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Old 05-20-2014, 11:49 AM   #1
jwhite
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Location: Boston

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Default R and Tcl/Tk system libraries

Hi,

For the past several days I've been fighting with R to install a software package "compcodeR". This package requires Tcl/Tk libraries be installed on the system. So I installed these libraries on our cluster (since they were not present). The install location is /usr/local/lib for Tcl/Tk 8.6.

Unfortunately, R will not install the compcodeR package because it cannot detect the Tcl or Tk libraries. (Yes, the libraries exists and are functional.) Adding /usr/local/lib to the $PATH and $LD_LIBRARY_PATH env. variables made no difference. Copying the .so library files to R's lib directory --as other libraries are--made no difference. R still complains that it cannot detect the tcl/tk libraries.

Has anyone else had a similar problem? Does anyone know why R cannot detect these libraries even after setting up the environment? Am I using the wrong env variable?

Any help is appreciated.
Thanks,
Joe White
MEEI
Boston
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Old 05-21-2014, 02:41 AM   #2
Jeremy
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Default

I think R needs to be compiled with tcl/tk already installed. Some packages need the dev version of tcl/tk and won't work with the normal version.

What does R say when you give it: capabilities("tcltk")
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Old 05-21-2014, 05:48 AM   #3
jwhite
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Default

Quote:
Originally Posted by Jeremy View Post
I think R needs to be compiled with tcl/tk already installed. Some packages need the dev version of tcl/tk and won't work with the normal version.

What does R say when you give it: capabilities("tcltk")
FALSE

possibly because the shared object libraries aren't available or in the right place.

This is the error returned during package installation:

[...snip...]
** preparing package for lazy loading
Warning: S3 methods as.character.tclObj, as.character.tclVar,
as.double.tclObj, as.integer.tclObj, as.logical.tclObj, as.raw.tclObj,
print.tclObj, [[.tclArray, [[<-.tclArray, $.tclArray, $<-.tclArray,
names.tclArray, names<-.tclArray, length.tclArray, length<-.tclArray,
tclObj.tclVar, tclObj<-.tclVar, tclvalue.default, tclvalue.tclObj,
tclvalue.tclVar, tclvalue<-.default, tclvalue<-.tclVar,
close.tkProgressBar were declared in NAMESPACE but not found
Error : .onLoad failed in loadNamespace() for 'tcltk', details:
call: fun(libname, pkgname)
error: Tcl/Tk support is not available on this system
ERROR: lazy loading failed for package compcodeR
* removing /opt/R-3.0.2/lib64/R/library/compcodeR
Warning message:
In install.packages("compcodeR_1.0.0.tar.gz") :
installation of package compcodeR_1.0.0.tar.gz had non-zero exit status

The same error occurs if the package is installed from the command-line.

Joe White
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Old 12-01-2014, 08:04 AM   #4
IsBeth
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Default Same error...

Hello!

I know this thread is a little bit old but I've got the same error with compcodeR now. The installation seems to work well, but when I try to load the library the following error appears:

sh: otool: command not found
Error : .onLoad failed in loadNamespace() for 'tcltk', details:
call: system2("otool", c("-L", shQuote(DLL)), stdout = TRUE)
error: error in running command

Do you know any trick to fix this? I've never had troubles with compcodeR before, so I'm a bit confused. It worked well until now

Last edited by IsBeth; 12-01-2014 at 08:06 AM.
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Old 12-01-2014, 08:09 AM   #5
Richard Finney
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otool is pretty much Apple Mac specific.
You need to install the developer tools to get access to otool. I'm not sure if you need Xcode, too.

http://superuser.com/questions/23550...mand-not-found
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