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.updateMethodsInTable(fdef, where, attach) : Couldn't find methods table for "conditional", package "Category" may be out of date 2: In .updateMethodsInTable(fdef, where, attach) : Methods list for generic "conditional" not found 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)
Please take this up with the RSPython maintainer (current address in the CC and in version 0.7-1). I think you have not built R as a shared library, and that symbol only exists when you do (it is not the default). The same happens in the released R: we will have to wait a couple of months to see what happens in 'R 2.6.0'. Even with R built as a shared library I get> library(RSPython)Error in ifelse(R.version$os == "Win32", ";", ":", ) : unused argument(s) () Error in library(RSPython) : .First.lib failed for 'RSPython' which is a bug in the package. (Duncan: that is what .Platform$path.sep is for, and on Windows R.version$os is "mingw32" - for 32-bit builds at least.) On Fri, 3 Aug 2007, 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) > > ______________________________________________ > R-help at stat.math.ethz.ch mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code. >-- Brian D. Ripley, ripley at stats.ox.ac.uk Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UK Fax: +44 1865 272595
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)
>>
>> ******************************************************************
>>
>>
>