Re: [galaxy-dev] RPy and R installation problems
Sorry, that's all I have. Le-Shin On Jul 15, 2012, at 4:41 AM, Morris Chukhman wrote: Yes! That seems to have worked! Thank you very much, Le-Shin! Are there any more of these dependencies that require these little patches to build and install properly? Morris On 7/14/2012 8:16 PM, Le-Shin Wu wrote: I forgot to mention the most important part. You have to modify line 100 in rpy_tools.py that is under the rpy package as version = re.search( +([0-9]+\.[0-9][0-9]+\.[0-9]+), output) Le-Shin On Jul 14, 2012, at 7:15 PM, Chukhman, Morris wrote: When I try to install rpy-1.0.3 against R-2.11.1 or R-2.15.1 I get the following error about the version number being unobtainable from R --version. python setup.py install --prefix=/path/to/shared/python RHOMES= [] DEBUG= True Setting RHOMES to ['/argus/app/rhel60/R_2.11.1/lib64/R'] Traceback (most recent call last): File setup.py, line 109, in module RVERSION = rpy_tools.get_R_VERSION(RHOME, force_exec=True) File /argus/app/src/rpy-1.0.3/rpy_tools.py, line 103, in get_R_VERSION raise RuntimeError(Couldn't obtain version number from output\n RuntimeError: Couldn't obtain version number from output of `R --version'. This is the R --version output: galaxy[rpy-1.0.3]$ R --version R version 2.11.1 (2010-05-31) Copyright (C) 2010 The R Foundation for Statistical Computing ISBN 3-900051-07-0 R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under the terms of the GNU General Public License version 2. For more information about these matters see http://www.gnu.org/licenses/. Although rpy2 builds and installs successfully the linear_regression.py module can't seem to use it. It is looking for the rpy module not the rpy2 module. If I ln -s rpy2 rpy, it appears to run but gives an name not defined error in a line like dat= r.list(... What is the proper procedure for installing the R and rpy dependencies? What versions are recommended with the current galaxy on mercurial? On Thu, June 28, 2012 3:51 pm, Susan Hester wrote: Hi, I'm trying to register in Galaxy on the public server and under the user tab register is greyed out? How do I register? Susan Hester, Ph.D. Research Biologist Systems Biology Branch Integrated Systems Toxicology Division (ISTD) National Health and Environmental Effects Research Lab US Environmental Protection Agency 109 T.W. Alexander Dr. MD-B143-06 Research Triangle Park, NC 27711 hester.susan@epa.gov___ 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/ ___ 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/ ___ 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/
Re: [galaxy-dev] RPy and R installation problems
To build R, you need readline, readline_devel, and gfortran have been installed already. Then, ./configure --enable-R-shlib --prefix=/YOUR_PATH_TO_WHERE_R_WILL_BE_INSTALLED/R make make install To build rpy, you need to first, add R/lib to $LD_LIBRARY_PATH and R/bin to $PATH; sencond, comment out RPY_DOWNLOAD_DIR/src/Rpy.h line 77 as #include Rdevices.h. Then, python setup.py install --prefix=/PATH_TO_WHERE_RPY_WILL_BE_INSTALLED hope this will help. Le-Shin On Jul 14, 2012, at 7:15 PM, Chukhman, Morris wrote: When I try to install rpy-1.0.3 against R-2.11.1 or R-2.15.1 I get the following error about the version number being unobtainable from R --version. python setup.py install --prefix=/path/to/shared/python RHOMES= [] DEBUG= True Setting RHOMES to ['/argus/app/rhel60/R_2.11.1/lib64/R'] Traceback (most recent call last): File setup.py, line 109, in module RVERSION = rpy_tools.get_R_VERSION(RHOME, force_exec=True) File /argus/app/src/rpy-1.0.3/rpy_tools.py, line 103, in get_R_VERSION raise RuntimeError(Couldn't obtain version number from output\n RuntimeError: Couldn't obtain version number from output of `R --version'. This is the R --version output: galaxy[rpy-1.0.3]$ R --version R version 2.11.1 (2010-05-31) Copyright (C) 2010 The R Foundation for Statistical Computing ISBN 3-900051-07-0 R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under the terms of the GNU General Public License version 2. For more information about these matters see http://www.gnu.org/licenses/. Although rpy2 builds and installs successfully the linear_regression.py module can't seem to use it. It is looking for the rpy module not the rpy2 module. If I ln -s rpy2 rpy, it appears to run but gives an name not defined error in a line like dat= r.list(... What is the proper procedure for installing the R and rpy dependencies? What versions are recommended with the current galaxy on mercurial? On Thu, June 28, 2012 3:51 pm, Susan Hester wrote: Hi, I'm trying to register in Galaxy on the public server and under the user tab register is greyed out? How do I register? Susan Hester, Ph.D. Research Biologist Systems Biology Branch Integrated Systems Toxicology Division (ISTD) National Health and Environmental Effects Research Lab US Environmental Protection Agency 109 T.W. Alexander Dr. MD-B143-06 Research Triangle Park, NC 27711 hester.susan@epa.gov___ 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/ ___ 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/ ___ 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/
Re: [galaxy-dev] RPy and R installation problems
I forgot to mention the most important part. You have to modify line 100 in rpy_tools.py that is under the rpy package as version = re.search( +([0-9]+\.[0-9][0-9]+\.[0-9]+), output) Le-Shin On Jul 14, 2012, at 7:15 PM, Chukhman, Morris wrote: When I try to install rpy-1.0.3 against R-2.11.1 or R-2.15.1 I get the following error about the version number being unobtainable from R --version. python setup.py install --prefix=/path/to/shared/python RHOMES= [] DEBUG= True Setting RHOMES to ['/argus/app/rhel60/R_2.11.1/lib64/R'] Traceback (most recent call last): File setup.py, line 109, in module RVERSION = rpy_tools.get_R_VERSION(RHOME, force_exec=True) File /argus/app/src/rpy-1.0.3/rpy_tools.py, line 103, in get_R_VERSION raise RuntimeError(Couldn't obtain version number from output\n RuntimeError: Couldn't obtain version number from output of `R --version'. This is the R --version output: galaxy[rpy-1.0.3]$ R --version R version 2.11.1 (2010-05-31) Copyright (C) 2010 The R Foundation for Statistical Computing ISBN 3-900051-07-0 R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under the terms of the GNU General Public License version 2. For more information about these matters see http://www.gnu.org/licenses/. Although rpy2 builds and installs successfully the linear_regression.py module can't seem to use it. It is looking for the rpy module not the rpy2 module. If I ln -s rpy2 rpy, it appears to run but gives an name not defined error in a line like dat= r.list(... What is the proper procedure for installing the R and rpy dependencies? What versions are recommended with the current galaxy on mercurial? On Thu, June 28, 2012 3:51 pm, Susan Hester wrote: Hi, I'm trying to register in Galaxy on the public server and under the user tab register is greyed out? How do I register? Susan Hester, Ph.D. Research Biologist Systems Biology Branch Integrated Systems Toxicology Division (ISTD) National Health and Environmental Effects Research Lab US Environmental Protection Agency 109 T.W. Alexander Dr. MD-B143-06 Research Triangle Park, NC 27711 hester.susan@epa.gov___ 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/ ___ 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/ ___ 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/
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 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 ‘=’, ‘,’, ‘;’,
Re: [galaxy-dev] rpy and R
Hi Ryan Our sysadmin spent quite some time on this problem...in the end, he gave up and installed R 2.9.0 on our new server. So, we ended up with two versions of R: one is used for rpy (we define: R_HOME=/***/***/galaxy/helpers/R/R-2.9.0 in the 'run.sh' script), and an up-to-date version of R (ie 2.13.0) is used to execute our self written Rscripts, which we have added. Regards, Hans On 06/22/2011 01:43 AM, Ryan Davis 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’
Re: [galaxy-dev] rpy and R
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.more...@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 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
Re: [galaxy-dev] rpy and R
Sarah Diehl wrote: Hi all, I'm currently working on setting up a fresh Galaxy server at our institute. 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. With some workarounds I managed to compile rpy, but when I try to import it in python, I get the following error: import rpy Traceback (most recent call last): File stdin, line 1, in module File rpy.py, line 134, in module % RVERSION) RuntimeError: No module named _rpy2122 RPy module can not be imported. Please check if your rpy installation supports R 2.12.2. If you have multiple R versions installed, you may need to set RHOME before importing rpy. For example: from rpy_options import set_options set_options(RHOME='c:/progra~1/r/rw2011/') from rpy import * It looks like my version of R isn't supported by rpy. Does anybody know which version of R still works with rpy? I couldn't find anything about it. What about rpy2? Is it not supported by Galaxy? Hi Sarah, Although I haven't tested with 2.12.2, I know it works with at least 2.11.0. The error above is indicating that rpy is installed somewhere on python's path but the C-extension module for the version of R found on your $PATH (2.12.2) is not present. Most likely this is because rpy was already installed, and is being found earlier on python's path than the version of rpy that you installed. The older rpy was built against a different version of R. If you find the original installation of rpy you should be able to determine from _rpyversion.so what version of R it was built against, and put that version of R ahead of 2.12.2 in your $PATH. Alternatively, you can find and uninstall the old version of rpy, which should allow your newer version to be found and used. python's path can be determined with: python -c 'import sys; print \n.join( sys.path )' There is some effort underway in the community to rewrite rpy tools to use rpy2, but this work is not yet complete. Hope this helps, --nate Thanks very much in advance for your help! Best regards, Sarah Diehl ___ To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ ___ To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-dev] rpy and R
Hi Nate, thank you very much for your help! I managed to figure out the problem. There seemed to be an old version of R and somehow (I still don't know how) the rpy installation did only find the old one. I hard-coded the directory of the new R in the setup.py (everything else failed) and then it compiled against the new R version. Best regards, Sarah On 03/03/2011 05:11 PM, Nate Coraor wrote: Sarah Diehl wrote: Hi all, I'm currently working on setting up a fresh Galaxy server at our institute. 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. With some workarounds I managed to compile rpy, but when I try to import it in python, I get the following error: import rpy Traceback (most recent call last): File stdin, line 1, inmodule File rpy.py, line 134, inmodule % RVERSION) RuntimeError: No module named _rpy2122 RPy module can not be imported. Please check if your rpy installation supports R 2.12.2. If you have multiple R versions installed, you may need to set RHOME before importing rpy. For example: from rpy_options import set_options set_options(RHOME='c:/progra~1/r/rw2011/') from rpy import * It looks like my version of R isn't supported by rpy. Does anybody know which version of R still works with rpy? I couldn't find anything about it. What about rpy2? Is it not supported by Galaxy? Hi Sarah, Although I haven't tested with 2.12.2, I know it works with at least 2.11.0. The error above is indicating that rpy is installed somewhere on python's path but the C-extension module for the version of R found on your $PATH (2.12.2) is not present. Most likely this is because rpy was already installed, and is being found earlier on python's path than the version of rpy that you installed. The older rpy was built against a different version of R. If you find the original installation of rpy you should be able to determine from _rpyversion.so what version of R it was built against, and put that version of R ahead of 2.12.2 in your $PATH. Alternatively, you can find and uninstall the old version of rpy, which should allow your newer version to be found and used. python's path can be determined with: python -c 'import sys; print \n.join( sys.path )' There is some effort underway in the community to rewrite rpy tools to use rpy2, but this work is not yet complete. Hope this helps, --nate Thanks very much in advance for your help! Best regards, Sarah Diehl ___ To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ ___ To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
