cl not found
stockett wrote on Feb 15, 2008
I've been running iraf in cygwin for a few months but yesterday I tried to start it up and got back
cl: command not found
Where'd it go? I tried re-installing everything but was confronted with
./install: command not found
I'm stumped. How do I get back in?
Thanks
cl: command not found
Where'd it go? I tried re-installing everything but was confronted with
./install: command not found
I'm stumped. How do I get back in?
Thanks
Mike Fitzpatrick wrote on Feb 15, 2008
Could just be that the 'cl' command isn't in your path. If you can access it directly as e.g. "/usr/local/bin/cl" then it still exists and you need to be sure that /usr/local/bin in your path variable (defined in .cshrc/.login for C-shell or .bashrc/.profile for Bash users). Did you recently switch shells or update Cygwin in some way (or are you logged in as a different user?)?
The 'install' script is in $iraf/unix/hlib and a "./install" will only work if you are in that directory.
-Mike
The 'install' script is in $iraf/unix/hlib and a "./install" will only work if you are in that directory.
-Mike
stockett wrote on Feb 15, 2008
So how exactly do I fix my path variable? I'm not a computer wiz, thanks for your help and patience.
Mike Fitzpatrick wrote on Feb 15, 2008
First, make sure that the 'cl' command still exists: Does starting it as /usr/local/bin/cl instead of just 'cl' work? If so, the command exists and you may just need to change your path; if not then you may need to re-run the install script.
You can check your path to see if it has /usr/local/bin by doing
The path should include /usr/local/bin for the commands to be found automatically. If not and you're using /bin/csh (or /bin/tcsh) then edit the file .cshrc or .login in your cygwin login directory and find a command like
and edit the path to include /usr/local/bin as well. For /bin/sh (or /bin/bash) the line will be something like
and will be set in your .bash_profile or .bashrc file. Note that you use a space between paths in a .cshrc, and a colon for bash. The choice of editor for the file is up to you.
-Mike
You can check your path to see if it has /usr/local/bin by doing
% echo $SHELL # to find out what shell you use
% echo $path # or for Bash
% echo $PATH
The path should include /usr/local/bin for the commands to be found automatically. If not and you're using /bin/csh (or /bin/tcsh) then edit the file .cshrc or .login in your cygwin login directory and find a command like
set path = (/bin /usr/bin)
and edit the path to include /usr/local/bin as well. For /bin/sh (or /bin/bash) the line will be something like
PATH=/bin:/usr/bin:${HOME}/binand will be set in your .bash_profile or .bashrc file. Note that you use a space between paths in a .cshrc, and a colon for bash. The choice of editor for the file is up to you.
-Mike
stockett wrote on Feb 15, 2008
/usr/local/bin is still in my path, but cl doesn't run when I try it in this directory. There's a cl.lnk file in that directory which is a shortcut to a cl.csh file in /iraf/iraf/unix/hlib, but cl wont run from that directory either. ./install also doesn't work from this directory, I get a message saying
bin/csh bad interpeter no such file...
bin/csh bad interpeter no such file...
Mike Fitzpatrick wrote on Feb 15, 2008
You need to use the Cygwin setup to install tcsh then, the 'cl' command and the install script are both C-shell scripts, the message is telling you that you don't have csh on your system.
-Mike
-Mike
stockett wrote on Feb 15, 2008
I reinstalled tcsh and was able to run ./install and mkiraf, but cl is still command not found. During the install I saw a lot of tput: command not found and it said installation was completed with errors.
I was able to run cl.e from the iraf/irafbin/bin.cygwin directory, but it couldn't run any commands because it couldn't link to any connected subprocesses or some such.
I was able to run cl.e from the iraf/irafbin/bin.cygwin directory, but it couldn't run any commands because it couldn't link to any connected subprocesses or some such.
Mike Fitzpatrick wrote on Feb 15, 2008
"Command not found" is a path problem (unless the /usr/local/bin/cl link points to a file that doesn't exist or can't be executed).
See the earlier postings: Can you start with /usr/local/bin/cl as the command directly? Is your .cshrc/.bashrc file setting the path, etc, etc.
-Mike
See the earlier postings: Can you start with /usr/local/bin/cl as the command directly? Is your .cshrc/.bashrc file setting the path, etc, etc.
-Mike
stockett wrote on Feb 15, 2008
echo path contains /usr/local/bin
cl does not run from /usr/local/bin
when run from /iraf/iraf/unix/hlib, cl.csh returns /iraf/iraf/bin.cygwin/ecl.e command not found. just cl (no .csh) doesn't run from this dir
If this were a path problem, would I be able to run mkiraf from /iraf/iraf/local?
Should I reinitialize uparm?
Do i need to do something to to .lnk files?
cl does not run from /usr/local/bin
when run from /iraf/iraf/unix/hlib, cl.csh returns /iraf/iraf/bin.cygwin/ecl.e command not found. just cl (no .csh) doesn't run from this dir
If this were a path problem, would I be able to run mkiraf from /iraf/iraf/local?
Should I reinitialize uparm?
Do i need to do something to to .lnk files?
Mike Fitzpatrick wrote on Feb 15, 2008
echo path contains /usr/local/bin
Good, so a (working) 'cl' command should be found.
cl does not run from /usr/local/bin
What is the error message? It should be the same as when you run the 'cl.csh' command directly. When you're in the /usr/local/bin directory, a command like "more cl" should page the script file if the link is valid.
when run from /iraf/iraf/unix/hlib, cl.csh returns /iraf/iraf/bin.cygwin/ecl.e command not found. just cl (no .csh) doesn't run from this dir
Does /iraf/iraf/bin.cygwin contain both a cl.e and an ecl.e binary?
If this were a path problem, would I be able to run mkiraf from /iraf/iraf/local?
Depends on the specific path problem: It may be that the mkiraf link is valid but the cl link isn't, or that there's a permissions problem on binaries and so mkiraf would work but cl wouldn't.
Should I reinitialize uparm?
Do i need to do something to to .lnk files?
Reinitializing the uparm directory only matters once you finally log in and isn't an issue here. From the /iraf/iraf/unix/hlib directory, try rerunning the install script with:
% ./installThis will re-establish the links and print out potential problems with paths so pay attention to the output. Post any error messages you might see.
-Mike
stockett wrote on Feb 15, 2008
/usr/local/bin
cl and cl.csh both give command not found. more cl gives more: command not found. It can't find more?
/iraf/iraf/bin.cygwin is a link to /iraf/irafbin/bin.cygwin, which contains both cl.e and ecl.e
I'll try ./install again
cl and cl.csh both give command not found. more cl gives more: command not found. It can't find more?
/iraf/iraf/bin.cygwin is a link to /iraf/irafbin/bin.cygwin, which contains both cl.e and ecl.e
I'll try ./install again
stockett wrote on Feb 15, 2008
During install, there was a tput: command not found message after pretty much every line. There was also a series of errors that went by too fast for me to read, the last few of which were things like
could not make link xyacc -> /iraf/iraf/unix/bin.cygwin/xyacc.e
All the other steps came out [OK]
Is there some sort of sharing violation that is blocking all my links? Is there a way to redo them manually?
could not make link xyacc -> /iraf/iraf/unix/bin.cygwin/xyacc.e
All the other steps came out [OK]
Is there some sort of sharing violation that is blocking all my links? Is there a way to redo them manually?
Mike Fitzpatrick wrote on Feb 15, 2008
Try the 'install.old' command, it does the same thing without the error checking and pretty output and if there's a user problem you'll see the error messages more clearly.
Any chance you did the original install with an 'iraf' user and you're trying this now as yourself? An 'ls -l' will list the owners of a file.
-Mike
Any chance you did the original install with an 'iraf' user and you're trying this now as yourself? An 'ls -l' will list the owners of a file.
-Mike
stockett wrote on Feb 15, 2008
install.old didn't give as many errors.
got a few cmp:command not found
chmod: no match
cannot find alloc.e (three times)
foreach: no match
This was the last printed item right after --check file permissions--, then back to tcsh prompt
I've been doing everything as iraf and all the files say they're owned by iraf, but I don't specifically recall who I was when I installed it the first time a few months ago, but I'd think i'd have been iraf.
The cl.e file in /iraf/irafbin/bin.cygwin has a string reading -wrxr-xr-x next to iraf when I do ls -l. Most of the other files in that dir don't have as many x's
got a few cmp:command not found
chmod: no match
cannot find alloc.e (three times)
foreach: no match
This was the last printed item right after --check file permissions--, then back to tcsh prompt
I've been doing everything as iraf and all the files say they're owned by iraf, but I don't specifically recall who I was when I installed it the first time a few months ago, but I'd think i'd have been iraf.
The cl.e file in /iraf/irafbin/bin.cygwin has a string reading -wrxr-xr-x next to iraf when I do ls -l. Most of the other files in that dir don't have as many x's
Mike Fitzpatrick wrote on Feb 15, 2008
I'm not sure where to begin:
The problems with the 'tput' command not being found can usually be fixed by running the script as
[code}% ./install -hl |& tee /tmp/install.log[/code]
to disable the highlighting (what the tput does). This will do the error checking of the iraf directory and copy the screen output to /tmp/install.log so you can review it later if you can't scroll the screen. Commands like 'cmp' and 'chmod' are in the /bin directory and should be part of the base Cygwin install.
The 'chmod: no match' and especially the 'foreach: no match' make me think that either the $iraf/unix/bin.cygwin directory is empty, your IRAFARCH is wrong, or maybe just that $iraf hasn't been defined. Before doing the ./install command, try running it all as:
Post (or email me) the install.log file if it still fails.
-Mike
The problems with the 'tput' command not being found can usually be fixed by running the script as
[code}% ./install -hl |& tee /tmp/install.log[/code]
to disable the highlighting (what the tput does). This will do the error checking of the iraf directory and copy the screen output to /tmp/install.log so you can review it later if you can't scroll the screen. Commands like 'cmp' and 'chmod' are in the /bin directory and should be part of the base Cygwin install.
The 'chmod: no match' and especially the 'foreach: no match' make me think that either the $iraf/unix/bin.cygwin directory is empty, your IRAFARCH is wrong, or maybe just that $iraf hasn't been defined. Before doing the ./install command, try running it all as:
% csh
% cd /iraf/iraf/unix/hlib
% setenv iraf /iraf/iraf/ <---- trailing '/' required!!!
% setenv IRAFARCH cygwin
% ./install -hl |& tee /tmp/install.log
Post (or email me) the install.log file if it still fails.
-Mike
stockett wrote on Feb 15, 2008
Here's the error-ridden parts of the install.log:
Editing the iraf user .login/.cshrc paths ... cmp: Command not found.
cmp: Command not found.
[ OK ]
Editing iraf/imdir paths into system files ... cmp: Command not found.
cmp: Command not found.
cmp: Command not found.
[ OK ]
Checking File Permissions
-------------------------
Checking iraf file permissions ... [ OK ]
Checking imdir permissions ... [ OK ]
Reset /tmp sticky bit setting ... [ OK ]
Checking alloc.e permissions ... chown: changing ownership of `/iraf/iraf/unix/bin.cygwin/alloc.e': Invalid argument
[ OK ]
Creating File Links
-------------------
Checking for /iraf symlink ... [ OK ]
Checking /usr/include directory ... [ OK ]
Creating <iraf.h> symlink ... ln: creating symbolic link `/usr/include/iraf.h': File exists
[ FAIL ]
Creating iraf command links in local bin dir ... ln: creating symbolic link `ecl': File exists
[ FAIL ]
*** Could not make link ecl -> /iraf/iraf/unix/ecl.e
ln: creating symbolic link `cl': File exists
*** Could not make link cl -> /iraf/iraf/unix/hlib/cl.csh
ln: creating symbolic link `mkiraf': File exists
*** Could not make link mkiraf -> /iraf/iraf/unix/hlib/mkiraf.csh
ln: creating symbolic link `mkmlist': File exists
*** Could not make link mkmlist -> /iraf/iraf/unix/hlib/mkmlist.csh
ln: creating symbolic link `generic': File exists
*** Could not make link generic -> /iraf/iraf/unix/bin.cygwin/generic.e
ln: creating symbolic link `mkpkg': File exists
*** Could not make link mkpkg -> /iraf/iraf/unix/bin.cygwin/mkpkg.e
ln: creating symbolic link `rmbin': File exists
*** Could not make link rmbin -> /iraf/iraf/unix/bin.cygwin/rmbin.e
ln: creating symbolic link `rmfiles': File exists
*** Could not make link rmfiles -> /iraf/iraf/unix/bin.cygwin/rmfiles.e
ln: creating symbolic link `rtar': File exists
*** Could not make link rtar -> /iraf/iraf/unix/bin.cygwin/rtar.e
ln: creating symbolic link `sgidispatch': File exists
*** Could not make link sgidispatch -> /iraf/iraf/unix/bin.cygwin/sgidispatch.e
ln: creating symbolic link `wtar': File exists
*** Could not make link wtar -> /iraf/iraf/unix/bin.cygwin/wtar.e
ln: creating symbolic link `rpp': File exists
*** Could not make link rpp -> /iraf/iraf/unix/bin.cygwin/rpp.e
ln: creating symbolic link `xpp': File exists
*** Could not make link xpp -> /iraf/iraf/unix/bin.cygwin/xpp.e
ln: creating symbolic link `xyacc': File exists
*** Could not make link xyacc -> /iraf/iraf/unix/bin.cygwin/xyacc.e
ln: creating symbolic link `xc': File exists
*** Could not make link xc -> /iraf/iraf/unix/bin.cygwin/xc.e
Marking system update time hlib$utime ... [ OK ]
Creating Graphics Device Files
------------------------------
Creating special graphcap file ... copy: Command not found.
[ OK ]
Checking /usr/local/lib directory ... [ OK ]
[ OK ]
Creating /usr/local/lib/imtoolrc link ... ln: creating symbolic link `imtoolrc': File exists
[ OK ]
I noticed that a lot of the files in the cygwin/bin dir were owned by me, not iraf, but all of the commands that weren't found are owned by iraf. Should I re-install cygwin as iraf and then re intall iraf as iraf? I guess it couldn't hurt.
Editing the iraf user .login/.cshrc paths ... cmp: Command not found.
cmp: Command not found.
[ OK ]
Editing iraf/imdir paths into system files ... cmp: Command not found.
cmp: Command not found.
cmp: Command not found.
[ OK ]
Checking File Permissions
-------------------------
Checking iraf file permissions ... [ OK ]
Checking imdir permissions ... [ OK ]
Reset /tmp sticky bit setting ... [ OK ]
Checking alloc.e permissions ... chown: changing ownership of `/iraf/iraf/unix/bin.cygwin/alloc.e': Invalid argument
[ OK ]
Creating File Links
-------------------
Checking for /iraf symlink ... [ OK ]
Checking /usr/include directory ... [ OK ]
Creating <iraf.h> symlink ... ln: creating symbolic link `/usr/include/iraf.h': File exists
[ FAIL ]
Creating iraf command links in local bin dir ... ln: creating symbolic link `ecl': File exists
[ FAIL ]
*** Could not make link ecl -> /iraf/iraf/unix/ecl.e
ln: creating symbolic link `cl': File exists
*** Could not make link cl -> /iraf/iraf/unix/hlib/cl.csh
ln: creating symbolic link `mkiraf': File exists
*** Could not make link mkiraf -> /iraf/iraf/unix/hlib/mkiraf.csh
ln: creating symbolic link `mkmlist': File exists
*** Could not make link mkmlist -> /iraf/iraf/unix/hlib/mkmlist.csh
ln: creating symbolic link `generic': File exists
*** Could not make link generic -> /iraf/iraf/unix/bin.cygwin/generic.e
ln: creating symbolic link `mkpkg': File exists
*** Could not make link mkpkg -> /iraf/iraf/unix/bin.cygwin/mkpkg.e
ln: creating symbolic link `rmbin': File exists
*** Could not make link rmbin -> /iraf/iraf/unix/bin.cygwin/rmbin.e
ln: creating symbolic link `rmfiles': File exists
*** Could not make link rmfiles -> /iraf/iraf/unix/bin.cygwin/rmfiles.e
ln: creating symbolic link `rtar': File exists
*** Could not make link rtar -> /iraf/iraf/unix/bin.cygwin/rtar.e
ln: creating symbolic link `sgidispatch': File exists
*** Could not make link sgidispatch -> /iraf/iraf/unix/bin.cygwin/sgidispatch.e
ln: creating symbolic link `wtar': File exists
*** Could not make link wtar -> /iraf/iraf/unix/bin.cygwin/wtar.e
ln: creating symbolic link `rpp': File exists
*** Could not make link rpp -> /iraf/iraf/unix/bin.cygwin/rpp.e
ln: creating symbolic link `xpp': File exists
*** Could not make link xpp -> /iraf/iraf/unix/bin.cygwin/xpp.e
ln: creating symbolic link `xyacc': File exists
*** Could not make link xyacc -> /iraf/iraf/unix/bin.cygwin/xyacc.e
ln: creating symbolic link `xc': File exists
*** Could not make link xc -> /iraf/iraf/unix/bin.cygwin/xc.e
Marking system update time hlib$utime ... [ OK ]
Creating Graphics Device Files
------------------------------
Creating special graphcap file ... copy: Command not found.
[ OK ]
Checking /usr/local/lib directory ... [ OK ]
[ OK ]
Creating /usr/local/lib/imtoolrc link ... ln: creating symbolic link `imtoolrc': File exists
[ OK ]
I noticed that a lot of the files in the cygwin/bin dir were owned by me, not iraf, but all of the commands that weren't found are owned by iraf. Should I re-install cygwin as iraf and then re intall iraf as iraf? I guess it couldn't hurt.
stockett wrote on Feb 15, 2008
Well I granted ownership of all cygwin files to iraf. I tried to run ./install but was told:
ERROR: invalid $iraf value (/iraf/iraf/)
I ran ./install.old and got the same output as before. cl still does not run.
ERROR: invalid $iraf value (/iraf/iraf/)
I ran ./install.old and got the same output as before. cl still does not run.
Last post on Feb 15, 2008