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Name |
Description |
Owner |
Revision |
Installation Status |
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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 |
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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'
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
Dependencies of this repository
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Name |
Revision |
Owner |
Installation status |
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5824d2b3bc8b |
devteam |
Installed |
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Name |
Version |
Type |
Installation status |
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2.11.0 |
package |
Installed |
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Name |
Version |
Type |
Installation status |
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1.0.3 |
package |
Error |
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Tool shed repository 'package_rpy_1_0_3' tool dependencies
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Name |
Version |
Type |
Status |
Error |
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2.11.0 |
package |
Installed |
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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 |
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
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 )..
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Test runs |
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2014-04-07 17:25:49 |
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Automated test environment
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Successful installations |
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Repository dependencies - installation of these additional repositories is required
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On Apr 8, 2014, at 3:28 PM, "Hayes, Curt" <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 |
|
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
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