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 isnt a prototype src/rpy_Rinterface.h:96: warning: function declaration isnt a prototype src/rpy_Rinterface.h:101: warning: function declaration isnt a prototype src/rpy_Rinterface.h:102: warning: function declaration isnt a prototype src/rpy_Rinterface.h:103: warning: function declaration isnt 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