/bin/env perl: bad interpreter: No such file or directory

[Matt]

Let me start this by saying, I'm a complete Perl newb (on Mac 10.6).
I've been working on installing everything for several days, because
I'd really love to use Circos. I think I've done everything correct up
to this point. Now I'm trying to compile my first graphic using code
from the readme as follows:

me$ bin/circos -conf tutorials/2/2/circos.conf
-bash: bin/circos: /bin/env: bad interpreter: No such file or
directory

I used the default directories when I installed Circos.

Any help? Thanks for your patience.

[Martin]

Hi Matt,

Mac OS X has a different location for the "env" binary, which is /usr/
bin/env. The problem you're seeing is not a Perl one, but a minor Mac
OS X difference.

To fix it, I suggest that you create a symlink to env from /bin/env,
which is a standard location for env.

To do this, in Terminal

> sudo ln -s /usr/bin/env /bin/env

This will guard against this problem in the future.

If you prefer, change the first line in bin/circos to

#!/usr/bin/env perl

Martin

[Matt]

You sir, are my hero. I ran into more problems after this, but figured
them out, and now we're up and running.

Matt

[andrew s]

I'm getting this error after having the same problems. what does this
mean?

bin/circos -conf tutorials/2/2/circos.conf
Can't locate Config/General.pm in @INC (@INC contains: /Users/
Shadowfunk/circos-0.52/bin/lib /Users/Shadowfunk/circos-0.52/bin/../
lib /Users/Shadowfunk/circos-0.52/bin /sw/lib/perl5 /sw/lib/perl5/
darwin /Library/Perl/Updates/5.10.0 /System/Library/Perl/5.10.0/darwin-
thread-multi-2level /System/Library/Perl/5.10.0 /Library/Perl/5.10.0/
darwin-thread-multi-2level /Library/Perl/5.10.0 /Network/Library/Perl/
5.10.0/darwin-thread-multi-2level /Network/Library/Perl/5.10.0 /
Network/Library/Perl /System/Library/Perl/Extras/5.10.0/darwin-thread-
multi-2level /System/Library/Perl/Extras/5.10.0 .) at /Users/
Shadowfunk/circos-0.52/bin/../lib/Circos.pm line 54.
BEGIN failed--compilation aborted at /Users/Shadowfunk/circos-0.52/
bin/../lib/Circos.pm line 54.
Compilation failed in require at bin/circos line 39.
BEGIN failed--compilation aborted at bin/circos line 39.

[Martin]

> Can't locate Config/General.pm

This means you're missing the Config::General module.

You'll need to install it, and any other modules that you're missing.

* Config::General
* GD::Polyline
* GD (requires to be compiled with TTF support)
* Math::Bezier
* Math::Round
* Math::VecStat
* Params::Validate
* Pod::Usage
* Set::IntSpan
* Statistics::Descriptive

To install on the command line:

> perl -MCPAN -e shell
...
cpan> install Config::General

Except for GD, none of the modules are tricky. For more information
about installing modules,

http://www.cpan.org/modules/INSTALL.html

Martin

[andrew s]

I am unable to install GD. do you know of a good tutorial to do that
for Mac OSX 10.6

[Martin]

Did you install the XCode utilities? These are an additional
(optional) install on top of Snow Leopard. Check your installation CD.

http://www.macworld.com/article/46286/2005/08/installxcode.html

[Phil Tatman]

I'm having the same problem as Matt, but I use Linux (Ubuntu). Will the same code work for me?

[Martin Krzywinski]

Depends on where your 'env' is. To find it use 'which'

> which env

Martin Krzywinski

science + art

http://mkweb.bcgsc.ca

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[Rakesh Netha Vadnala]

i got like this
Sort subroutine didn't return single value at /home/crrao/software/circos/circos-0.67/bin/../lib/Circos/Debug.pm line 143.
what is the problem? what can i do to proceed further.

[Martin Krzywinski]

This is likely due to the fact that you don't have /bin/env on your system.

Please see this tutorial

http://circos.ca/tutorials/lessons/configuration/distribution_and_installation/

Make use of the search box in the tutorials -- in this case, searching for "/bin/env" provides the solution.

Martin Krzywinski

science + art

http://mkweb.bcgsc.ca

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[Raf Czlonka]

Dear Martin,

I had gone through the groups'/mailing-lists' archives and see your preference for /bin/env :^)

Every modern unix operating system out there has 'env' in /usr/bin - be it POSIX-certified (i.e. Solaris, OS X, etc.) or POSIX-compliant (Linux, NetBSD, FreeBSD, OpenBSD).

Why /bin/env, then?

INVHO, it doesn't make any sense to ask people to alter their operating systems by creating symbolic links (something they may not have control over) rather than simply *fix* the scripts and start using *standrard* /usr/bin/env - it's everywhere, so you're not "breaking" any compatibility :^)

Also, every single guide on how to crate portable scripts, be it Perl or Python, users '#!/usr/bin/env ...' - I am yet to encounter one using '#!/bin/env ...'.

Therefore, I kindly ask if you could change /bin/env to /usr/bin/env in the next release.

Best regards,

Raf

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[Martin Krzywinski]

Sure, I'll make this change.

Martin Krzywinski

science + art

http://mkweb.bcgsc.ca

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[msimb...@dnanexus.com]

Hi Martin,

Can you please make this change in Circos Tools, as well?

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[Martin Krzywinski]

Done for all tools in circos-tools-v0.22 

http://www.circos.ca/distribution/circos-tools-0.22.tgz

Martin Krzywinski

science + art

http://mkweb.bcgsc.ca

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