[R] RSPython won't load in R 2.6.0 under Linux

[Mark W Kimpel]

Duncan,

Thanks for the update on the update. I downloaded and installed it and 
receive the following messages on installation and require(RSPython). 
Also, checked to make sure python was on my path and working and it is 
(also below). I am running openSuse 10.2. sessionInfo() follows as well.

Mark

* DONE (RSPython)

The downloaded packages are in
	/tmp/Rtmp4QozuD/downloaded_packages
Warning message:
In install.packages(pkgs = "RSPython", repos = 
"http://www.omegahat.org/R") :
   dependency ‘Python’ is not available
 > require(RSPython)
Loading required package: RSPython

Attaching package: 'RSPython'


	The following object(s) are masked from package:base :

	 .Call

Warning message:
In .Call("InitPython") :
   the Python callback manager has been registered implicitly using the 
defaults (referenceManager())!
 >


Python is installed on my system and can be invoked from the command line:
mkimpel at m-90:~> python
Python 2.5 (r25:51908, May 25 2007, 16:14:04)
[GCC 4.1.2 20061115 (prerelease) (SUSE Linux)] on linux2
Type "help", "copyright", "credits" or "license" for more information.
 >>> quit()
mkimpel at m-90:~> whereis python
python: /usr/bin/python2.5 /usr/bin/python2.5-config /usr/bin/python 
/usr/lib/python2.5 /usr/lib/python /usr/bin/X11/python2.5 
/usr/bin/X11/python2.5-config /usr/bin/X11/python /usr/include/python2.5 
/usr/include/python /usr/share/man/man1/python.1.gz
mkimpel at m-90:~>

 > sessionInfo()
R version 2.6.0 Under development (unstable) (2007-08-01 r42387)
i686-pc-linux-gnu

locale:
LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=en_US.UTF-8;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C

attached base packages:
[1] splines   tools     stats     graphics  grDevices utils     datasets
[8] methods   base

other attached packages:
  [1] RSPython_0.8-0         affycoretools_1.9.3    annaffy_1.9.1
  [4] xtable_1.5-0           gcrma_2.9.1            matchprobes_1.9.10
  [7] biomaRt_1.11.4         RCurl_0.8-1            XML_1.9-0
[10] GOstats_2.3.8          Category_2.3.18        genefilter_1.15.9
[13] survival_2.32          KEGG_1.17.0            RBGL_1.13.3
[16] annotate_1.15.3        AnnotationDbi_0.0.88   RSQLite_0.6-0
[19] DBI_0.2-3              GO_1.17.0              limma_2.11.9
[22] affy_1.15.7            preprocessCore_0.99.12 affyio_1.5.6
[25] Biobase_1.15.23        graph_1.15.10

loaded via a namespace (and not attached):
[1] cluster_1.11.7
 >

Mark W. Kimpel MD  ** Neuroinformatics ** Dept. of Psychiatry
Indiana University School of Medicine

15032 Hunter Court, Westfield, IN  46074

(317) 490-5129 Work, & Mobile & VoiceMail
(317) 663-0513 Home (no voice mail please)

******************************************************************

Duncan Temple Lang wrote:
> 
> Mark,
>   Just thought I'd let you know that I did get a chance to
> make the changes and some others besides and there is a new
> RSPython release on the Omegahat web site.
> 
>  Thanks,
>    D.
> 
> Mark W Kimpel wrote:
>> I can compile RSPython without difficulty, been when I try to load it, I
>> get the error messages below. Also below are some cryptic warnings I get
>> on R boot (in case these are pertinent) and my sessionInfo().
>>
>> Any help is appreciated. Thanks, Mark
>>
>> Warning messages:
>> 1: In .updateMethodsInTable(fdef, where, attach) :
>>   Couldn't find methods table for "conditional", package "Category" may
>> be out of date
>> 2: In .updateMethodsInTable(fdef, where, attach) :
>>   Methods list for generic "conditional" not found
>>> require(RSPython)
>> Loading required package: RSPython
>> Error in dyn.load(file, ...) :
>>   unable to load shared library
>> '/home/mkimpel/R_HOME/site-library/RSPython/libs/RSPython.so':
>>   /home/mkimpel/R_HOME/site-library/RSPython/libs/RSPython.so:
>> undefined symbol: Rf_initEmbeddedR
>>> sessionInfo()
>> R version 2.6.0 Under development (unstable) (2007-08-01 r42387)
>> i686-pc-linux-gnu
>>
>> locale:
>> LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=en_US.UTF-8;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C 
>>
>>
>> attached base packages:
>> [1] splines   tools     stats     graphics  grDevices utils     datasets
>> [8] methods   base
>>
>> other attached packages:
>>  [1] affycoretools_1.9.3    annaffy_1.9.1          xtable_1.5-0
>>  [4] gcrma_2.9.1            matchprobes_1.9.10     biomaRt_1.11.4
>>  [7] RCurl_0.8-1            XML_1.9-0              GOstats_2.3.8
>> [10] Category_2.3.18        genefilter_1.15.9      survival_2.32
>> [13] KEGG_1.17.0            RBGL_1.13.3            annotate_1.15.3
>> [16] AnnotationDbi_0.0.88   RSQLite_0.6-0          DBI_0.2-3
>> [19] GO_1.17.0              limma_2.11.9           affy_1.15.7
>> [22] preprocessCore_0.99.12 affyio_1.5.6           Biobase_1.15.23
>> [25] graph_1.15.10
>>
>> loaded via a namespace (and not attached):
>> [1] cluster_1.11.7  rcompgen_0.1-15
>>
>>
>> ---
>>
>> Mark W. Kimpel MD  ** Neuroinformatics ** Dept. of Psychiatry
>> Indiana University School of Medicine
>>
>> 15032 Hunter Court, Westfield, IN  46074
>>
>> (317) 490-5129 Work, & Mobile & VoiceMail
>> (317) 663-0513 Home (no voice mail please)
>>
>> ******************************************************************
>>
>>
>