpy/_neighborhood_iterator_imp.h:55: error: 'npy_intp' undeclared (first use in this function) /usr/lib64/python2.6/site-packages/numpy/core/include/numpy/_neighborhood_iterator_imp.h:55: error: expected ';' before 'wb' /usr/lib64/python2.6/site-packages/numpy/core/include/numpy/_neighborhood_iterator_imp.h:57: error: 'wb' undeclared (first use in this function) /usr/lib64/python2.6/site-packages/numpy/core/include/numpy/_neighborhood_iterator_imp.h:57: error: 'PyArrayNeighborhoodIterObject' has no member named 'coordinates' /usr/lib64/python2.6/site-packages/numpy/core/include/numpy/_neighborhood_iterator_imp.h:57: error: 'PyArrayNeighborhoodIterObject' has no member named 'bounds' /usr/lib64/python2.6/site-packages/numpy/core/include/numpy/_neighborhood_iterator_imp.h:57: error: 'PyArrayNeighborhoodIterObject' has no member named 'coordinates' /usr/lib64/python2.6/site-packages/numpy/core/include/numpy/_neighborhood_iterator_imp.h:57: error: 'PyArrayNeighborhoodIterObject' has no member named 'coordinates' /usr/lib64/python2.6/site-packages/numpy/core/include/numpy/_neighborhood_iterator_imp.h:57: error: 'PyArrayNeighborhoodIterObject' has no member named 'bounds' /usr/lib64/python2.6/site-packages/numpy/core/include/numpy/_neighborhood_iterator_imp.h:58: error: 'PyArrayNeighborhoodIterObject' has no member named 'coordinates' /usr/lib64/python2.6/site-packages/numpy/core/include/numpy/_neighborhood_iterator_imp.h:58: error: 'PyArrayNeighborhoodIterObject' has no member named 'bounds' /usr/lib64/python2.6/site-packages/numpy/core/include/numpy/_neighborhood_iterator_imp.h:58: error: 'PyArrayNeighborhoodIterObject' has no member named 'coordinates' /usr/lib64/python2.6/site-packages/numpy/core/include/numpy/_neighborhood_iterator_imp.h:58: error: 'PyArrayNeighborhoodIterObject' has no member named 'coordinates' /usr/lib64/python2.6/site-packages/numpy/core/include/numpy/_neighborhood_iterator_imp.h:58: error: 'PyArrayNeighborhoodIterObject' has no member named 'bounds' /usr/lib64/python2.6/site-packages/numpy/core/include/numpy/_neighborhood_iterator_imp.h: In function 'PyArrayNeighborhoodIter_Next': /usr/lib64/python2.6/site-packages/numpy/core/include/numpy/_neighborhood_iterator_imp.h:71: error: 'PyArrayNeighborhoodIterObject' has no member named 'dataptr' /usr/lib64/python2.6/site-packages/numpy/core/include/numpy/_neighborhood_iterator_imp.h:71: error: 'PyArrayNeighborhoodIterObject' has no member named 'translate' /usr/lib64/python2.6/site-packages/numpy/core/include/numpy/_neighborhood_iterator_imp.h:71: error: 'PyArrayNeighborhoodIterObject' has no member named 'coordinates' /usr/lib64/python2.6/site-packages/numpy/core/include/numpy/_neighborhood_iterator_imp.h: In function 'PyArrayNeighborhoodIter_Reset': /usr/lib64/python2.6/site-packages/numpy/core/include/numpy/_neighborhood_iterator_imp.h:82: error: 'npy_intp' undeclared (first use in this function) /usr/lib64/python2.6/site-packages/numpy/core/include/numpy/_neighborhood_iterator_imp.h:82: error: expected ';' before 'i' /usr/lib64/python2.6/site-packages/numpy/core/include/numpy/_neighborhood_iterator_imp.h:84: error: 'i' undeclared (first use in this function) /usr/lib64/python2.6/site-packages/numpy/core/include/numpy/_neighborhood_iterator_imp.h:84: error: 'PyArrayNeighborhoodIterObject' has no member named 'nd' /usr/lib64/python2.6/site-packages/numpy/core/include/numpy/_neighborhood_iterator_imp.h:85: error: 'PyArrayNeighborhoodIterObject' has no member named 'coordinates' /usr/lib64/python2.6/site-packages/numpy/core/include/numpy/_neighborhood_iterator_imp.h:85: error: 'PyArrayNeighborhoodIterObject' has no member named 'bounds' /usr/lib64/python2.6/site-packages/numpy/core/include/numpy/_neighborhood_iterator_imp.h:87: error: 'PyArrayNeighborhoodIterObject' has no member named 'dataptr' /usr/lib64/python2.6/site-packages/numpy/core/include/numpy/_neighborhood_iterator_imp.h:87: error: 'PyArrayNeighborhoodIterObject' has no member named 'translate' /usr/lib64/python2.6/site-packages/numpy/core/include/numpy/_neighborhood_iterator_imp.h:87: error: 'PyArrayNeighborhoodIterObject' has no member named 'coordinates' In file included from /usr/lib64/python2.6/site-packages/numpy/core/include/numpy/arrayobject.h:14, from src/RPy.h:89, from src/rpymodule2130.c:51: /usr/lib64/python2.6/site-packages/numpy/core/include/numpy/ndarrayobject.h: At top level: /usr/lib64/python2.6/site-packages/numpy/core/include/numpy/ndarrayobject.h:1223: error: expected specifier-qualifier-list before 'npy_intp' In file included from /usr/lib64/python2.6/site-packages/numpy/core/include/numpy/ndarrayobject.h:1238, from /usr/lib64/python2.6/site-packages/numpy/core/include/numpy/arrayobject.h:14, from src/RPy.h:89, from src/rpymodule2130.c:51: /usr/lib64/python2.6/site-packages/numpy/core/include/numpy/__multiarray_api.h: In function '_import_array': /usr/lib64/python2.6/site-packages/numpy/core/include/numpy/__multiarray_api.h:1190: error: 'PyObject' undeclared (first use in this function) /usr/lib64/python2.6/site-packages/numpy/core/include/numpy/__multiarray_api.h:1190: error: 'numpy' undeclared (first use in this function) /usr/lib64/python2.6/site-packages/numpy/core/include/numpy/__multiarray_api.h:1190: warning: implicit declaration of function 'PyImport_ImportModule' /usr/lib64/python2.6/site-packages/numpy/core/include/numpy/__multiarray_api.h:1191: error: 'c_api' undeclared (first use in this function) /usr/lib64/python2.6/site-packages/numpy/core/include/numpy/__multiarray_api.h:1193: warning: implicit declaration of function 'PyObject_GetAttrString' /usr/lib64/python2.6/site-packages/numpy/core/include/numpy/__multiarray_api.h:1194: warning: implicit declaration of function 'Py_DECREF' /usr/lib64/python2.6/site-packages/numpy/core/include/numpy/__multiarray_api.h:1195: warning: implicit declaration of function 'PyCObject_Check' /usr/lib64/python2.6/site-packages/numpy/core/include/numpy/__multiarray_api.h:1196: warning: implicit declaration of function 'PyCObject_AsVoidPtr' /usr/lib64/python2.6/site-packages/numpy/core/include/numpy/__multiarray_api.h:1203: warning: implicit declaration of function 'PyErr_Format' /usr/lib64/python2.6/site-packages/numpy/core/include/numpy/__multiarray_api.h:1203: error: 'PyExc_RuntimeError' undeclared (first use in this function) In file included from src/rpymodule2130.c:51: src/RPy.h: At top level: src/RPy.h:91: error: expected '=', ',', ';', 'asm' or '__attribute__' before 'n_intp' In file included from src/RPy.h:105, from src/rpymodule2130.c:51: src/robjobject.h:46: error: expected specifier-qualifier-list before 'PyObject_HEAD' src/robjobject.h:57: warning: return type defaults to 'int' src/robjobject.h: In function 'DL_IMPORT': src/robjobject.h:57: error: expected declaration specifiers before 'Robj_Type' In file included from src/rpymodule2130.c:51: src/RPy.h:112: error: expected ')' before '*' token src/RPy.h:113: error: expected declaration specifiers before 'PyObject' src/RPy.h:114: error: expected declaration specifiers before 'PyObject' src/RPy.h:115: error: expected declaration specifiers before 'PyObject' src/RPy.h:131: error: expected '=', ',', ';', 'asm' or '__attribute__' before '*' token src/RPy.h:132: error: expected '=', ',', ';', 'asm' or '__attribute__' before '*' token src/RPy.h:133: error: expected '=', ',', ';', 'asm' or '__attribute__' before '*' token src/RPy.h:138: error: storage class specified for parameter 'Rf_initEmbeddedR' src/RPy.h:139: error: storage class specified for parameter 'init_io_routines' src/RPy.h:145: error: storage class specified for parameter 'R_Outputfile' src/RPy.h:153: error: storage class specified for parameter 'ptr_R_WriteConsole' src/RPy.h:154: error: storage class specified for parameter 'ptr_R_ReadConsole' src/RPy.h:155: error: storage class specified for parameter 'ptr_R_ShowFiles' src/RPy.h:172: error: expected declaration specifiers before 'PyObject' src/RPy.h:173: error: expected declaration specifiers before 'PyObject' src/RPy.h:174: error: expected declaration specifiers before 'PyObject' src/RPy.h:175: error: expected declaration specifiers before 'PyObject' src/RPy.h:176: error: expected declaration specifiers before 'PyObject' src/RPy.h:177: error: expected declaration specifiers before 'PyObject' src/RPy.h:183: error: expected '=', ',', ';', 'asm' or '__attribute__' before 'python_sigint' src/RPy.h:186: error: storage class specified for parameter 'jump_now' src/RPy.h:189: error: expected '=', ',', ';', 'asm' or '__attribute__' before '*' token src/RPy.h:192: error: storage class specified for parameter 'R_interact' src/RPy.h:195: error: expected '=', ',', ';', 'asm' or '__attribute__' before '*' token src/RPy.h:197: error: expected '=', ',', ';', 'asm' or '__attribute__' before '*' token src/RPy.h:205: error: expected declaration specifiers or '...' before 'PyObject' src/RPy.h:205: error: storage class specified for parameter 'to_Pyobj_proc' src/RPy.h:206: error: expected declaration specifiers or '...' before 'PyObject' src/RPy.h:206: error: storage class specified for parameter 'to_Pyobj_class' src/RPy.h:207: error: expected declaration specifiers or '...' before 'PyObject' src/RPy.h:207: error: storage class specified for parameter 'to_Pyobj_basic' src/RPy.h:208: error: expected declaration specifiers or '...' before 'PyObject' src/RPy.h:208: error: storage class specified for parameter 'to_Pyobj_vector' src/rpymodule2130.c:63: error: storage class specified for parameter 'use_numeric' src/rpymodule2130.c:63: error: parameter 'use_numeric' is initialized src/rpymodule2130.c:67: error: expected declaration specifiers before 'DL_EXPORT' src/rpymodule2130.c:68: error: expected '=', ',', ';', 'asm' or '__attribute__' before '*' token src/rpymodule2130.c:70: error: expected '=', ',', ';', 'asm' or '__attribute__' before '*' token src/rpymodule2130.c:77: error: storage class specified for parameter 'get_item' src/rpymodule2130.c:78: error: storage class specified for parameter 'set_item' src/rpymodule2130.c:79: error: storage class specified for parameter 'length' src/rpymodule2130.c:80: error: storage class specified for parameter 'aperm' src/rpymodule2130.c:81: error: expected '=', ',', ';', 'asm' or '__attribute__' before '*' token src/rpymodule2130.c:82: error: expected '=', ',', ';', 'asm' or '__attribute__' before '*' token src/rpymodule2130.c:83: error: storage class specified for parameter 'default_mode' src/rpymodule2130.c:84: error: expected '=', ',', ';', 'asm' or '__attribute__' before '*' token src/rpymodule2130.c:85: error: expected declaration specifiers before 'PyObject' src/rpymodule2130.c:86: error: expected declaration specifiers before 'PyObject' src/rpymodule2130.c:87: error: expected declaration specifiers before 'PyObject' src/rpymodule2130.c:89: error: storage class specified for parameter 'RHOME' src/rpymodule2130.c:90: error: storage class specified for parameter 'RVERSION' src/rpymodule2130.c:91: error: storage class specified for parameter 'RVER' src/rpymodule2130.c:92: error: storage class specified for parameter 'RUSER' src/rpymodule2130.c:93: error: parameter 'defaultargv' is initialized src/rpymodule2130.c:93: warning: initialization from incompatible pointer type src/rpymodule2130.c:93: warning: excess elements in scalar initializer src/rpymodule2130.c:93: warning: (near initialization for 'defaultargv') src/rpymodule2130.c:93: warning: excess elements in scalar initializer src/rpymodule2130.c:93: warning: (near initialization for 'defaultargv') src/rpymodule2130.c:94: error: parameter 'defaultargc' is initialized src/rpymodule2130.c:97: error: expected declaration specifiers before 'PyInterpreterState' src/rpymodule2130.c:100: error: redefinition of parameter 'R_interact' src/RPy.h:192: note: previous definition of 'R_interact' was here src/rpymodule2130.c:103: error: expected declaration specifiers before 'PyObject' src/rpymodule2130.c:104: error: expected declaration specifiers before 'PyObject' src/rpymodule2130.c:108: error: expected '=', ',', ';', 'asm' or '__attribute__' before '*' token src/rpymodule2130.c:113: error: storage class specified for parameter 'R_References' src/rpymodule2130.c:117: error: expected '=', ',', ';', 'asm' or '__attribute__' before '{' token src/rpymodule2130.c:131: error: expected '=', ',', ';', 'asm' or '__attribute__' before '{' token src/rpymodule2130.c:141: error: expected '=', ',', ';', 'asm' or '__attribute__' before '{' token src/rpymodule2130.c:160: error: expected '=', ',', ';', 'asm' or '__attribute__' before '*' token src/rpymodule2130.c:183: error: expected ')' before '*' token src/rpymodule2130.c:207: error: expected ')' before '*' token src/rpymodule2130.c:292: error: expected ')' before '*' token src/rpymodule2130.c:330: error: expected ')' before '*' token src/rpymodule2130.c:510: error: expected ')' before '*' token src/rpymodule2130.c:626: error: expected '=', ',', ';', 'asm' or '__attribute__' before '*' token src/rpymodule2130.c:652: error: expected '=', ',', ';', 'asm' or '__attribute__' before '*' token src/rpymodule2130.c:686: error: expected '=', ',', ';', 'asm' or '__attribute__' before '*' token src/rpymodule2130.c:710: error: expected '=', ',', ';', 'asm' or '__attribute__' before '*' token src/rpymodule2130.c:751: error: expected declaration specifiers or '...' before 'PyObject' src/rpymodule2130.c:752: error: expected '=', ',', ';', 'asm' or '__attribute__' before '{' token src/rpymodule2130.c:774: error: expected declaration specifiers or '...' before 'PyObject' src/rpymodule2130.c:775: error: expected '=', ',', ';', 'asm' or '__attribute__' before '{' token src/rpymodule2130.c:900: error: expected declaration specifiers before 'PyObject' src/rpymodule2130.c:939: error: expected declaration specifiers or '...' before 'PyObject' src/rpymodule2130.c:940: error: expected '=', ',', ';', 'asm' or '__attribute__' before '{' token src/rpymodule2130.c:977: error: expected declaration specifiers or '...' before 'PyObject' src/rpymodule2130.c:978: error: expected '=', ',', ';', 'asm' or '__attribute__' before '{' token src/rpymodule2130.c:999: error: expected declaration specifiers or '...' before 'PyObject' src/rpymodule2130.c:1000: error: expected '=', ',', ';', 'asm' or '__attribute__' before '{' token src/rpymodule2130.c:1015: error: expected declaration specifiers before 'PyObject' src/rpymodule2130.c:1048: error: expected declaration specifiers or '...' before 'PyObject' src/rpymodule2130.c:1049: error: expected '=', ',', ';', 'asm' or '__attribute__' before '{' token src/rpymodule2130.c:1067: error: expected '=', ',', ';', 'asm' or '__attribute__' before '{' token src/rpymodule2130.c:1092: error: expected declaration specifiers or '...' before 'PyObject' src/rpymodule2130.c:1093: error: expected '=', ',', ';', 'asm' or '__attribute__' before '{' token src/rpymodule2130.c:1139: error: expected '=', ',', ';', 'asm' or '__attribute__' before '*' token src/rpymodule2130.c:1191: error: expected declaration specifiers or '...' before 'PyObject' src/rpymodule2130.c:1192: error: expected '=', ',', ';', 'asm' or '__attribute__' before '{' token src/rpymodule2130.c:1276: error: expected '=', ',', ';', 'asm' or '__attribute__' before '*' token src/rpymodule2130.c:1342: error: expected '=', ',', ';', 'asm' or '__attribute__' before '*' token src/rpymodule2130.c:1369: error: expected '=', ',', ';', 'asm' or '__attribute__' before '*' token src/rpymodule2130.c:1392: error: expected '=', ',', ';', 'asm' or '__attribute__' before 'Robj_methods' src/rpymodule2130.c:1398: error: expected declaration specifiers before ';' token src/rpymodule2130.c:1404: error: expected ')' before '*' token src/rpymodule2130.c:1423: error: expected ')' before '*' token src/rpymodule2130.c:1449: error: expected '=', ',', ';', 'asm' or '__attribute__' before '*' token src/rpymodule2130.c:1490: error: expected '=', ',', ';', 'asm' or '__attribute__' before '*' token src/rpymodule2130.c:1564: error: expected '=', ',', ';', 'asm' or '__attribute__' before 'Robj_as_sequence' src/rpymodule2130.c:1575: error: expected declaration specifiers before ';' token src/rpymodule2130.c:1589: error: expected declaration specifiers before 'PyTypeObject' src/rpymodule2130.c:1656: error: expected declaration specifiers before ';' token src/rpymodule2130.c:1663: error: expected '=', ',', ';', 'asm' or '__attribute__' before '*' token src/rpymodule2130.c:1682: error: expected '=', ',', ';', 'asm' or '__attribute__' before '*' token src/rpymodule2130.c:1700: error: expected '=', ',', ';', 'asm' or '__attribute__' before '*' token src/rpymodule2130.c:1709: error: expected '=', ',', ';', 'asm' or '__attribute__' before '*' token src/rpymodule2130.c:1739: error: expected '=', ',', ';', 'asm' or '__attribute__' before '{' token src/rpymodule2130.c:1754: error: expected '=', ',', ';', 'asm' or '__attribute__' before '{' token src/rpymodule2130.c:1774: error: expected '=', ',', ';', 'asm' or '__attribute__' before '{' token src/rpymodule2130.c:1807: error: expected '=', ',', ';', 'asm' or '__attribute__' before '*' token src/rpymodule2130.c:1818: error: expected '=', ',', ';', 'asm' or '__attribute__' before '{' token src/rpymodule2130.c:1834: error: expected '=', ',', ';', 'asm' or '__attribute__' before '*' token src/rpymodule2130.c:1863: error: expected '=', ',', ';', 'asm' or '__attribute__' before 'rpy_methods' src/rpymodule2130.c:1877: error: expected declaration specifiers before ';' token src/rpymodule2130.c:1972: error: expected declaration specifiers before 'DL_EXPORT' src/rpymodule2130.c:113: error: declaration for parameter 'R_References' but no such parameter src/rpymodule2130.c:100: error: declaration for parameter 'R_interact' but no such parameter src/rpymodule2130.c:94: error: declaration for parameter 'defaultargc' but no such parameter src/rpymodule2130.c:93: error: declaration for parameter 'defaultargv' but no such parameter src/rpymodule2130.c:92: error: declaration for parameter 'RUSER' but no such parameter src/rpymodule2130.c:91: error: declaration for parameter 'RVER' but no such parameter src/rpymodule2130.c:90: error: declaration for parameter 'RVERSION' but no such parameter src/rpymodule2130.c:89: error: declaration for parameter 'RHOME' but no such parameter src/rpymodule2130.c:83: error: declaration for parameter 'default_mode' but no such parameter src/rpymodule2130.c:80: error: declaration for parameter 'aperm' but no such parameter src/rpymodule2130.c:79: error: declaration for parameter 'length' but no such parameter src/rpymodule2130.c:78: error: declaration for parameter 'set_item' but no such parameter src/rpymodule2130.c:77: error: declaration for parameter 'get_item' but no such parameter src/rpymodule2130.c:63: error: declaration for parameter 'use_numeric' but no such parameter src/RPy.h:208: error: declaration for parameter 'to_Pyobj_vector' but no such parameter src/RPy.h:207: error: declaration for parameter 'to_Pyobj_basic' but no such parameter src/RPy.h:206: error: declaration for parameter 'to_Pyobj_class' but no such parameter src/RPy.h:205: error: declaration for parameter 'to_Pyobj_proc' but no such parameter src/RPy.h:201: error: declaration for parameter 'start_events' but no such parameter src/RPy.h:200: error: declaration for parameter 'stop_events' but no such parameter src/RPy.h:192: error: declaration for parameter 'R_interact' but no such parameter src/RPy.h:186: error: declaration for parameter 'jump_now' but no such parameter src/RPy.h:180: error: declaration for parameter 'interrupt_R' but no such parameter src/RPy.h:155: error: declaration for parameter 'ptr_R_ShowFiles' but no such parameter src/RPy.h:154: error: declaration for parameter 'ptr_R_ReadConsole' but no such parameter src/RPy.h:153: error: declaration for parameter 'ptr_R_WriteConsole' but no such parameter src/RPy.h:145: error: declaration for parameter 'R_Outputfile' but no such parameter src/RPy.h:139: error: declaration for parameter 'init_io_routines' but no such parameter src/RPy.h:138: error: declaration for parameter 'Rf_initEmbeddedR' but no such parameter src/RPy.h:135: error: declaration for parameter 'get_last_error_msg' but no such parameter src/RPy.h:128: error: declaration for parameter 'get_fun_from_name' but no such parameter src/RPy.h:127: error: declaration for parameter 'do_eval_fun' but no such parameter src/RPy.h:126: error: declaration for parameter 'do_eval_expr' but no such parameter src/setenv.h:46: error: declaration for parameter 'setenv' but no such parameter src/robjobject.h:62: error: declaration for parameter 'Robj_new' but no such parameter src/rpymodule2130.c:2104: error: expected '{' at end of input error: command 'gcc' failed with exit status 1 Top of Form Check each tool dependency that you want to uninstall and click Uninstall. Select/unselect all tool dependencies R version 2.11.0 rpy version 1.0.3 Bottom of Form From: Greg Von Kuster [mailto:greg@bx.psu.edu] Sent: Tuesday, April 08, 2014 1:27 PM To: Hayes, Curt Cc: 'galaxy-dev@lists.bx.psu.edu' Subject: Re: [galaxy-dev] Package/Module RPY Hello Curt, I believe that version 1.0.3 of the rpy package should be installing successfully from the main tool shed if you have a repository that contains a tool that defines a dependency to the rpy repository owned by devteam at http://toolshed.g2.bx.psu.edu/view/devteam/package_rpy_1_0_3 Here is the last test run for the tool shed's install and test framework for that repository. I believe tis should install correctly using the dist repository, but if you're seeing problems, let us know. Also, the next release is coming soon ( tentatively a week or so from now ).. Test runs 2014-04-07 17:25:49 Automated test environment Successful installations Repository dependencies - installation of these additional repositories is required Tool shed Name Owner Changeset revision toolshed.g2.bx.psu.edu<http://bx.psu.edu> package_r_2_11_0 devteam 5824d2b3bc8b Tool dependencies Type Name Version R package 2.11.0 Installation directory /ToolDepsMain/R/2.11.0/devteam/package_rpy_1_0_3/82170c94ca7c Type Name Version rpy package 1.0.3 Installation directory /ToolDepsMain/rpy/1.0.3/devteam/package_rpy_1_0_3/82170c94ca7c On Apr 8, 2014, at 3:28 PM, "Hayes, Curt" <curt.hayes@seattlechildrens.org<mailto:curt.hayes@seattlechildrens.org>> wrote: Hi there all, Does anyone have RPY working? I install via toolshed and the folder is empty, and shows missing dependencies. I have searched previous posts, nothing since 2010. I have a local install (production config - postgres, etc - on CENTOS 6.5). I posted last week and it fell off the list.
From Galaxy User interface: Dataset generation errors Dataset 81: Build base quality distribution on data 9
Tool execution generated the following error message: Traceback (most recent call last): File "/apps/galaxy/galaxy-dist/tools/metag_tools/short_reads_figure_score.py", line 12, in <module> from rpy import * ImportError: No module named rpy I have attempted to download/install the scripts but they fail with multiple errors (most posts out there have a bad URL) - http://getgalaxyp.org/install.html says use: curlhttp://rpy.svn.sourceforge.net/viewvc/rpy/trunk/rpy/?view=tar > rpy.tar.gz if you view that it redirects you to another URL. Via shell: R is installed: R version 2.13.0 (2011-04-13) Can someone provide me some help please to get it working via Galaxy? I understand it works in Central.
From Toolshed: Name
Version Type Installation status rpy<http://seachildrenslinuxvm.cloudapp.net:8080/admin_toolshed/manage_repository_tool_dependencies?tool_dependency_ids=fb85969571388350> 1.0.3 package Error Toolshed Error: In file included from src/rpymodule2110.c:51: src/RPy.h:56:20: error: Python.h: No such file or directory In file included from /usr/lib64/python2.6/site-packages/numpy/core/include/numpy/ndarrayobject.h:68, from /usr/lib64/python2.6/site-packages/numpy/core/include/numpy/arrayobject.h:14, from src/RPy.h:89, from src/rpymodule2110.c:51: /usr/lib64/python2.6/site-packages/numpy/core/include/numpy/npy_common.h:79:2: error: #error Must use Python with unicode enabled. <truncated> Thanks, Curt CONFIDENTIALITY NOTICE: This e-mail message, including any attachments, is for the sole use of the intended recipient(s) and may contain confidential and privileged information protected by law. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, please contact the sender by reply e-mail and destroy all copies of the original message. ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ CONFIDENTIALITY NOTICE: This e-mail message, including any attachments, is for the sole use of the intended recipient(s) and may contain confidential and privileged information protected by law. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, please contact the sender by reply e-mail and destroy all copies of the original message.