[R-sig-Debian] Rscript path problem on R 2.13.1 for Ubuntu 11.04?

[Michael Rutter]

On 09/19/2011 09:54 AM, Syrus Nemat-Nasser wrote:
> Hi Johan,
>
> I have 2.13 installed on my Ubuntu 11.04 machine, but Rscript is located in
> /usr/bin:
>
> snn at d630snn:~/bin$ which Rscript
> /usr/bin/Rscript
>
> I installed R from CRAN using the instructions at
> http://cran.r-project.org/bin/linux/ubuntu/README
>
> Perhaps it has something to do with how you installed R 2.13 on your
> machine?
>
> Regards, --Syrus
>

When I look at my installed files list for r-base-core (2.13.1-1lucid2), 
it lists the following:

/usr/bin/Rscript

Johan, did you do an upgrade to 11.04 or a clean install of 11.04? 
Upgrades from one release of Ubuntu to another can sometimes cause 
strange issues.  This could a side effect of doing an upgrade.

Are there any other R related programs in /usr/local/bin?  What is 
strange is that when I ask for the version of Rscript, I get

 > Rscript --version
R scripting front-end version 2.13.1 (2011-07-08)

I am not even sure where "version 49838" is coming from.  It seems to be 
to a leftover file from another install.  Is Rscript also in /usr/bin? I 
would delete the /usr/local/bin/Rscript manually, and then reinstall R.

Michael

>> Dear all,
>>
>> finally decided to do an Ubuntu upgrade and a new clean R install from
>> http://cran.r-project.org/bin/linux/ubuntu/.
>>
>> However, while trying to install a package from R-forge I encountered
>> problems, involving error messages saying "Rscript execution error: No
>> such file or directory" (see below).
>>
>> The same procedure works on Ubuntu 11.04 running R 2.12.1-1 from the
>> Ubuntu repositories.
>>
>> The behavior of Rscript on my (11.04 + 2.13.1) machine:
>>   $ which Rscript
>>   /usr/local/bin/Rscript
>>   $ Rscript --version
>>   R scripting front-end version 49838
>>   $ Rscript -e 'rnorm(1)'
>>   Rscript execution error: No such file or directory
>>
>> on my 11.04 + 2.12.1:
>>   $ which Rscript
>>   /usr/bin/Rscript
>>   $ Rscript --version
>>   R scripting front-end version 2.12.1 (2010-12-16)
>>   $ Rscript -e 'rnorm(1)'
>>   [1] 0.9278564
>>
>> Seems like this problem has been seen before
>> (http://bugs.r-project.org/bugzilla3/show_bug.cgi?id=14493), and that the
>> wrong PATH and/or RHOME is involved.
>>
>> Any suggestions? Solutions?
>>
>> Cheers
>> Johan
>>
>> --------------------------------------------
>> Install Error output (On Ubuntu Linux 11.04 64bit, R version 2.13.1
>> (2011-07-08). R installed from CRAN Ubuntu bin repositories.)
>>
>> $ sudo R
>>>
>>> install.packages("earthmovdist", repos = "http://R-forge.R-project.org")
>> Installing package(s) into ‘/usr/local/lib/R/site-library’
>> (as ‘lib’ is unspecified)
>> trying URL
>> 'http://R-forge.R-project.org/src/contrib/earthmovdist_0.1.1.tar.gz'
>> Content type 'application/x-gzip' length 15819 bytes (15 Kb)
>> opened URL
>> ==================================================
>> downloaded 15 Kb
>>
>> * installing *source* package ‘earthmovdist’ ...
>> ** libs
>> g++ -I/usr/share/R/include
>> -I"/usr/local/lib/R/site-library/Rcpp/include"   -fpic  -O3 -pipe  -g -c
>> emdL1.cpp -o emdL1.o
>> g++ -I/usr/share/R/include
>> -I"/usr/local/lib/R/site-library/Rcpp/include"   -fpic  -O3 -pipe  -g -c
>> emdL1_R.cpp -o emdL1_R.o
>> Rscript execution error: No such file or directory
>> Rscript execution error: No such file or directory
>> g++ -shared -o earthmovdist.so emdL1.o emdL1_R.o -L/usr/lib64/R/lib -lR
>> installing to /usr/local/lib/R/site-library/earthmovdist/libs
>> ** R
>> ** inst
>> ** preparing package for lazy loading
>> ** help
>> *** installing help indices
>> ** building package indices ...
>> ** testing if installed package can be loaded
>> Error in dyn.load(file, DLLpath = DLLpath, ...) :
>>   unable to load shared object
>> '/usr/local/lib/R/site-library/earthmovdist/libs/earthmovdist.so':
>>   /usr/local/lib/R/site-library/earthmovdist/libs/earthmovdist.so:
>> undefined symbol: _ZTIN4Rcpp7RObjectE
>> Error: loading failed
>> Execution halted
>> ERROR: loading failed
>> * removing ‘/usr/local/lib/R/site-library/earthmovdist’
>>
>> The downloaded packages are in
>>         ‘/tmp/RtmpdFcoSz/downloaded_packages’
>> Warning message:
>> In install.packages("earthmovdist", repos = "http://R-forge.R-project.org")
>> :
>>   installation of package 'earthmovdist' had non-zero exit status
>>>
>>
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-- 
Dr. Michael A. Rutter
School of Science
Penn State Erie, The Behrend College
Station Road
Erie, PA 16563
http://math.bd.psu.edu/faculty/rutter