Re: [galaxy-dev] Package/Module RPY

2014-04-08 Thread Greg Von Kuster 
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 )..

Test runs  
2014-04-07 17:25:49  
Automated test environment  
Successful installations  
Repository dependencies - installation of these additional repositories is 
required  
Tool shed   NameOwner   Changeset revision
toolshed.g2.bx.psu.edu  package_r_2_11_0devteam 5824d2b3bc8b
Tool dependencies  
TypeNameVersion
R   package 2.11.0
Installation directory
/ToolDepsMain/R/2.11.0/devteam/package_rpy_1_0_3/82170c94ca7c
TypeNameVersion
rpy package 1.0.3
Installation directory
/ToolDepsMain/rpy/1.0.3/devteam/package_rpy_1_0_3/82170c94ca7c



On Apr 8, 2014, at 3:28 PM, "Hayes, Curt"  
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 
> 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
> rpy
> 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. 
> 
> Thanks,
> Curt
>  
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[galaxy-dev] Package/Module RPY

2014-04-08 Thread Hayes, Curt 
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 
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: curl 
http://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

rpy

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. 

Thanks,
Curt

CONFIDENTIALITY NOTICE: This e-mail message, including any attachments, is for 
the sole use of the intended recipient(s) and may contain confidential and 
privileged information protected by law. Any unauthorized review, use, 
disclosure or distribution is prohibited. If you are not the intended 
recipient, please contact the sender by reply e-mail and destroy all copies of 
the original message.

___
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/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/

[galaxy-dev] Package/Module RPY

2014-04-02 Thread Hayes, Curt 
Hi there all,

I have searched previous posts, nothing since 2010. I have a local install 
(production config - postgres, etc - on CENTOS 6.5).
Does anyone have RPY working? I install via toolshed and the folder is empty, 
and shows missing dependencies.

>From Galaxy User:
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 
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: curl 
http://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

rpy

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. 

Thanks,
Curt

CONFIDENTIALITY NOTICE: This e-mail message, including any attachments, is for 
the sole use of the intended recipient(s) and may contain confidential and 
privileged information protected by law. Any unauthorized review, use, 
disclosure or distribution is prohibited. If you are not the intended 
recipient, please contact the sender by reply e-mail and destroy all copies of 
the original message.

[root@seachlinux rpy]# python setup.py install
RHOMES= []
DEBUG= False
Setting RHOMES to  ['/usr/lib64/R']
### Using R verion 2.13.0 installed at /usr/lib64/R ###
RHOME= /usr/lib64/R
copying src/rpymodule.c -> src/rpymodule2130.c
copying src/R_eval.c -> src/R_eval2130.c
copying src/io.c -> src/io2130.c
running install
running build
running build_py
running build_ext
building '_rpy2130' extension
gcc -pthread -fno-strict-aliasing -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 
-fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic 
-D_GNU_SOURCE -fPIC -fwrapv -DNDEBUG -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 
-fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic 
-D_GNU_SOURCE -fPIC -fwrapv -fPIC -DWITH_NUMERIC=3 
-DPY_ARRAY_TYPES_PREFIX=PyArray_ -DRPY_SHNAME=_rpy2130 -DINIT_RPY=init_rpy2130 
-UPRE_2_2 -I/usr/lib64/R/include -Isrc -I/usr/share/R/include 
-I/usr/lib64/python2.6/site-packages/numpy/core/include 
-I/usr/include/python2.6 -c src/rpymodule2130.c -o 
build/temp.linux-x86_64-2.6/src/rpymodule2130.o -shared -llapack
In file included from src/rpymodule2130.c:51:
src/RPy.h:63:20: 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:99,
 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:99,
 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 ‘...’