[EMBOSS] Can not install emboss on mandrake 9.2

[D. Joe Anderson]

On Wed, May 26, 2004 at 07:01:57AM -0400, Sony wrote:
> Dear friends
> 
> I try to install emboss 2.8.0 on my mandrake 9.2, I have already done 
> ./configure prefix=/usr/local/emboss/, make, make install, but after I 
> modify bashrc with the following suggested code " 
> PLPLOT_LIB=/site/prog/emboss/lib PATH=/site/prog/emboss/bin:\$PATH export 
> PLPLOT_LIB PATH" then the command line can not recognized common command 
> such as ls, cp, etc except cd. 

Just for clarity, let's unwrap those commands onto one line per command:

PLPLOT_LIB=/site/prog/emboss/lib 
PATH=/site/prog/emboss/bin:\$PATH 
export PLPLOT_LIB PATH



Leave out the \

Instead of adding something to your PATH, you are obliterating your PATH and
replacing it with directories that lack useful and necessary programs.

With the \, the $ is escaped and not recognized as a special character. 
This keeps the $PATH variable from being interpreted and its value included.

You want to include PATH's former value, as it tells the system where to
find ls, cp, etc.  It finds cd just fine because that is a command built-in
to the bash shell.

Also, you should not have to set the prefix, if ./configure's defaults are
set right, it should put things in /usr/local.

At that point, what you want to add to PATH is not /site/proc/emboss/bin but
rather /usr/local/bin.

You can set the PATH variable from the shell prompt.  Doing so is a good way
to test a PATH setting before committing it to a configuration file like
bashrc

For instance, if you manage to again get a shell prompt, issuing this
command may restore your path to a useable state:

export PATH=/bin:/sbin:/usr/bin:/usr/sbin

you can then try issuing 

export PATH=/bin:/sbin:/usr/bin:/usr/sbin:/usr/local/emboss/bin

to see if you can execute any of the programs installed by your earlier
invocation of "make install"

> When I try to log out, I can not back to my 
> x windows because mandrake system reject my username and password (before 
> changing the bashrc the username and password are working properly).

Which bashrc file did you modify?  You are better off to modify the bashrc
file in the home directory of a non-root account.  For instance, if you have
a regular user account called "sony" then this would be /home/sony/.bashrc
or ~sony/.bashrc for short.  Or, if you are logged-in as "sony" then this
would be ~/.bashrc

Once this file is modified to work properly, and if you need to make this
change effective systemwide (for instance, if other people are to use this
machine and you want them to be able to use the copy of emboss you have
installed), then it might be appropriate to edit the system-wide copies in
/etc

Also, what account's do and don't work for you?  If you have a regular user
account that isn't working, you should be able to log in as the root user
and make any changes.  If what you have done have made it impossible for you
to log in as root, then more drastic measures may be necessary.


> Does anyone know how to solve the problem? 

You could try logging-in through a virtual terminal, instead of via X Windows. 
Hit Ctl-Alt-F1 to switch to a virtual terminal.  Log in to the console
window there and make any repairs necessary.  When done, log out and switch
back to X with Alt-F7.

You could try booting into single-user mode, and to reverse your changes
using that. 

You might try to boot the system with the Mandrake installation CD in rescue
mode, and try to find the bashrc file you changed, and to change it back. 
It's been a while since I used Mandrake so I can't offer more detailed
instructions.

You might also try to choose GNOME or some other window manager from the X
Windows login screen, instead of KDE.  It might be that, with screwed-up
dotfiles, KDE cannot find certain subdirectories in your home directory that
it needs, and so login fails. 

> Do I have to change my 
> distribution, once I have ever installed it in redhat 9, and it work 
> properly without experiencing this case

My guess is the success with redhat 9 was due more to happenstance than to
any advantage emboss has on that distribution.  So, I don't see that
changing back to Redhat 9 would help per se.  It might be that GNOME is more
forgiving of dotfile configuration mishaps and that it therefore lets you
log in via X Windows.

You may find it easiest to re-install Mandrake (or any other distribution)
but a change in distribution won't solve the basic difficulty, which seems
to be an unfamiliarity with the basic system administration.

You may be best to seek out local help with Linux basics.  Linux.org shows 7
user groups in Indonesia:

http://www.linux.org/groups/indonesia.html

among which, this one ranks high in google:

http://www.linux.or.id/

They may be better positioned to help you with answers and advice
troubleshooting general problems like these with running X Windows, GNU
software, and Linux.

Regards,

--Joe