Hi Ryan,
it seems like your compiler can't find the R header files. I don't know on
which linux distro your're running Galaxy and if you installed with a
package manager it or compiled it, but you should try to install R headers
(the development packages). For example in Ubuntu an apt-get install
r-base-dev should fix the problem.
Hope it helps.
---
Marco
On 22 June 2011 01:43, Ryan Davis <rrda...@ucdavis.edu> wrote:
>
> Hi all,
>
> I'm currently working on setting up a Galaxy on our local server. I'm going
> through the tool dependencies list and install everything on it. I
> installed the latest R version (2.12.2) and now I'm trying to install rpy
> 1.0.3.
>
> I have installed R with --enable-R-shlib and also done this step:
>
> export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/lib64/R/lib/
>
> However I get the following error with the install of rpy 1.0.3.
>
> Thanks for the help,
>
> Ryan
>
> [cgtepper@hobbes rpy-1.0.3]$ python setup.py install
> RHOMES= []
> DEBUG= True
> Setting RHOMES to ['/usr/lib64/R']
> ### Using R verion 2.12.2 installed at /usr/lib64/R ###
> RHOME= /usr/lib64/R
> copying src/rpymodule.c -> src/rpymodule2122.c
> copying src/R_eval.c -> src/R_eval2122.c
> copying src/io.c -> src/io2122.c
> running install
> running build
> running build_py
> running build_ext
> building '_rpy2122' extension
> gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O3 -Wall
> -Wstrict-prototypes -fPIC -DRPY_SHNAME=_rpy2122 -DINIT_RPY=init_rpy2122
> -UPRE_2_2 -UWITH_NUMERIC -I/usr/lib64/R/include -Isrc
> -I/usr/share/R/include -I/usr/local/include/python2.6 -c
> src/rpymodule2122.c -o build/temp.linux-x86_64-2.6/src/rpymodule2122.o
> -shared
> src/rpymodule2122.c:42:23: error: Rversion.h: No such file or directory
> src/rpymodule2122.c:43:28: error: missing binary operator before token "("
> In file included from src/rpymodule2122.c:51:
> src/RPy.h:51:15: error: R.h: No such file or directory
> src/RPy.h:52:22: error: Rdefines.h: No such file or directory
> src/RPy.h:53:24: error: Rinternals.h: No such file or directory
> src/RPy.h:57:28: error: R_ext/Rdynload.h: No such file or directory
> src/RPy.h:58:29: error: R_ext/eventloop.h: No such file or directory
> In file included from src/RPy.h:71,
> from src/rpymodule2122.c:51:
> src/rpy_Rinterface.h:51:27: error: R_ext/Boolean.h: No such file or
> directory
> In file included from src/rpy_Rinterface.h:61,
> from src/RPy.h:71,
> from src/rpymodule2122.c:51:
> src/rpy_Startup.h:70: error: expected specifier-qualifier-list before
> ‘Rboolean’
> In file included from src/RPy.h:71,
> from src/rpymodule2122.c:51:
> src/rpy_Rinterface.h:70: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or
> ‘__attribute__’ before ‘R_Interactive’
> src/rpy_Rinterface.h:71: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or
> ‘__attribute__’ before ‘R_Quiet’
> src/rpy_Rinterface.h:72: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or
> ‘__attribute__’ before ‘R_Slave’
> src/rpy_Rinterface.h:73: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or
> ‘__attribute__’ before ‘R_Verbose’
> src/rpy_Rinterface.h:76: error: expected declaration specifiers or ‘...’
> before ‘Rboolean’
> src/rpy_Rinterface.h:85: warning: function declaration isn’t a prototype
> src/rpy_Rinterface.h:96: warning: function declaration isn’t a prototype
> src/rpy_Rinterface.h:101: warning: function declaration isn’t a prototype
> src/rpy_Rinterface.h:102: warning: function declaration isn’t a prototype
> src/rpy_Rinterface.h:103: warning: function declaration isn’t a prototype
> src/rpy_Rinterface.h:112: warning: parameter names (without types) in
> function declaration
> In file included from src/rpymodule2122.c:51:
> src/RPy.h:77:51: error: Rdevices.h: No such file or directory
> In file included from src/RPy.h:108,
> from src/rpymodule2122.c:51:
> src/robjobject.h:47: error: expected specifier-qualifier-list before ‘SEXP’
> src/robjobject.h:62: error: expected ‘)’ before ‘int’
> In file included from src/rpymodule2122.c:51:
> src/RPy.h:115: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’
> before ‘to_Robj’
> src/RPy.h:116: warning: parameter names (without types) in function
> declaration
> src/RPy.h:117: warning: parameter names (without types) in function
> declaration
> src/RPy.h:118: error: expected ‘)’ before ‘int’
> src/RPy.h:129: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’
> before ‘do_eval_expr’
> src/RPy.h:130: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’
> before ‘do_eval_fun’
> src/RPy.h:131: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’
> before ‘get_fun_from_name’
> src/RPy.h:208: error: expected ‘)’ before ‘robj’
> src/RPy.h:209: error: expected ‘)’ before ‘robj’
> src/RPy.h:210: error: expected ‘)’ before ‘robj’
> src/RPy.h:211: error: expected ‘)’ before ‘robj’
> src/rpymodule2122.c:77: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or
> ‘__attribute__’ before ‘get_item’
> src/rpymodule2122.c:78: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or
> ‘__attribute__’ before ‘set_item’
> src/rpymodule2122.c:79: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or
> ‘__attribute__’ before ‘length’
> src/rpymodule2122.c:80: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or
> ‘__attribute__’ before ‘aperm’
> src/rpymodule2122.c:113: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or
> ‘__attribute__’ before ‘R_References’
> src/rpymodule2122.c:116: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or
> ‘__attribute__’ before ‘RecursiveRelease’
> src/rpymodule2122.c: In function ‘Robj_dealloc’:
> src/rpymodule2122.c:133: error: ‘R_References’ undeclared (first use in
> this function)
> src/rpymodule2122.c:133: error: (Each undeclared identifier is reported
> only once
> src/rpymodule2122.c:133: error: for each function it appears in.)
> src/rpymodule2122.c:133: warning: implicit declaration of function
> ‘RecursiveRelease’
> src/rpymodule2122.c:133: error: ‘RobjObject’ has no member named ‘R_obj’
> src/rpymodule2122.c:134: warning: implicit declaration of function
> ‘SET_SYMVALUE’
> src/rpymodule2122.c:134: warning: implicit declaration of function
> ‘install’
> src/rpymodule2122.c: At top level:
> src/rpymodule2122.c:140: error: expected ‘)’ before ‘robj’
> src/rpymodule2122.c:207: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or
> ‘__attribute__’ before ‘seq_to_R’
> src/rpymodule2122.c:292: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or
> ‘__attribute__’ before ‘dict_to_R’
> src/rpymodule2122.c:510: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or
> ‘__attribute__’ before ‘to_Robj’
> src/rpymodule2122.c:627: error: expected declaration specifiers or ‘...’
> before ‘SEXP’
> src/rpymodule2122.c: In function ‘to_PyDict’:
> src/rpymodule2122.c:641: warning: implicit declaration of function ‘CHAR’
> src/rpymodule2122.c:641: warning: implicit declaration of function
> ‘STRING_ELT’
> src/rpymodule2122.c:641: error: ‘names’ undeclared (first use in this
> function)
> src/rpymodule2122.c:641: warning: assignment makes pointer from integer
> without a cast
> src/rpymodule2122.c: At top level:
> src/rpymodule2122.c:751: error: expected ‘)’ before ‘robj’
> src/rpymodule2122.c:774: error: expected ‘)’ before ‘robj’
> src/rpymodule2122.c:901: error: expected ‘)’ before ‘robj’
> src/rpymodule2122.c:939: error: expected ‘)’ before ‘robj’
> src/rpymodule2122.c:977: error: expected ‘)’ before ‘robj’
> src/rpymodule2122.c:999: error: expected ‘)’ before ‘robj’
> src/rpymodule2122.c:1016: error: expected ‘)’ before ‘robj’
> src/rpymodule2122.c:1048: error: expected declaration specifiers or ‘...’
> before ‘SEXP’
> src/rpymodule2122.c: In function ‘make_args’:
> src/rpymodule2122.c:1050: error: ‘SEXP’ undeclared (first use in this
> function)
> src/rpymodule2122.c:1050: error: expected ‘;’ before ‘r’
> src/rpymodule2122.c:1054: error: ‘r’ undeclared (first use in this
> function)
> src/rpymodule2122.c:1054: warning: implicit declaration of function
> ‘to_Robj’
> src/rpymodule2122.c:1057: warning: implicit declaration of function
> ‘SETCAR’
> src/rpymodule2122.c:1057: error: ‘e’ undeclared (first use in this
> function)
> src/rpymodule2122.c:1058: warning: implicit declaration of function ‘CDR’
> src/rpymodule2122.c: At top level:
> src/rpymodule2122.c:1092: error: expected declaration specifiers or ‘...’
> before ‘SEXP’
> src/rpymodule2122.c: In function ‘make_kwds’:
> src/rpymodule2122.c:1094: error: ‘SEXP’ undeclared (first use in this
> function)
> src/rpymodule2122.c:1094: error: expected ‘;’ before ‘r’
> src/rpymodule2122.c:1108: error: ‘r’ undeclared (first use in this
> function)
> src/rpymodule2122.c:1113: error: ‘e’ undeclared (first use in this
> function)
> src/rpymodule2122.c:1125: warning: implicit declaration of function
> ‘SET_TAG’
> src/rpymodule2122.c:1125: warning: implicit declaration of function
> ‘Rf_install’
> src/rpymodule2122.c: In function ‘Robj_call’:
> src/rpymodule2122.c:1142: error: ‘SEXP’ undeclared (first use in this
> function)
> src/rpymodule2122.c:1142: error: expected ‘;’ before ‘exp’
> src/rpymodule2122.c:1155: warning: implicit declaration of function
> ‘PROTECT’
> src/rpymodule2122.c:1155: warning: implicit declaration of function
> ‘allocVector’
> src/rpymodule2122.c:1155: error: ‘LANGSXP’ undeclared (first use in this
> function)
> src/rpymodule2122.c:1155: error: invalid lvalue in assignment
> src/rpymodule2122.c:1156: error: ‘e’ undeclared (first use in this
> function)
> src/rpymodule2122.c:1157: error: ‘RobjObject’ has no member named ‘R_obj’
> src/rpymodule2122.c:1160: error: too many arguments to function ‘make_args’
> src/rpymodule2122.c:1161: warning: implicit declaration of function
> ‘UNPROTECT’
> src/rpymodule2122.c:1164: error: too many arguments to function ‘make_kwds’
> src/rpymodule2122.c:1169: error: ‘res’ undeclared (first use in this
> function)
> src/rpymodule2122.c:1169: warning: implicit declaration of function
> ‘do_eval_expr’
> src/rpymodule2122.c:1176: error: ‘RobjObject’ has no member named
> ‘conversion’
> src/rpymodule2122.c:1180: warning: implicit declaration of function
> ‘to_Pyobj_with_mode’
> src/rpymodule2122.c:1180: warning: assignment makes pointer from integer
> without a cast
> src/rpymodule2122.c: At top level:
> src/rpymodule2122.c:1191: error: expected declaration specifiers or ‘...’
> before ‘SEXP’
> src/rpymodule2122.c: In function ‘make_argl’:
> src/rpymodule2122.c:1193: error: ‘SEXP’ undeclared (first use in this
> function)
> src/rpymodule2122.c:1193: error: expected ‘;’ before ‘rvalue’
> src/rpymodule2122.c:1239: error: ‘rvalue’ undeclared (first use in this
> function)
> src/rpymodule2122.c:1247: error: ‘e’ undeclared (first use in this
> function)
> src/rpymodule2122.c: In function ‘Robj_lcall’:
> src/rpymodule2122.c:1279: error: ‘SEXP’ undeclared (first use in this
> function)
> src/rpymodule2122.c:1279: error: expected ‘;’ before ‘exp’
> src/rpymodule2122.c:1308: error: ‘LANGSXP’ undeclared (first use in this
> function)
> src/rpymodule2122.c:1308: error: invalid lvalue in assignment
> src/rpymodule2122.c:1309: error: ‘e’ undeclared (first use in this
> function)
> src/rpymodule2122.c:1310: error: ‘RobjObject’ has no member named ‘R_obj’
> src/rpymodule2122.c:1314: error: too many arguments to function ‘make_argl’
> src/rpymodule2122.c:1320: error: ‘res’ undeclared (first use in this
> function)
> src/rpymodule2122.c:1328: error: ‘RobjObject’ has no member named
> ‘conversion’
> src/rpymodule2122.c:1332: warning: assignment makes pointer from integer
> without a cast
> src/rpymodule2122.c: In function ‘Robj_autoconvert’:
> src/rpymodule2122.c:1359: error: ‘RobjObject’ has no member named
> ‘conversion’
> src/rpymodule2122.c:1361: error: ‘RobjObject’ has no member named
> ‘conversion’
> src/rpymodule2122.c: In function ‘Robj_as_py’:
> src/rpymodule2122.c:1388: error: ‘RobjObject’ has no member named ‘R_obj’
> src/rpymodule2122.c:1388: warning: assignment makes pointer from integer
> without a cast
> src/rpymodule2122.c: In function ‘Robj_len’:
> src/rpymodule2122.c:1406: error: ‘SEXP’ undeclared (first use in this
> function)
> src/rpymodule2122.c:1406: error: expected ‘;’ before ‘e’
> src/rpymodule2122.c:1408: error: ‘e’ undeclared (first use in this
> function)
> src/rpymodule2122.c:1408: error: ‘LANGSXP’ undeclared (first use in this
> function)
> src/rpymodule2122.c:1409: error: ‘length’ undeclared (first use in this
> function)
> src/rpymodule2122.c:1410: error: ‘RobjObject’ has no member named ‘R_obj’
> src/rpymodule2122.c:1412: error: ‘robj’ undeclared (first use in this
> function)
> src/rpymodule2122.c:1418: warning: implicit declaration of function
> ‘INTEGER_DATA’
> src/rpymodule2122.c:1418: error: subscripted value is neither array nor
> pointer
> src/rpymodule2122.c: In function ‘Robj_ass_item’:
> src/rpymodule2122.c:1425: error: ‘SEXP’ undeclared (first use in this
> function)
> src/rpymodule2122.c:1425: error: expected ‘;’ before ‘e’
> src/rpymodule2122.c:1427: error: ‘e’ undeclared (first use in this
> function)
> src/rpymodule2122.c:1427: error: ‘LANGSXP’ undeclared (first use in this
> function)
> src/rpymodule2122.c:1428: error: ‘ri’ undeclared (first use in this
> function)
> src/rpymodule2122.c:1428: warning: implicit declaration of function
> ‘NEW_INTEGER’
> src/rpymodule2122.c:1429: error: subscripted value is neither array nor
> pointer
> src/rpymodule2122.c:1430: error: ‘set_item’ undeclared (first use in this
> function)
> src/rpymodule2122.c:1431: error: ‘RobjObject’ has no member named ‘R_obj’
> src/rpymodule2122.c:1438: error: ‘robj’ undeclared (first use in this
> function)
> src/rpymodule2122.c:1443: error: ‘RobjObject’ has no member named ‘R_obj’
> src/rpymodule2122.c: In function ‘Robj_item’:
> src/rpymodule2122.c:1452: error: ‘SEXP’ undeclared (first use in this
> function)
> src/rpymodule2122.c:1452: error: expected ‘;’ before ‘ri’
> src/rpymodule2122.c:1463: error: ‘ri’ undeclared (first use in this
> function)
> src/rpymodule2122.c:1464: error: subscripted value is neither array nor
> pointer
> src/rpymodule2122.c:1465: error: ‘e’ undeclared (first use in this
> function)
> src/rpymodule2122.c:1465: error: ‘LANGSXP’ undeclared (first use in this
> function)
> src/rpymodule2122.c:1466: error: ‘get_item’ undeclared (first use in this
> function)
> src/rpymodule2122.c:1467: error: ‘RobjObject’ has no member named ‘R_obj’
> src/rpymodule2122.c:1470: error: ‘robj’ undeclared (first use in this
> function)
> src/rpymodule2122.c:1482: warning: assignment makes pointer from integer
> without a cast
> src/rpymodule2122.c: In function ‘Robj_slice’:
> src/rpymodule2122.c:1493: error: ‘SEXP’ undeclared (first use in this
> function)
> src/rpymodule2122.c:1493: error: expected ‘;’ before ‘robj’
> src/rpymodule2122.c:1532: error: ‘INTSXP’ undeclared (first use in this
> function)
> src/rpymodule2122.c:1532: error: invalid lvalue in assignment
> src/rpymodule2122.c:1535: warning: implicit declaration of function
> ‘INTEGER_POINTER’
> src/rpymodule2122.c:1535: error: subscripted value is neither array nor
> pointer
> src/rpymodule2122.c:1538: error: ‘e’ undeclared (first use in this
> function)
> src/rpymodule2122.c:1538: error: ‘LANGSXP’ undeclared (first use in this
> function)
> src/rpymodule2122.c:1539: error: ‘get_item’ undeclared (first use in this
> function)
> src/rpymodule2122.c:1540: error: ‘RobjObject’ has no member named ‘R_obj’
> src/rpymodule2122.c:1543: error: ‘robj’ undeclared (first use in this
> function)
> src/rpymodule2122.c:1555: warning: assignment makes pointer from integer
> without a cast
> src/rpymodule2122.c: At top level:
> src/rpymodule2122.c:1565: warning: initialization from incompatible pointer
> type
> src/rpymodule2122.c:1568: warning: ‘intargfunc’ is deprecated
> src/rpymodule2122.c:1568: warning: initialization from incompatible pointer
> type
> src/rpymodule2122.c:1569: warning: ‘intintargfunc’ is deprecated
> src/rpymodule2122.c:1569: warning: initialization from incompatible pointer
> type
> src/rpymodule2122.c:1570: warning: initialization from incompatible pointer
> type
> src/rpymodule2122.c: In function ‘get_fun’:
> src/rpymodule2122.c:1668: error: ‘SEXP’ undeclared (first use in this
> function)
> src/rpymodule2122.c:1668: error: expected ‘;’ before ‘robj’
> src/rpymodule2122.c:1675: error: ‘robj’ undeclared (first use in this
> function)
> src/rpymodule2122.c:1675: warning: implicit declaration of function
> ‘get_fun_from_name’
> src/rpymodule2122.c:1679: warning: implicit declaration of function
> ‘Robj_new’
> src/rpymodule2122.c:1679: warning: cast to pointer from integer of
> different size
> src/rpymodule2122.c: In function ‘r_events’:
> src/rpymodule2122.c:1727: warning: implicit declaration of function
> ‘R_checkActivity’
> src/rpymodule2122.c:1727: warning: assignment makes pointer from integer
> without a cast
> src/rpymodule2122.c:1728: warning: implicit declaration of function
> ‘R_runHandlers’
> src/rpymodule2122.c:1728: error: ‘R_InputHandlers’ undeclared (first use in
> this function)
> src/rpymodule2122.c: In function ‘r_finalize’:
> src/rpymodule2122.c:1778: warning: implicit declaration of function
> ‘R_dot_Last’
> src/rpymodule2122.c:1779: warning: implicit declaration of function
> ‘R_RunExitFinalizers’
> src/rpymodule2122.c:1781:28: error: missing binary operator before token
> "("
> src/rpymodule2122.c:1784: warning: implicit declaration of function
> ‘KillAllDevices’
> src/rpymodule2122.c:1787:28: error: missing binary operator before token
> "("
> src/rpymodule2122.c:1798: warning: implicit declaration of function
> ‘R_system’
> src/rpymodule2122.c:1803: warning: implicit declaration of function ‘R_gc’
> src/rpymodule2122.c: In function ‘init_rpy2122’:
> src/rpymodule2122.c:1980: error: ‘SEXP’ undeclared (first use in this
> function)
> src/rpymodule2122.c:1980: error: expected ‘;’ before ‘interact’
> src/rpymodule2122.c:2070: error: ‘get_item’ undeclared (first use in this
> function)
> src/rpymodule2122.c:2071: error: ‘set_item’ undeclared (first use in this
> function)
> src/rpymodule2122.c:2072: error: ‘length’ undeclared (first use in this
> function)
> src/rpymodule2122.c:2075: error: ‘aperm’ undeclared (first use in this
> function)
> src/rpymodule2122.c:2078: error: ‘R_References’ undeclared (first use in
> this function)
> src/rpymodule2122.c:2078: error: ‘R_NilValue’ undeclared (first use in this
> function)
> src/rpymodule2122.c:2085: error: ‘interact’ undeclared (first use in this
> function)
> src/rpymodule2122.c:2085: warning: implicit declaration of function
> ‘do_eval_fun’
> src/rpymodule2122.c:2086: warning: implicit declaration of function
> ‘INTEGER’
> src/rpymodule2122.c:2086: error: subscripted value is neither array nor
> pointer
> error: command 'gcc' failed with exit status 1
>
>
>
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