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[ferret_users] Having trouble setting up Ferret on Mac - can't save ferret_paths to /usr/local
Hello Ferret Users!
I am having some issues installing Ferret on my iMac with Snow Leopard 10.6.2
First off, I installed Fink and then proceeded to follow the directions on the Ferret for Mac OS X instruction page. I am using the older version of Ferret (which is supposed to be good for up to 10.5.4). I'm not too computer savvy and didn't want to/know how to do the binary install for 10.6 and build the system.
According to the instructions provided on the Ferret for Mac OS X page, it would be better to use the tcsh shell, however, I couldn't seem to change the startup shell to tcsh (though I tried numerous time through System Preferences/Account/Advanced Options. etc.), so I am stuck using the bash shell. I didn't seem to have a /usr/local directory so I created one using the instructions on the webpage:
In the unlikely event that /usr/local does not exist, please make it, and give "other" read and execute permissions (in my case, using the bash shell):
sudo bash
mkdir /usr/local
chmod go+rx /usr/local
I then followed the directions to install Ferret:
sudo bash
cd /usr/local
tar zxvf ~/Desktop/ferret.tgz
The Ferret download is now located in /usr/local/ferret
I was trying to fix the ferret_paths file as per the instructions on the bottom of the webpage by using the /usr/local/ferret/bin/ferret_paths_bash_template. I created a .bash_profile and put in the line /usr/local/ferret/bin/ferret_paths in it. However, when I tried to modify the /usr/local/ferret/bin/ferret_paths_bash_template and save it as ferret_paths, it wouldn't let me save it to /usr/local. Apparently I do not have permissions to do that, which is unusual as I am the administrator of my computer. I was trying to modify the template using gedit. Every time I try to save the modified document, I get the message "Could not save the file /usr/local/ferret_paths. You do not have the permissions necessary to save the file. Please check that you typed the location correctly and try again." Recall that this is a message I get in gedit. I am at a loss on how to save this file. I know I can use emacs or something, although when I open that, at the bottom it says "opening directory: permission denied, /Users/lclab/.emacs.d/auto-save-list." And I can't figure out how to save things in emacs and get back to the bash - Terminal.
I downloaded gedit to use to modify the ferret_paths template and simply dragged the gedit icon to the applications folder, which is what I was supposed to do, according to the instructions that I downloaded with gedit. I had been using gedit on a NOAA Mac computer when I originally worked with Ferret (but that one had been set up for me by a really smart computer whiz). When I typed gedit into the Terminal, a window opened and I could access and save files using gedit. On the computer that I am using outside of NOAA (I am a graduate student), when I type gedit it says command not found. Do I need to modify some code in my bash startup file? And what is my bash startup file (.bash_profile?) What is the command to get it to understand the gedit command and open gedit from my Terminal session? And how can I get the proper permissions to get gedit to save the file to /usr/local?
Also, now when I am in the / directory and type ls -l, one of the columns has root the whole way down, while the other column says admin and wheel. I am the administrator on this computer, but I don't seem to have any permissions. Please help!!!!
bash-3.2$ ls -l
total 36525
drwxrwxr-x+ 37 root admin 1258 Jan 5 13:50 Applications
drwxrwxr-x@ 15 root admin 510 Dec 22 16:02 Developer
drwxrwxr-t+ 57 root admin 1938 Jan 4 17:25 Library
drwxr-xr-x@ 2 root wheel 68 Oct 4 21:42 Network
drwxr-xr-x 4 root wheel 136 Nov 19 20:45 System
lrwxr-xr-x 1 root admin 60 Dec 17 11:12 User Guides And Information -> /Library/Documentation/User Guides and Information.localized
drwxr-xr-x 5 root admin 170 Dec 17 11:12 Users
drwxrwxrwt@ 5 root admin 170 Jan 5 13:50 Volumes
drwxr-xr-x@ 39 root wheel 1326 Nov 19 20:44 bin
drwxrwxr-t@ 2 root admin 68 Oct 4 21:42 cores
dr-xr-xr-x 3 root wheel 4107 Jan 4 17:36 dev
lrwxr-xr-x@ 1 root wheel 11 Nov 19 20:44 etc -> private/etc
dr-xr-xr-x 2 root wheel 1 Jan 4 17:36 home
-rw-r--r--@ 1 root wheel 18676624 Nov 3 23:10 mach_kernel
dr-xr-xr-x 2 root wheel 1 Jan 4 17:36 net
drwxr-xr-x@ 6 root wheel 204 Nov 19 20:46 private
drwxr-xr-x@ 64 root wheel 2176 Nov 19 20:44 sbin
drwxr-xr-x 11 root admin 374 Dec 22 16:20 sw
lrwxr-xr-x@ 1 root wheel 11 Nov 19 20:44 tmp -> private/tmp
drwxrwxrwx@ 13 root wheel 442 Jan 4 17:54 usr
lrwxr-xr-x@ 1 root wheel 11 Nov 19 20:44 var -> private/var
When I used to open a Terminal window, I got:
Last login: Mon Jan 4 17:45:55 on ttys000
-bash: /usr/local/ferret_paths: No such file or directory
catmac:~ lclab$ bash
bash-3.2$
I think I got that message because I couldn't save the modified template because I don't have the proper permissions. I tried to get one of my computer programmer friends to help, but he was at a loss! I am including our session below. I also contacted the very patient, kind, and understanding NOAA computer whiz who instructed me to go into /System/Library/CoreServices and Directory Utility to enable me as the root user, however, no matter what I do, I am unable to save the modified ferret_paths template using gedit to /usr/local.
Now when I open a new Terminal window, I get the message:
Last login: Tue Jan 5 17:41:20 on ttys001
bash
[catmac:~] lclab% bash
bash-3.2$
Somewhere along the line, the message "-bash: /usr/local/ferret_paths: No such file or directory" has disappeared.
I know that many people love Ferret and from what I've managed to do with it (at NOAA), it seems like a great tool, but I am getting extremely frustrated. I would love an easy install for Mac users!!! By the way, if anyone does offer me some assistance in this matter, I am not too familiar with computer lingo and shells and Unix systems, so please, please, please offer suggestions in very basic, easy to follow steps. Like those you would give to a small child as I am not a computer whiz. If this fails....I'm going to have to switch back to R.
Much thanks in advance!!!
I am including my Terminal sessions for anyone that is interested in my struggle!
Last login: Mon Jan 4 17:41:03 on ttys000
bash
-bash: /usr/local/ferret_paths: No such file or directory
catmac:~ lclab$ bash
bash-3.2$ cd ..
bash-3.2$ ls
Shared lclab
bash-3.2$ sudo chown root:admin /
Password:
bash-3.2$ ls -l
total 0
drwxrwxrwt 4 root wheel 136 Dec 17 11:33 Shared
drwxr-xr-x+ 30 lclab staff 1020 Jan 4 17:35 lclab
bash-3.2$ cd lclab
bash-3.2$ ls
Desktop Movies Send Registration
Documents Music Sites
Downloads Pictures fink-0.29.10
Library Public
bash-3.2$ cd /usr
bash-3.2$ ls -l
total 8
drwxr-xr-x 8 root wheel 272 Nov 19 20:55 X11
lrwxr-xr-x 1 root wheel 3 Nov 19 20:55 X11R6 -> X11
drwxr-xr-x 1068 root wheel 36312 Dec 22 16:05 bin
drwxr-xr-x 271 root wheel 9214 Dec 22 16:03 include
drwxr-xr-x 383 root wheel 13022 Dec 22 16:04 lib
drwxr-xr-x 103 root wheel 3502 Dec 22 16:04 libexec
drwxr-xr-x 3 root wheel 102 Jan 4 14:13 local
drwxr-xr-x 236 root wheel 8024 Dec 22 16:04 sbin
drwxr-xr-x 74 root wheel 2516 Dec 22 16:04 share
drwxr-xr-x 4 root wheel 136 Nov 19 20:44 standalone
bash-3.2$ cd ..
bash-3.2$ sudo chown root:admin /
bash-3.2$ xxxxxx
bash: xxxxxx: event not found
bash-3.2$ sudo chown root:admin /
bash-3.2$ ls
Applications etc
Developer home
Library mach_kernel
Network net
System private
User Guides And Information sbin
Users sw
Volumes tmp
bin usr
cores var
dev
bash-3.2$ ls -l
total 36524
drwxrwxr-x+ 37 root admin 1258 Jan 4 14:23 Applications
drwxrwxr-x@ 15 root admin 510 Dec 22 16:02 Developer
drwxrwxr-t+ 57 root admin 1938 Jan 4 17:25 Library
drwxr-xr-x@ 2 root wheel 68 Oct 4 21:42 Network
drwxr-xr-x 4 root wheel 136 Nov 19 20:45 System
lrwxr-xr-x 1 root admin 60 Dec 17 11:12 User Guides And Information -> /Library/Documentation/User Guides and Information.localized
drwxr-xr-x 5 root admin 170 Dec 17 11:12 Users
drwxrwxrwt@ 4 root admin 136 Jan 4 17:36 Volumes
drwxr-xr-x@ 39 root wheel 1326 Nov 19 20:44 bin
drwxrwxr-t@ 2 root admin 68 Oct 4 21:42 cores
dr-xr-xr-x 3 root wheel 4080 Jan 4 17:36 dev
lrwxr-xr-x@ 1 root wheel 11 Nov 19 20:44 etc -> private/etc
dr-xr-xr-x 2 root wheel 1 Jan 4 17:36 home
-rw-r--r--@ 1 root wheel 18676624 Nov 3 23:10 mach_kernel
dr-xr-xr-x 2 root wheel 1 Jan 4 17:36 net
drwxr-xr-x@ 6 root wheel 204 Nov 19 20:46 private
drwxr-xr-x@ 64 root wheel 2176 Nov 19 20:44 sbin
drwxr-xr-x 11 root admin 374 Dec 22 16:20 sw
lrwxr-xr-x@ 1 root wheel 11 Nov 19 20:44 tmp -> private/tmp
drwxr-xr-x@ 12 root wheel 408 Jan 4 14:12 usr
lrwxr-xr-x@ 1 root wheel 11 Nov 19 20:44 var -> private/var
bash-3.2$ cd usr
bash-3.2$ ls
X11 bin lib local share
X11R6 include libexec sbin standalone
bash-3.2$ mkdir temp
mkdir: temp: Permission denied
bash-3.2$ su
Password:
su: Sorry
bash-3.2$
bash-3.2$
bash-3.2$ ls -l
total 8
drwxr-xr-x 8 root wheel 272 Nov 19 20:55 X11
lrwxr-xr-x 1 root wheel 3 Nov 19 20:55 X11R6 -> X11
drwxr-xr-x 1068 root wheel 36312 Dec 22 16:05 bin
drwxr-xr-x 271 root wheel 9214 Dec 22 16:03 include
drwxr-xr-x 383 root wheel 13022 Dec 22 16:04 lib
drwxr-xr-x 103 root wheel 3502 Dec 22 16:04 libexec
drwxr-xr-x 3 root wheel 102 Jan 4 14:13 local
drwxr-xr-x 236 root wheel 8024 Dec 22 16:04 sbin
drwxr-xr-x 74 root wheel 2516 Dec 22 16:04 share
drwxr-xr-x 4 root wheel 136 Nov 19 20:44 standalone
bash-3.2$ cd ..
bash-3.2$ ls
Applications etc
Developer home
Library mach_kernel
Network net
System private
User Guides And Information sbin
Users sw
Volumes tmp
bin usr
cores var
dev
bash-3.2$ ls -l
total 36524
drwxrwxr-x+ 37 root admin 1258 Jan 4 14:23 Applications
drwxrwxr-x@ 15 root admin 510 Dec 22 16:02 Developer
drwxrwxr-t+ 57 root admin 1938 Jan 4 17:25 Library
drwxr-xr-x@ 2 root wheel 68 Oct 4 21:42 Network
drwxr-xr-x 4 root wheel 136 Nov 19 20:45 System
lrwxr-xr-x 1 root admin 60 Dec 17 11:12 User Guides And Information -> /Library/Documentation/User Guides and Information.localized
drwxr-xr-x 5 root admin 170 Dec 17 11:12 Users
drwxrwxrwt@ 4 root admin 136 Jan 4 17:36 Volumes
drwxr-xr-x@ 39 root wheel 1326 Nov 19 20:44 bin
drwxrwxr-t@ 2 root admin 68 Oct 4 21:42 cores
dr-xr-xr-x 3 root wheel 4080 Jan 4 17:36 dev
lrwxr-xr-x@ 1 root wheel 11 Nov 19 20:44 etc -> private/etc
dr-xr-xr-x 2 root wheel 1 Jan 4 17:36 home
-rw-r--r--@ 1 root wheel 18676624 Nov 3 23:10 mach_kernel
dr-xr-xr-x 2 root wheel 1 Jan 4 17:36 net
drwxr-xr-x@ 6 root wheel 204 Nov 19 20:46 private
drwxr-xr-x@ 64 root wheel 2176 Nov 19 20:44 sbin
drwxr-xr-x 11 root admin 374 Dec 22 16:20 sw
lrwxr-xr-x@ 1 root wheel 11 Nov 19 20:44 tmp -> private/tmp
drwxr-xr-x@ 12 root wheel 408 Jan 4 14:12 usr
lrwxr-xr-x@ 1 root wheel 11 Nov 19 20:44 var -> private/var
bash-3.2$ chmod 777 usr
chmod: Unable to change file mode on usr: Operation not permitted
bash-3.2$ sudo chmod 777 usr
bash-3.2$ ls -l
total 36524
drwxrwxr-x+ 37 root admin 1258 Jan 4 14:23 Applications
drwxrwxr-x@ 15 root admin 510 Dec 22 16:02 Developer
drwxrwxr-t+ 57 root admin 1938 Jan 4 17:25 Library
drwxr-xr-x@ 2 root wheel 68 Oct 4 21:42 Network
drwxr-xr-x 4 root wheel 136 Nov 19 20:45 System
lrwxr-xr-x 1 root admin 60 Dec 17 11:12 User Guides And Information -> /Library/Documentation/User Guides and Information.localized
drwxr-xr-x 5 root admin 170 Dec 17 11:12 Users
drwxrwxrwt@ 4 root admin 136 Jan 4 17:36 Volumes
drwxr-xr-x@ 39 root wheel 1326 Nov 19 20:44 bin
drwxrwxr-t@ 2 root admin 68 Oct 4 21:42 cores
dr-xr-xr-x 3 root wheel 4080 Jan 4 17:36 dev
lrwxr-xr-x@ 1 root wheel 11 Nov 19 20:44 etc -> private/etc
dr-xr-xr-x 2 root wheel 1 Jan 4 17:36 home
-rw-r--r--@ 1 root wheel 18676624 Nov 3 23:10 mach_kernel
dr-xr-xr-x 2 root wheel 1 Jan 4 17:36 net
drwxr-xr-x@ 6 root wheel 204 Nov 19 20:46 private
drwxr-xr-x@ 64 root wheel 2176 Nov 19 20:44 sbin
drwxr-xr-x 11 root admin 374 Dec 22 16:20 sw
lrwxr-xr-x@ 1 root wheel 11 Nov 19 20:44 tmp -> private/tmp
drwxrwxrwx@ 12 root wheel 408 Jan 4 14:12 usr
lrwxr-xr-x@ 1 root wheel 11 Nov 19 20:44 var -> private/var
bash-3.2$ cd usr
bash-3.2$ mkdir tttt
bash-3.2$ rd tttt
bash: rd: command not found
bash-3.2$ rmdir tttt
bash-3.2$ ls -l
total 8
drwxr-xr-x 8 root wheel 272 Nov 19 20:55 X11
lrwxr-xr-x 1 root wheel 3 Nov 19 20:55 X11R6 -> X11
drwxr-xr-x 1068 root wheel 36312 Dec 22 16:05 bin
drwxr-xr-x 271 root wheel 9214 Dec 22 16:03 include
drwxr-xr-x 383 root wheel 13022 Dec 22 16:04 lib
drwxr-xr-x 103 root wheel 3502 Dec 22 16:04 libexec
drwxr-xr-x 3 root wheel 102 Jan 4 14:13 local
drwxr-xr-x 236 root wheel 8024 Dec 22 16:04 sbin
drwxr-xr-x 74 root wheel 2516 Dec 22 16:04 share
drwxr-xr-x 4 root wheel 136 Nov 19 20:44 standalone
bash-3.2$ cd ..
bash-3.2$ ls -l
total 36524
drwxrwxr-x+ 37 root admin 1258 Jan 4 14:23 Applications
drwxrwxr-x@ 15 root admin 510 Dec 22 16:02 Developer
drwxrwxr-t+ 57 root admin 1938 Jan 4 17:25 Library
drwxr-xr-x@ 2 root wheel 68 Oct 4 21:42 Network
drwxr-xr-x 4 root wheel 136 Nov 19 20:45 System
lrwxr-xr-x 1 root admin 60 Dec 17 11:12 User Guides And Information -> /Library/Documentation/User Guides and Information.localized
drwxr-xr-x 5 root admin 170 Dec 17 11:12 Users
drwxrwxrwt@ 4 root admin 136 Jan 4 17:36 Volumes
drwxr-xr-x@ 39 root wheel 1326 Nov 19 20:44 bin
drwxrwxr-t@ 2 root admin 68 Oct 4 21:42 cores
dr-xr-xr-x 3 root wheel 4080 Jan 4 17:36 dev
lrwxr-xr-x@ 1 root wheel 11 Nov 19 20:44 etc -> private/etc
dr-xr-xr-x 2 root wheel 1 Jan 4 17:36 home
-rw-r--r--@ 1 root wheel 18676624 Nov 3 23:10 mach_kernel
dr-xr-xr-x 2 root wheel 1 Jan 4 17:36 net
drwxr-xr-x@ 6 root wheel 204 Nov 19 20:46 private
drwxr-xr-x@ 64 root wheel 2176 Nov 19 20:44 sbin
drwxr-xr-x 11 root admin 374 Dec 22 16:20 sw
lrwxr-xr-x@ 1 root wheel 11 Nov 19 20:44 tmp -> private/tmp
drwxrwxrwx@ 12 root wheel 408 Jan 4 17:50 usr
lrwxr-xr-x@ 1 root wheel 11 Nov 19 20:44 var -> private/var
bash-3.2$ sudo chmod 755 usr
bash-3.2$ ls -l
total 36524
drwxrwxr-x+ 37 root admin 1258 Jan 4 14:23 Applications
drwxrwxr-x@ 15 root admin 510 Dec 22 16:02 Developer
drwxrwxr-t+ 57 root admin 1938 Jan 4 17:25 Library
drwxr-xr-x@ 2 root wheel 68 Oct 4 21:42 Network
drwxr-xr-x 4 root wheel 136 Nov 19 20:45 System
lrwxr-xr-x 1 root admin 60 Dec 17 11:12 User Guides And Information -> /Library/Documentation/User Guides and Information.localized
drwxr-xr-x 5 root admin 170 Dec 17 11:12 Users
drwxrwxrwt@ 4 root admin 136 Jan 4 17:36 Volumes
drwxr-xr-x@ 39 root wheel 1326 Nov 19 20:44 bin
drwxrwxr-t@ 2 root admin 68 Oct 4 21:42 cores
dr-xr-xr-x 3 root wheel 4080 Jan 4 17:36 dev
lrwxr-xr-x@ 1 root wheel 11 Nov 19 20:44 etc -> private/etc
dr-xr-xr-x 2 root wheel 1 Jan 4 17:36 home
-rw-r--r--@ 1 root wheel 18676624 Nov 3 23:10 mach_kernel
dr-xr-xr-x 2 root wheel 1 Jan 4 17:36 net
drwxr-xr-x@ 6 root wheel 204 Nov 19 20:46 private
drwxr-xr-x@ 64 root wheel 2176 Nov 19 20:44 sbin
drwxr-xr-x 11 root admin 374 Dec 22 16:20 sw
lrwxr-xr-x@ 1 root wheel 11 Nov 19 20:44 tmp -> private/tmp
drwxr-xr-x@ 12 root wheel 408 Jan 4 17:50 usr
lrwxr-xr-x@ 1 root wheel 11 Nov 19 20:44 var -> private/var
bash-3.2$ cd usr
bash-3.2$ mkdir temp
mkdir: temp: Permission denied
bash-3.2$ cd ..
bash-3.2$ sudo chmod 777 usr
bash-3.2$ whoami
lclab
bash-3.2$ cd usr
bash-3.2$
bash-3.2$
bash-3.2$
bash-3.2$ mkdir temp
bash-3.2$ cd ..
bash-3.2$ gedit
bash: gedit: command not found
bash-3.2$ sudo chmod 777 usr
Password:
bash-3.2$ rmdir usr
rmdir: usr: Permission denied
bash-3.2$ chgrp admin usr
chgrp: usr: Operation not permitted
bash-3.2$ chown lclab usr
chown: usr: Operation not permitted
bash-3.2$ ls -l
total 36525
drwxrwxr-x+ 37 root admin 1258 Jan 5 13:50 Applications
drwxrwxr-x@ 15 root admin 510 Dec 22 16:02 Developer
drwxrwxr-t+ 57 root admin 1938 Jan 4 17:25 Library
drwxr-xr-x@ 2 root wheel 68 Oct 4 21:42 Network
drwxr-xr-x 4 root wheel 136 Nov 19 20:45 System
lrwxr-xr-x 1 root admin 60 Dec 17 11:12 User Guides And Information -> /Library/Documentation/User Guides and Information.localized
drwxr-xr-x 5 root admin 170 Dec 17 11:12 Users
drwxrwxrwt@ 5 root admin 170 Jan 5 13:50 Volumes
drwxr-xr-x@ 39 root wheel 1326 Nov 19 20:44 bin
drwxrwxr-t@ 2 root admin 68 Oct 4 21:42 cores
dr-xr-xr-x 3 root wheel 4107 Jan 4 17:36 dev
lrwxr-xr-x@ 1 root wheel 11 Nov 19 20:44 etc -> private/etc
dr-xr-xr-x 2 root wheel 1 Jan 4 17:36 home
-rw-r--r--@ 1 root wheel 18676624 Nov 3 23:10 mach_kernel
dr-xr-xr-x 2 root wheel 1 Jan 4 17:36 net
drwxr-xr-x@ 6 root wheel 204 Nov 19 20:46 private
drwxr-xr-x@ 64 root wheel 2176 Nov 19 20:44 sbin
drwxr-xr-x 11 root admin 374 Dec 22 16:20 sw
lrwxr-xr-x@ 1 root wheel 11 Nov 19 20:44 tmp -> private/tmp
drwxrwxrwx@ 13 root wheel 442 Jan 4 17:54 usr
lrwxr-xr-x@ 1 root wheel 11 Nov 19 20:44 var -> private/var
bash-3.2$ pwd
/
bash-3.2$
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