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

[Andrew Noble]

Today, I downloaded the most recent binary for R.app. I'm running on
MacOSX 10.4.11.

Downloading packages fail. I've tried it at the command line and
using the "Packages & Data" menu. In both cases, trying to
downloaded the "emdbook" binary, I get the following error.

-----
Warning in install.packages("emdbook") :
argument 'lib' is missing: using '/Users/andrewnoble/Library/R/2.7/library'
trying URL
'http://cran.mirrors.hoobly.com/bin/macosx/universal/contrib/2.7/emdbook_1.1.1.tgz'
Content type 'application/x-tgz' length 126320 bytes (123 Kb)
opened URL
==================================================
downloaded 123 Kb

/bin/sh: line 1: tar: command not found
Error in sprintf(gettext(fmt, domain = domain), ...) :
argument is missing, with no default---
-----

Any help would be greatly appreciated. Thank you!
Andrew

[Ben Bolker]

This is my package, but I don't think there's anything wrong with
the package (the check summary on CRAN says it's OK). Does this happen
with all packages? Have you tried a different mirror? (123 K seems
like a reasonable size for this package).

On the other hand, the specific error message says the problem
is that R can't find the "tar" command -- is it in your path?

Ben Bolker (not a Mac person)

Post by Andrew Noble
Today, I downloaded the most recent binary for R.app. I'm running on
MacOSX 10.4.11.
Downloading packages fail. I've tried it at the command line and using
the "Packages & Data" menu. In both cases, trying to downloaded the
"emdbook" binary, I get the following error.
-----
argument 'lib' is missing: using
'/Users/andrewnoble/Library/R/2.7/library'
trying URL
'http://cran.mirrors.hoobly.com/bin/macosx/universal/contrib/2.7/emdbook_1.1.1.tgz'
Content type 'application/x-tgz' length 126320 bytes (123 Kb)
opened URL
==================================================
downloaded 123 Kb
/bin/sh: line 1: tar: command not found
argument is missing, with no default---
-----
Any help would be greatly appreciated. Thank you!
Andrew
_______________________________________________
R-SIG-Mac mailing list
https://stat.ethz.ch/mailman/listinfo/r-sig-mac

[[Ricardo Rodriguez] Your XEN ICT Team]

Hi Ben, Andrew,

I am facing the same problem (R 2.7.2 running on Mac OS X 10.5.5 Build
9F33; MacBook Pro Intel Core 2 Duo, 2.5 GHz); tar is in the path...

GMXUX-Ricardo-Rodriguez:~ rrodriguez$ tar
tar: You must specify one of the `-Acdtrux' options
Try `tar --help' or `tar --usage' for more information.

Here an error. This installation usually does work...

*****

install.packages("reshape")

also installing the dependency 'plyr'

trying URL
'http://cran.us.r-project.org/bin/macosx/universal/contrib/2.7/plyr_0.1.tgz'
Content type 'application/x-gzip' length 544654 bytes (531 Kb)
opened URL
==================================================
downloaded 531 Kb

trying URL
'http://cran.us.r-project.org/bin/macosx/universal/contrib/2.7/reshape_0.8.1.tgz'
Content type 'application/x-gzip' length 94353 bytes (92 Kb)
opened URL
==================================================
downloaded 92 Kb

/bin/sh: tar: command not found
Error in sprintf(gettext(fmt, domain = domain), ...) :
argument is missing, with no default
*****

Any idea, please? Thanks!

Greetings,

Ricardo

This is my package, but I don't think there's anything wrong with
the package (the check summary on CRAN says it's OK). Does this happen
with all packages? Have you tried a different mirror? (123 K seems
like a reasonable size for this package).
On the other hand, the specific error message says the problem
is that R can't find the "tar" command -- is it in your path?
Ben Bolker (not a Mac person)

[Ben Bolker]

Post by [Ricardo Rodriguez] Your XEN ICT Team
Hi Ben, Andrew,
I am facing the same problem (R 2.7.2 running on Mac OS X 10.5.5 Build
9F33; MacBook Pro Intel Core 2 Duo, 2.5 GHz); tar is in the path...
GMXUX-Ricardo-Rodriguez:~ rrodriguez$ tar
tar: You must specify one of the `-Acdtrux' options
Try `tar --help' or `tar --usage' for more information.
Here an error. This installation usually does work...
*****

install.packages("reshape")

also installing the dependency 'plyr'
trying URL
'http://cran.us.r-project.org/bin/macosx/universal/contrib/2.7/plyr_0.1.tgz'
Content type 'application/x-gzip' length 544654 bytes (531 Kb)
opened URL
==================================================
downloaded 531 Kb
trying URL
'http://cran.us.r-project.org/bin/macosx/universal/contrib/2.7/reshape_0.8.1.tgz'
Content type 'application/x-gzip' length 94353 bytes (92 Kb)
opened URL
==================================================
downloaded 92 Kb
/bin/sh: tar: command not found
argument is missing, with no default
*****
Any idea, please? Thanks!
Greetings,
Ricardo

This is my package, but I don't think there's anything wrong with
the package (the check summary on CRAN says it's OK). Does this happen
with all packages? Have you tried a different mirror? (123 K seems
like a reasonable size for this package).
On the other hand, the specific error message says the problem
is that R can't find the "tar" command -- is it in your path?
Ben Bolker (not a Mac person)

Since this is not my package (and I'm still not a Mac user),
I really have no idea ... I never heard back from Andrew, don't
know if he found a solution or if the problem went away by itself

good luck
Ben

[Kasper Daniel Hansen]

Clearly tar is not in the PATH. Your PATH variable can be different
from application to application and in this case however you have
started R (GUI?), tar is not being picked up. And which tar are you
using? Xcode, FInk, Macports.

Kasper

Post by Ben Bolker

Post by [Ricardo Rodriguez] Your XEN ICT Team
Hi Ben, Andrew,
I am facing the same problem (R 2.7.2 running on Mac OS X 10.5.5 Build
9F33; MacBook Pro Intel Core 2 Duo, 2.5 GHz); tar is in the path...
GMXUX-Ricardo-Rodriguez:~ rrodriguez$ tar
tar: You must specify one of the `-Acdtrux' options
Try `tar --help' or `tar --usage' for more information.
Here an error. This installation usually does work...
*****

install.packages("reshape")

also installing the dependency 'plyr'
trying URL
'http://cran.us.r-project.org/bin/macosx/universal/contrib/2.7/plyr_0.1.tgz'
Content type 'application/x-gzip' length 544654 bytes (531 Kb)
opened URL
==================================================
downloaded 531 Kb
trying URL
'http://cran.us.r-project.org/bin/macosx/universal/contrib/2.7/reshape_0.8.1.tgz'
Content type 'application/x-gzip' length 94353 bytes (92 Kb)
opened URL
==================================================
downloaded 92 Kb
/bin/sh: tar: command not found
argument is missing, with no default
*****
Any idea, please? Thanks!
Greetings,
Ricardo

This is my package, but I don't think there's anything wrong with
the package (the check summary on CRAN says it's OK). Does this happen
with all packages? Have you tried a different mirror? (123 K seems
like a reasonable size for this package).
On the other hand, the specific error message says the problem
is that R can't find the "tar" command -- is it in your path?
Ben Bolker (not a Mac person)

Since this is not my package (and I'm still not a Mac user),
I really have no idea ... I never heard back from Andrew, don't
know if he found a solution or if the problem went away by itself
good luck
Ben
_______________________________________________
R-SIG-Mac mailing list
https://stat.ethz.ch/mailman/listinfo/r-sig-mac

[[Ricardo Rodriguez] Your XEN ICT Team]

Hi Kasper,

Post by Kasper Daniel Hansen
Clearly tar is not in the PATH. Your PATH variable can be different
from application to application and in this case however you have
started R (GUI?), tar is not being picked up. And which tar are you
using? Xcode, FInk, Macports.

I must recognize that to set PATH keeps being a mystery for me.

How could I print out the PATH R is using? In a terminal:

sh-3.2# echo $PATH
/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/usr/X11/bin:/usr/local/apache-maven/apache-maven-2.1.0-M1/bin
sh-3.2#

sh-3.2# find . -name tar
./Applications/Fetch.app/Contents/Frameworks/StuffItCore.framework/Versions/A/Plug-Ins/tar.bundle/Contents/MacOS/tar
./Applications/StuffIt 11/StuffIt
Expander.app/Contents/Frameworks/StuffItCore.framework/Versions/A/Plug-Ins/tar.bundle/Contents/MacOS/tar
./System/Library/Tcl/tcllib1.8/tar
./usr/bin/tar
./usr/share/ant/docs/javadocs/org/apache/tools/tar

No GUI, just R Console.

Thanks for your help,

Ricardo

[Kasper Daniel Hansen]

You can print and set environment variables from within R by doing

Sys.getenv("PATH")
Sys.setenv(PATH = "SOMETHING")

When you start R from the command line it should inherit the PATH
(although that depends on how you set it - and note that it looks as
if you are using SH and not say BASH).

Since you are installing a binary from Bioconductor under something I
guess is the CRAN binary (I cannot be 100% with the info you are
providing), it really should work. You should not need to have the
DevTools installed.

Kasper

Post by [Ricardo Rodriguez] Your XEN ICT Team
Hi Kasper,

Post by Kasper Daniel Hansen
Clearly tar is not in the PATH. Your PATH variable can be different
from application to application and in this case however you have
started R (GUI?), tar is not being picked up. And which tar are you
using? Xcode, FInk, Macports.

I must recognize that to set PATH keeps being a mystery for me.
sh-3.2# echo $PATH
/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/usr/X11/bin:/usr/local/
apache-maven/apache-maven-2.1.0-M1/bin
sh-3.2#
sh-3.2# find . -name tar
./Applications/Fetch.app/Contents/Frameworks/StuffItCore.framework/
Versions/A/Plug-Ins/tar.bundle/Contents/MacOS/tar
./Applications/StuffIt 11/StuffIt Expander.app/Contents/Frameworks/
StuffItCore.framework/Versions/A/Plug-Ins/tar.bundle/Contents/MacOS/
tar
./System/Library/Tcl/tcllib1.8/tar
./usr/bin/tar
./usr/share/ant/docs/javadocs/org/apache/tools/tar
No GUI, just R Console.
Thanks for your help,
Ricardo
--
Ricardo Rodríguez
Your XEN ICT Team

[[Ricardo Rodriguez] Your XEN ICT Team]

Thanks Kasper,

Post by Kasper Daniel Hansen
You can print and set environment variables from within R by doing
Sys.getenv("PATH")
Sys.setenv(PATH = "SOMETHING")
When you start R from the command line it should inherit the PATH
(although that depends on how you set it - and note that it looks as
if you are using SH and not say BASH).

It is a bit weird to receive a message concerning sh. As far as I know,
I am using BASH. In fact, I have recently modified /etc/bashrc to
include some Maven variables. I now reads...

*****
sh-3.2# cat bashrc
# System-wide .bashrc file for interactive bash(1) shells.
if [ -z "$PS1" ]; then
return
fi

PS1='\h:\W \u\$ '
# Make bash check its window size after a process completes
shopt -s checkwinsize

# Maven Settings
export M2_HOME=/usr/local/apache-maven/apache-maven-2.1.0-M1
export M2=$M2_HOME/bin
export PATH=$PATH:$M2
export MAVEN_OPTS=-Xmx600m
sh-3.2#

*****
sh-3.2# echo $PATH
/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/usr/X11/bin:/usr/local/apache-maven/apache-maven-2.1.0-M1/bin
*****

[Kasper Daniel Hansen]

Post by [Ricardo Rodriguez] Your XEN ICT Team
Thanks Kasper,

Post by Kasper Daniel Hansen
You can print and set environment variables from within R by doing
Sys.getenv("PATH")
Sys.setenv(PATH = "SOMETHING")
When you start R from the command line it should inherit the PATH
(although that depends on how you set it - and note that it looks
as if you are using SH and not say BASH).

It is a bit weird to receive a message concerning sh. As far as I
know, I am using BASH. In fact, I have recently modified /etc/bashrc
to include some Maven variables. I now reads...
*****
sh-3.2# cat bashrc
# System-wide .bashrc file for interactive bash(1) shells.
if [ -z "$PS1" ]; then
return
fi
PS1='\h:\W \u\$ '
# Make bash check its window size after a process completes
shopt -s checkwinsize
# Maven Settings
export M2_HOME=/usr/local/apache-maven/apache-maven-2.1.0-M1
export M2=$M2_HOME/bin
export PATH=$PATH:$M2
export MAVEN_OPTS=-Xmx600m
sh-3.2#
*****
sh-3.2# echo $PATH
/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/usr/X11/bin:/usr/local/
apache-maven/apache-maven-2.1.0-M1/bin
*****
*****

Post by Kasper Daniel Hansen
Sys.getenv("PATH")

PATH
"$M2:$PATH:/usr/local/bin"
*****

Ok, this is clearly wrong. As you can see in your output, this PATH
does not contain /usr/bin where tar is. In my case I get
R> Sys.getenv("PATH")
PATH
"/Users/khansen/Bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/usr/
texbin:/usr/X11/bin"

This looks like a failed attempt at setting the PATH somewhere. What
you see is where similar to the syntax you use in your .bashrc file
but with stuff jumbled a bit. So my wild guess is that you have tried
setting your PATH somewhere else and that this gets picked up. Do you
have a .profile file. In fact I would do something like

# cd
# grep PATH * .*
(star space dot star), to see if you are playing with the PATH
somewhere else.

Are you on a multi-user system? (Could your sys admin have played with
site-settings?)

My comment about BASH and SH was just based on your prompt. It is
normal that R uses SH for its purposes, that is pretty standard.

The reason why people are talking about DevTools is that this is
needed in order to compile from source. And a lot of tools are found
in the DevTools. And most of us cannot remember if tar came from
DevTools or with a standard Mac OS X. But I am pretty sure it is part
of standard OS X.

Kasper

Post by [Ricardo Rodriguez] Your XEN ICT Team
From your comments, I've done...

Post by Kasper Daniel Hansen
Sys.setenv(PATH = "$M2:$PATH:/usr/bin:/usr/local/bin")

And now the installation works smoothly...
*****

Post by Kasper Daniel Hansen
install.packages("zoo",repos="http://R-Forge.R-project.org")

trying URL 'http://R-Forge.R-project.org/bin/macosx/universal/contrib/2.7/zoo_1.6-0.tgz'
Content type 'application/x-gzip' length 651045 bytes (635 Kb)
opened URL
==================================================
downloaded 635 Kb
The downloaded packages are in
/var/folders/6h/6hyderV4GAmSiGLPDwB16k+++TI/-Tmp-//Rtmp8eeprZ/
downloaded_packages

Post by Kasper Daniel Hansen
require(zoo)

Loading required package: zoo
*****
So, I think the question could be, is R correctly inheriting PATH?
It seems that it is not able to understand the syntax $M2:$PATH:/usr/
local/bin

Post by Kasper Daniel Hansen
Since you are installing a binary from Bioconductor under something
I guess is the CRAN binary (I cannot be 100% with the info you are
providing), it really should work. You should not need to have the
DevTools installed.

I required DevTools for several buildings here not related with R.
Thanks for your help!
Ricardo
--
Ricardo Rodríguez
Your XEN ICT Team

[[Ricardo Rodriguez] Your XEN ICT Team]

Hi Kasper

Post by Kasper Daniel Hansen
Ok, this is clearly wrong. As you can see in your output, this PATH
does not contain /usr/bin where tar is. In my case I get
R> Sys.getenv("PATH")
PATH
"/Users/khansen/Bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/usr/texbin:/usr/X11/bin"
This looks like a failed attempt at setting the PATH somewhere. What
you see is where similar to the syntax you use in your .bashrc file
but with stuff jumbled a bit. So my wild guess is that you have tried
setting your PATH somewhere else and that this gets picked up. Do you
have a .profile file. In fact I would do something like
# cd
# grep PATH * .*
(star space dot star), to see if you are playing with the PATH
somewhere else.

Here the output of this command...

GMXUX-Ricardo-Rodriguez:~ rrodriguez$ sudo grep PATH * .*
Password:
.Rhistory:Sys.getenv("PATH")
.bash_history:echo $PATH
.bash_history:echo $PATH
.bash_history:echo $PATH
.bash_history:echo $PATH
.bash_history:echo $PATH
.bash_history:echo $PATH
.bash_history:echo $PATH
.bash_history:echoc$PATH
.bash_history:$echo PATH
.bash_history:echo $PATH
.bash_history:echo $PATH
.bash_history:echo $PATH
.bash_profile.bak:export PATH=$PATH:$M2
.viminfo: export PATH=$PATH:$M2
.viminfo: export PATH=$PATH:$M2
GMXUX-Ricardo-Rodriguez:~ rrodriguez$

In fact I realized that I was using the wrong order of variables! The
right one is $M2:$PATH. But this has nothing to do with the issue we are
dealing with now.

Could this .bash_profile.bak be the problem? I have left this file there
while trying to set some variables I need to work with Maven in
/etc/.bashrc.

Post by Kasper Daniel Hansen
Are you on a multi-user system? (Could your sys admin have played with
site-settings?)

I am using a brand new MacBook Pro laptop. I am the only user and
administrator.

Post by Kasper Daniel Hansen
My comment about BASH and SH was just based on your prompt. It is
normal that R uses SH for its purposes, that is pretty standard.

I think years ago Mac OS X used tcsh as default shell. But today bash is
the default one. The "funny" thing is that sudo su apparently switch to
sh. I can not say much on this. Just that your comment called my
attention on this.

Post by Kasper Daniel Hansen
The reason why people are talking about DevTools is that this is
needed in order to compile from source. And a lot of tools are found
in the DevTools. And most of us cannot remember if tar came from
DevTools or with a standard Mac OS X. But I am pretty sure it is part
of standard OS X.

I got it! tar is part of the standard OS X distribution as ./usr/bin/tar

Thanks for your help!

Ricardo

[Kasper Daniel Hansen]

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.

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?

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)

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:

3) You have played with the R installation (unlikely)

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.

Kasper

Post by [Ricardo Rodriguez] Your XEN ICT Team
Hi Kasper

Post by Kasper Daniel Hansen
Ok, this is clearly wrong. As you can see in your output, this PATH
does not contain /usr/bin where tar is. In my case I get
R> Sys.getenv("PATH")
PATH
"/Users/khansen/Bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/
usr/texbin:/usr/X11/bin"
This looks like a failed attempt at setting the PATH somewhere.
What you see is where similar to the syntax you use in your .bashrc
file but with stuff jumbled a bit. So my wild guess is that you
have tried setting your PATH somewhere else and that this gets
picked up. Do you have a .profile file. In fact I would do
something like
# cd
# grep PATH * .*
(star space dot star), to see if you are playing with the PATH
somewhere else.

Here the output of this command...
GMXUX-Ricardo-Rodriguez:~ rrodriguez$ sudo grep PATH * .*
.Rhistory:Sys.getenv("PATH")
.bash_history:echo $PATH
.bash_history:echo $PATH
.bash_history:echo $PATH
.bash_history:echo $PATH
.bash_history:echo $PATH
.bash_history:echo $PATH
.bash_history:echo $PATH
.bash_history:echoc$PATH
.bash_history:$echo PATH
.bash_history:echo $PATH
.bash_history:echo $PATH
.bash_history:echo $PATH
.bash_profile.bak:export PATH=$PATH:$M2
.viminfo: export PATH=$PATH:$M2
.viminfo: export PATH=$PATH:$M2
GMXUX-Ricardo-Rodriguez:~ rrodriguez$
In fact I realized that I was using the wrong order of variables!
The right one is $M2:$PATH. But this has nothing to do with the
issue we are dealing with now.
Could this .bash_profile.bak be the problem? I have left this file
there while trying to set some variables I need to work with Maven
in /etc/.bashrc.

Post by Kasper Daniel Hansen
Are you on a multi-user system? (Could your sys admin have played
with site-settings?)

I am using a brand new MacBook Pro laptop. I am the only user and
administrator.

Post by Kasper Daniel Hansen
My comment about BASH and SH was just based on your prompt. It is
normal that R uses SH for its purposes, that is pretty standard.

I think years ago Mac OS X used tcsh as default shell. But today
bash is the default one. The "funny" thing is that sudo su
apparently switch to sh. I can not say much on this. Just that your
comment called my attention on this.

Post by Kasper Daniel Hansen
The reason why people are talking about DevTools is that this is
needed in order to compile from source. And a lot of tools are
found in the DevTools. And most of us cannot remember if tar came
from DevTools or with a standard Mac OS X. But I am pretty sure it
is part of standard OS X.

I got it! tar is part of the standard OS X distribution as ./usr/bin/
tar
Thanks for your help!
Ricardo
--
Ricardo Rodríguez
Your XEN ICT Team

[[Ricardo Rodriguez] Your XEN ICT Team]

Thanks for your patience!

Post by Kasper Daniel Hansen
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.

Post by Kasper Daniel Hansen
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.

Post by Kasper Daniel Hansen
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
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$

Post by Kasper Daniel Hansen
2) You have messed with your system wide settings in /etc. You could
look for the M2 problem you have by doing
# cd /etc

Yes, I've done this as well. This was the .bashrc I was speaking about
in my previous messages.

Post by Kasper Daniel Hansen
3) You have played with the R installation (unlikely)

Fortunately I've had no time to screw up my R installation.

Post by Kasper Daniel Hansen
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:

*****

Post by Kasper Daniel Hansen
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 Rodriguez] Your XEN ICT Team]

Post by [Ricardo Rodriguez] Your XEN ICT Team
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.

This is what I get...

GMXUX-Ricardo-Rodriguez:~ rrodriguez$ sudo grep $M2:$PATH: -R * .*
grep(784) malloc: *** mmap(size=1241518080) failed (error code=12)
*** error: can't allocate region
*** set a breakpoint in malloc_error_break to debug
grep: memory exhausted
GMXUX-Ricardo-Rodriguez:~ rrodriguez$

Am I doing anything (else) wrong? Thanks.

Thanks,

Ricardo

[Stefan Evert]

Post by [Ricardo Rodriguez] Your XEN ICT Team
I've modified the system wied .bashrc in /etc. Note that I've do cd,
not cd / previous to grep. Look now...

If I understand the Leopard architecture correctly, you don't want to
mess around with /etc/bashrc to set additional paths. Rather, add a
new file to /etc/paths.d/ which contains _only_ the extra search path.
This should be included automatically in $PATH when you start a new
Terminal session, but won't work for R.app either.

Post by [Ricardo Rodriguez] Your XEN ICT Team
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$

This looks pretty wrong to me, although I'm not really familiar with
Apple's property lists. You seem to assume that property lists
understand bash's $XXX notation for variable interpolation, which I'm
quite sure won't work. I suspect that you have to insert the FULL,
EXPANDED path list here, as printed when you type "echo $PATH" in the
Terminal.

Hope this helps,
Stefan

[Charilaos Skiadas]

Post by Stefan Evert

Post by [Ricardo Rodriguez] Your XEN ICT Team
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$

This looks pretty wrong to me, although I'm not really familiar
with Apple's property lists. You seem to assume that property lists
understand bash's $XXX notation for variable interpolation, which
I'm quite sure won't work. I suspect that you have to insert the
FULL, EXPANDED path list here, as printed when you type "echo
$PATH" in the Terminal.

You are correct Stefan, the $PATH would not expand itself, which is
why Ricardo saw seeing what he was seeing as a path within R.app.
Ricardo, you should avoid using the environment.plist file. After you
delete it, which I think you have done already, you MUST restart the
system for the changes to take effect. Your systems should be back to
normal then, and R.app should be able to find /usr/bin/tar just fine
on its own after that.

Post by Stefan Evert
Hope this helps,
Stefan

Haris Skiadas
Department of Mathematics and Computer Science
Hanover College

[[Ricardo Rodriguez] Your XEN ICT Team]

Post by Charilaos Skiadas
You are correct Stefan, the $PATH would not expand itself, which is
why Ricardo saw seeing what he was seeing as a path within R.app.
Ricardo, you should avoid using the environment.plist file. After you
delete it, which I think you have done already, you MUST restart the
system for the changes to take effect. Your systems should be back to
normal then, and R.app should be able to find /usr/bin/tar just fine
on its own after that.

Thanks Haris! But the restart seems to have no effect on these values as
posted before. Please, any idea?

Greetings,

Ricardo

[[Ricardo Rodriguez] Your XEN ICT Team]

Hi,

Post by Stefan Evert
If I understand the Leopard architecture correctly, you don't want to
mess around with /etc/bashrc to set additional paths. Rather, add a
new file to /etc/paths.d/ which contains _only_ the extra search path.
This should be included automatically in $PATH when you start a new
Terminal session, but won't work for R.app either.

This works fine, thank you. Please, is it possible to modify the
position where the new path will be inserted in $PATH? It is added at
the end of the string by default. I would like to insert in at the
beginning.

Post by Stefan Evert

Post by [Ricardo Rodriguez] Your XEN ICT Team
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$

This looks pretty wrong to me, although I'm not really familiar with
Apple's property lists. You seem to assume that property lists
understand bash's $XXX notation for variable interpolation, which I'm
quite sure won't work. I suspect that you have to insert the FULL,
EXPANDED path list here, as printed when you type "echo $PATH" in the
Terminal.

This makes sense. Thanks for the tip. What I am not able to work out now
is to know how and why R.app is picking up this valeu for PATH...

Post by Stefan Evert
Sys.getenv("PATH")

PATH
"$M2:$PATH:/usr/local/bin"
I am not able to figure out where am I setting this value for PATH. M2,
M2_HOME and MAVEN_OPTS, the variable I've been dealing with, are not set
in the shell...

GMXUX-Ricardo-Rodriguez:~ rrodriguez$ echo $M2

GMXUX-Ricardo-Rodriguez:~ rrodriguez$ echo $M2_HOME

GMXUX-Ricardo-Rodriguez:~ rrodriguez$ echo $MAVEN_OPTS


But all three are set in R!

Post by Stefan Evert
Sys.getenv("PATH")

PATH
"$M2:$PATH:/usr/local/bin"

Post by Stefan Evert
Sys.getenv("M2")

M2
"/usr/local/apache-maven/apache-maven-2.0.9/bin"

Post by Stefan Evert
Sys.getenv("M2_HOME")

M2_HOME
"/usr/local/apache-maven/apache-maven-2.0.9"

Post by Stefan Evert
Sys.getenv("MAVEN_OPTS")

MAVEN_OPTS
"-Xms256m -Xmx512m"


.Rprofile works fine and I am able to control variables with this file
but, I there is not .Rprofile, where could am I be setting these
variables? Does .RData store these values?


I would like to understand where am I wrong. Thanks for your help!

Ricardo

[Stefan Evert]

Post by [Ricardo Rodriguez] Your XEN ICT Team

Post by Stefan Evert
If I understand the Leopard architecture correctly, you don't want
to mess around with /etc/bashrc to set additional paths. Rather,
add a new file to /etc/paths.d/ which contains _only_ the extra
search path. This should be included automatically in $PATH when
you start a new Terminal session, but won't work for R.app either.

This works fine, thank you. Please, is it possible to modify the
position where the new path will be inserted in $PATH? It is added
at the end of the string by default. I would like to insert in at
the beginning.

Good question, I'd like to know this myself!

Any Mac experts out there who can help us? Are the extra paths in /etc/
paths.d/ included alphabetically (by file name)? I suppose it's
intentional that they go _after_ the standard system directories,
otherwise you might mess up your OS X installation pretty badly ...

Post by [Ricardo Rodriguez] Your XEN ICT Team

Post by Stefan Evert

Post by [Ricardo Rodriguez] Your XEN ICT Team
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$

This looks pretty wrong to me, although I'm not really familiar
with Apple's property lists. You seem to assume that property lists
understand bash's $XXX notation for variable interpolation, which
I'm quite sure won't work. I suspect that you have to insert the
FULL, EXPANDED path list here, as printed when you type "echo
$PATH" in the Terminal.

This makes sense. Thanks for the tip. What I am not able to work out
now is to know how and why R.app is picking up this valeu for PATH...

Post by Stefan Evert
Sys.getenv("PATH")

PATH
"$M2:$PATH:/usr/local/bin"

It's obvious where you get the $M2:$PATH from -- that's what you've
specified in environment.plist. I don't know where /usr/local/bin has
been added, though. Perhaps something that R does automatically so you
always have access to the GNU Fortran installed with R?

Post by [Ricardo Rodriguez] Your XEN ICT Team
I am not able to figure out where am I setting this value for PATH.
M2, M2_HOME and MAVEN_OPTS, the variable I've been dealing with, are
not set in the shell...

Well, they're set in your environment.plist file above. When you start
R.app, it gets its environment variables from this property list,
while the Terminal uses the "normal" .bashrc-based mechanism and seem
to ignore environment.plist.


Best,
Stefan

[[Ricardo Rodriguez] Your XEN ICT Team]

Post by Stefan Evert
It's obvious where you get the $M2:$PATH from -- that's what you've
specified in environment.plist. I don't know where /usr/local/bin has
been added, though. Perhaps something that R does automatically so you
always have access to the GNU Fortran installed with R?

You are completely right! I "thought" that I deleted this
environment.plist in my ~/.MacOSX folder. I didn't! Sorry for the noise!
Once I delete this file and restarted R (to restart the box/session was
not required), the PATH in R has been set as expected.

Thanks for your help. Let's see if others can help us with the paths.d
related question!

Cheers,

Ricardo

[Kasper Daniel Hansen]

Ok, I guess I was being a bit unhelpful. You are trying to install a
binary from Bioconductor. This should work out of the box. What
version of R are you using. If you are doing 64bit computing you need
to install from source. Of course, that does not change that tar seems
to be missing which is a mystery. But my guess is that you have done
something non-standard since for most people it works out of the box.

Kasper

Post by Ben Bolker

Post by [Ricardo Rodriguez] Your XEN ICT Team
Hi Ben, Andrew,
I am facing the same problem (R 2.7.2 running on Mac OS X 10.5.5 Build
9F33; MacBook Pro Intel Core 2 Duo, 2.5 GHz); tar is in the path...
GMXUX-Ricardo-Rodriguez:~ rrodriguez$ tar
tar: You must specify one of the `-Acdtrux' options
Try `tar --help' or `tar --usage' for more information.
Here an error. This installation usually does work...
*****

install.packages("reshape")

also installing the dependency 'plyr'
trying URL
'http://cran.us.r-project.org/bin/macosx/universal/contrib/2.7/plyr_0.1.tgz'
Content type 'application/x-gzip' length 544654 bytes (531 Kb)
opened URL
==================================================
downloaded 531 Kb
trying URL
'http://cran.us.r-project.org/bin/macosx/universal/contrib/2.7/reshape_0.8.1.tgz'
Content type 'application/x-gzip' length 94353 bytes (92 Kb)
opened URL
==================================================
downloaded 92 Kb
/bin/sh: tar: command not found
argument is missing, with no default
*****
Any idea, please? Thanks!
Greetings,
Ricardo

This is my package, but I don't think there's anything wrong with
the package (the check summary on CRAN says it's OK). Does this happen
with all packages? Have you tried a different mirror? (123 K seems
like a reasonable size for this package).
On the other hand, the specific error message says the problem
is that R can't find the "tar" command -- is it in your path?
Ben Bolker (not a Mac person)

Since this is not my package (and I'm still not a Mac user),
I really have no idea ... I never heard back from Andrew, don't
know if he found a solution or if the problem went away by itself
good luck
Ben
_______________________________________________
R-SIG-Mac mailing list
https://stat.ethz.ch/mailman/listinfo/r-sig-mac

[[Ricardo Rodriguez] Your XEN ICT Team]

Post by Kasper Daniel Hansen
Ok, I guess I was being a bit unhelpful. You are trying to install a
binary from Bioconductor. This should work out of the box. What
version of R are you using. If you are doing 64bit computing you need
to install from source. Of course, that does not change that tar seems
to be missing which is a mystery. But my guess is that you have done
something non-standard since for most people it works out of the box.
version

_
platform i386-apple-darwin8.11.1
arch i386
os darwin8.11.1
system i386, darwin8.11.1
status
major 2
minor 7.2
year 2008
month 08
day 25
svn rev 46428
language R
version.string R version 2.7.2 (2008-08-25)
I am working in a MacBook Pro, Mac OS X 10.5.5 Build 9F33

Model Name: MacBook Pro
Model Identifier: MacBookPro4,1
Processor Name: Intel Core 2 Duo
Processor Speed: 2.5 GHz
Number Of Processors: 1
Total Number Of Cores: 2
L2 Cache: 6 MB
Memory: 4 GB
Bus Speed: 800 MHz
Boot ROM Version: MBP41.00C1.B03
SMC Version: 1.27f1
Serial Number: W88251TWYJY
Sudden Motion Sensor:
State: Enabled

Hope this gives you some clue.

[[Ricardo Rodriguez] Your XEN ICT Team]

Hi Phil,

Ricarcdo -
Do you have the Developer Tools installed on your Mac?

Yeap! I have them. And when I installed reshape, weren't installed.
Please, how could I fix my installation? What does DevTools modify that
affects install.packages functioning?

Thanks!

Ricardo

[hadley wickham]

Ricardo,

Have you tried reinstalling the latest version of R? That would seem
to be the first step to take.

Hadley

On Fri, Oct 3, 2008 at 5:08 PM, [Ricardo Rodriguez] Your XEN ICT Team

Post by [Ricardo Rodriguez] Your XEN ICT Team
Hi Phil,

Ricarcdo -
Do you have the Developer Tools installed on your Mac?

Yeap! I have them. And when I installed reshape, weren't installed. Please,
how could I fix my installation? What does DevTools modify that affects
install.packages functioning?
Thanks!
Ricardo
--
Ricardo Rodríguez
Your XEN ICT Team
_______________________________________________
R-SIG-Mac mailing list
https://stat.ethz.ch/mailman/listinfo/r-sig-mac

[[Ricardo Rodriguez] Your XEN ICT Team]

Post by hadley wickham
Ricardo,
Have you tried reinstalling the latest version of R? That would seem
to be the first step to take.
Hadley

Reinstallationg didn't help. Thanks!

[[Ricardo Rodriguez] Your XEN ICT Team]

Hi Phil,

Ricardo -
I was just responding to the subject line, i.e. tar not found.
The Developer Tools contain the compilers and other utilities that
are used to build packages from source code. They don't have any
affect on installation of pre-compiled (binary) packages.
- Phil

I'm afraid I don't understand your answer.Why to have or not to have
DevTools installed does matter here? Thanks!

[Steve Revilak]

Date: Fri, 03 Oct 2008 23:08:16 +0200
Subject: Re: [R-SIG-Mac] /bin/sh: tar: command not found
Hi Ben, Andrew,
I am facing the same problem (R 2.7.2 running on Mac OS X 10.5.5 Build 9F33;
MacBook Pro Intel Core 2 Duo, 2.5 GHz); tar is in the path...
GMXUX-Ricardo-Rodriguez:~ rrodriguez$ tar
tar: You must specify one of the `-Acdtrux' options
Try `tar --help' or `tar --usage' for more information.

[...]

Here an error. This installation usually does work...

[...]

==================================================
downloaded 92 Kb
/bin/sh: tar: command not found

It seems as though tar is in bash's PATH, but not R's PATH. How are
you starting R?

If you're starting R by clicking R.app, you might try running
"open /Applications/R.app" from a terminal instead. This way, open inherits
PATH from bash, and R.app will inherit PATH from open.

[[Ricardo Rodriguez] Your XEN ICT Team]

Hi Steve, thanks for your answer.

Post by Steve Revilak
It seems as though tar is in bash's PATH, but not R's PATH. How are
you starting R?
If you're starting R by clicking R.app, you might try running "open
/Applications/R.app" from a terminal instead. This way, open inherits
PATH from bash, and R.app will inherit PATH from open.

I was starting R by clicking the R.app icon. To run "open
/Applications/R.app" did the trick. Thanks.

I've just replied to the last message posted by Kasper. I've been
dealing with PATH to get Maven integrated in my environment. Perhaps
some of this actions has affected the way R get its environment. I can
not explain what is happening here and why there is this difference
between R environments when launched from the terminal or by clicking
the R.app icon. I keep trying.

Thanks.

Ricardo