Re: [galaxy-dev] rpy and R

22 Jun 2011

      Thank you Marco and Hans for your solutions.  I installed the R-devel and it
fixed the issues.  I now have R 2.12.2 and rpy 1.0.3 running smoothly.
Thanks!

From: Marco Moretto [mailto:marco.moretto@gmail.com] 
Sent: Tuesday, June 21, 2011 11:49 PM
To: Ryan Davis
Cc: galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] rpy and R

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 <rrdavis@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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