[R-SIG-Mac] /bin/sh: tar: command not found

[[Ricardo Rodriguez] Your XEN ICT Team]

Thanks for your patience!

Kasper Daniel Hansen wrote:
> Ok, I think I know what went wrong now
>
> The key information was that you are using R.app (the GUI) which was 
> not clear to me until now.

:-( Ok, I was calling console to the graphical console... R 2.7.2 GUI 
1.25 (5217) :-( again. Sorry about this.
>
> First I would say however that you seem to be messing around a bit. In 
> your previous email you said you had modified .bashrc to include the 
> long PATH setting, but in your grep below, bashrc is not mentioned. So 
> I assume you have deleted it in the meantime?

I've modified the system wied .bashrc in /etc. Note that I've do cd, not 
cd / previous to grep. Look now...

GMXUX-Ricardo-Rodriguez:etc rrodriguez$ sudo grep PATH * .*
Password:
bashrc:export PATH=$M2:$PATH
locate.rc:#SEARCHPATHS="/"
locate.rc:#PRUNEPATHS="/tmp /var/tmp"
locate.rc:# and if the SEARCHPATHS starts in such a filesystem locate 
will build
man.conf:# when MANPATH contains an empty substring), to find out where 
the cat
man.conf:# and to map each PATH element to a manpath element.
man.conf:# MANPATH        manpath_element    [corresponding_catdir]
man.conf:# MANPATH_MAP        path_element    manpath_element
man.conf:# Every automatically generated MANPATH includes these fields
man.conf:MANPATH    /usr/share/man
man.conf:MANPATH    /usr/local/share/man
man.conf:MANPATH    /usr/X11/man
man.conf:# MANPATH    /opt/*/man
man.conf:# MANPATH    /usr/lib/*/man
man.conf:# MANPATH    /usr/share/*/man
man.conf:# MANPATH    /usr/kerberos/man
man.conf:# Set up PATH to MANPATH mapping
man.conf:# If people ask for "man foo" and have "/dir/bin/foo" in their PATH
man.conf:MANPATH_MAP    /bin            /usr/share/man
man.conf:MANPATH_MAP    /sbin            /usr/share/man
man.conf:MANPATH_MAP    /usr/bin        /usr/share/man
man.conf:MANPATH_MAP    /usr/sbin        /usr/share/man
man.conf:MANPATH_MAP    /usr/local/bin        /usr/local/share/man
man.conf:MANPATH_MAP    /usr/local/sbin        /usr/local/share/man
man.conf:MANPATH_MAP    /usr/X11/bin        /usr/X11/man
man.conf:MANPATH_MAP    /usr/bin/X11        /usr/X11/man
man.conf:MANPATH_MAP    /usr/bin/mh        /usr/share/man
man.conf:# NOAUTOPATH keeps man from automatically adding directories 
that look like
man.conf:#NOAUTOPATH
php.ini.default:safe_mode_protected_env_vars = LD_LIBRARY_PATH
php.ini.default:; cgi.fix_pathinfo provides *real* 
PATH_INFO/PATH_TRANSLATED support for CGI.  PHP's
php.ini.default:; previous behaviour was to set PATH_TRANSLATED to 
SCRIPT_FILENAME, and to not grok
php.ini.default:; what PATH_INFO is.  For more information on PATH_INFO, 
see the cgi specs.  Setting
php.ini.default:; to use SCRIPT_FILENAME rather than PATH_TRANSLATED.
rc.common:PATH=/bin:/sbin:/usr/bin:/usr/sbin:/usr/libexec:/System/Library/CoreServices; 
export PATH
sshd_config:# This sshd was compiled with PATH=/usr/bin:/bin:/usr/sbin:/sbin
GMXUX-Ricardo-Rodriguez:etc rrodriguez$

bashrc has been modified. This also answer question 2) below.

>
> Anyways, you seem to have been playing around a bit with your 
> environment variables and how to set them. In general graphical 
> applications on OS X does not care about what you do in your .bashrc 
> or .bash_profile, period. But you have still managed to kind of screw 
> things up :). And whatever you do in your .bashrc or .bash_profile 
> won't have any effect on R.app because it does not care about these 
> files (so you may answer, how come that # open -a R.app ... worked? 
> Well, that is because you launched R from inside Terminal, and in that 
> case it inherits stuff from Terminal).
>
> So what are the options for what you could have done
> 1) You have created an environment.plist variable inside inside 
> ~/.MacOS like described in the following note:
>   http://developer.apple.com/qa/qa2001/qa1067.html
> In order to check for this you could do something like
>   # find ~/ -iname "environment.plist"
> (this will take a while)

I've done it. I hasn't effect on the PATH. I forgot to delete it. I 
deleted it now.

GMXUX-Ricardo-Rodriguez:.MacOSX rrodriguez$ cat environment.plist
<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE plist PUBLIC "-//Apple//DTD PLIST 1.0//EN" 
"http://www.apple.com/DTDs/PropertyList-1.0.dtd">
<plist version="1.0">
<dict>
    <key>M2</key>
    <string>/usr/local/apache-maven/apache-maven-2.0.9/bin</string>
    <key>M2_HOME</key>
    <string>/usr/local/apache-maven/apache-maven-2.0.9</string>
    <key>MAVEN_OPTS</key>
    <string>-Xms256m -Xmx512m</string>
    <key>PATH</key>
    <string>$M2:$PATH</string>
</dict>
</plist>
GMXUX-Ricardo-Rodriguez:.MacOSX rrodriguez$

>
> 2) You have messed with your system wide settings in /etc. You could 
> look for the M2 problem you have by doing
>   # cd /etc
>   #grep -R M2:

Yes, I've done this as well. This was the .bashrc I was speaking about 
in my previous messages.
>
> 3) You have played with the R installation (unlikely)

Fortunately I've had no time to screw up my R installation.
>
> If you are truly desperate, you could execute the grep command from /, 
> but that will take ages.
>
> So once you have located it, what is your fix?
>
> 0) delete or restore the file you located above
> 1) keep everything in .profile instead of .bashrc and .bash_profile
> 2) You may have to log out and log in again.
> 3) If you really want to use your apache-maven PATH in R, do the 
> following: create a file called ~/.Rprofile and put the following in it
> Sys.putenv(PATH=SOMETHING)
> Thats is probably the best long term solution.

I don't to use the apache-maven PATH in R. This problem arises when 
trying to install a packages and R was not able to find tar.

Now that I have:

1. deleted ~/.MacOSX/environment.plist
2. restored the original /etc/bashrc script
3. created a ~/.profile script with the following content that allow me 
to have access to the Maven release I do need:

# Maven Settings
export M2_HOME=/usr/local/apache-maven/apache-maven-2.1.0-M1
export M2=$M2_HOME/bin
export PATH=$M2:$PATH
export MAVEN_OPTS=-Xmx600m

In spite of this, I keep getting this in R:

*****
 > Sys.getenv("PATH")
                      PATH
"$M2:$PATH:/usr/local/bin"
 >
*****

If I launch R from a terminal all runs smoothly.

The ~/.Rprofile didn't work. Here the content of the ~/.Rprofile file:

Sys.putenv(PATH=/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/usr/X11/bin:/usr/local/bin)


I am running sudo grep $M2:$PATH: -R  * .* in the root directory now. I 
will keep this thread posted. I am not able to figure out where is the 
problem. Thank you so much for your help.

Best,

Ricardo

-- 
Ricardo Rodríguez
Your XEN ICT Team