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python/sage scripts

asked 2012-10-09 09:52:29 -0600

rmp251 gravatar image

updated 2012-10-09 16:41:51 -0600

First of all, my apologies for being a noob and a windows user. I'm using sage in virtualbox. I'm at this part of the tutorial:

I'm having 2 problems:

(1) I can't execute "./factor 2006". It says "no such file or directory", but the file is definitely there, and "sage -python factor 2006" works.

(2) factoring polynomials doesn't seem to work for me in sage. If I call factor on a string I get a TypeError: "unable to factor n".

Edit: Part of the problem may have been that the script was in a shared folder in VirtualBox. Here is some exact input/output, working completely locally (this changes the error in (2)).

>./factor 2006

/usr/bin/env: sage -python: No such file or directory

>sage -python factor "32*x^5-1"

NameError: name 'x' is not defined

Any assistance is much appreciated!

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Hi! I can guess what your problems are, but it would be better if you posted *exact commands* that you tried that didn't work. That makes it easier for others to be helped by your question too!

kcrisman gravatar imagekcrisman ( 2012-10-09 10:37:33 -0600 )edit

See my edit, thanks.

rmp251 gravatar imagermp251 ( 2012-10-09 16:48:49 -0600 )edit

Thanks. Gee, this really suggests that `from sage.all import *` isn't being done, not to mention the enigmatic no such file problem.

kcrisman gravatar imagekcrisman ( 2012-10-09 16:55:26 -0600 )edit

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answered 2012-10-12 16:15:05 -0600

updated 2012-10-12 16:19:54 -0600

Edit: try replacing the first line with #!/usr/bin/env sage. That might bypass all of the problems described below.

One more attempt at an answer: perhaps the shell in VirtualBox doesn't accept the syntax #!/usr/bin/env sage -python — some shells balk at having more than one term after "/usr/bin/env". So changing this first line to #!/usr/bin/env python and executing it with sage -sh -c './factor 2012' should work, as should first running sage -sh and then ./factor 2012. In either case, sage -sh tells /usr/bin/env python to use Sage's version of Python, which knows how to import the Sage library (from the line from sage.all import *).

That's my guess. See Wikipedia's article on 'Shebang (Unix)' – I don't know how to add the link here, since the link has a right parenthesis in it, which conflicts with the markup here for links – and in particular the part which says

Another portability problem is the interpretation of the command arguments. Some systems, including Linux, do not split up the arguments;[11] for example, when running the script with the first line like,

`#!/usr/bin/env python -c`

That is, python -c will be passed as one argument to /usr/bin/env, rather than two arguments. Cygwin also behaves this way.

While the original script (with #!/usr/bin/env sage -python) works on my OS X box, it doesn't work on a linux machine that I have access to. This part of the tutorial needs to be fixed, I think.

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See for a ticket tracking this problem.

John Palmieri gravatar imageJohn Palmieri ( 2012-10-12 16:21:39 -0600 )edit

Thanks a lot - this works. (As to WHY it works I'm still confused... I guess I don't understand the meaning of the hash-bang and /usr/bin/env)

rmp251 gravatar imagermp251 ( 2012-10-15 07:10:42 -0600 )edit

"#!/usr/bin/env sage" as the first line in the script says what program should be used to process the script, in this case "/usr/bin/env sage", so it is equivalent to running "sage factor". Some programs might start with "#!/usr/bin/python", for example, but it's more portable to use "#!/usr/bin/env python" -- the first only finds python if it's in /usr/bin, while the second finds python if it's anywhere in the user's PATH. In this case, the documentation suggested using "#!/usr/bin/env sage -python", to use Sage's installation of Python, but Linux apparently doesn't handle having more than one word after "#!/usr/bin/env" very well.

John Palmieri gravatar imageJohn Palmieri ( 2012-10-15 08:07:09 -0600 )edit

I see - thanks.

rmp251 gravatar imagermp251 ( 2012-10-15 10:19:42 -0600 )edit

answered 2012-10-09 10:41:37 -0600

kcrisman gravatar image

Here's a link that everyone can access: the tutorial on standalone scripts.

1) Is it possible that you aren't in the appropriate directory? Just a guess. What happens if you type ls? Sorry if this is too naive of question.

2) Strings can't be factored; polynomials can.

sage: P = 'x^2+x'
sage: P.factor()
AttributeError: 'str' object has no attribute 'factor'
sage: (x^2+x).factor()
(x + 1)*x
sage: R.<y> = ZZ[]
sage: R
Univariate Polynomial Ring in y over Integer Ring
sage: (y^2+y).factor()
y * (y + 1)

Of course, I didn't get your error message, so maybe something else is going on.

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Thanks for the response. 1) I'm in the appropriate directory and ls verifies that. 2) I see. I guess it is passed as a string argument but then is converted to an expression for sage. Please see my edit. Since the tutorial is for "standalone scripts" I would expect this to work.

rmp251 gravatar imagermp251 ( 2012-10-09 16:43:12 -0600 )edit

Yes, see my comment - `from sage.all import *` should make `x` predefined as a variable.

kcrisman gravatar imagekcrisman ( 2012-10-09 16:55:53 -0600 )edit

answered 2012-10-09 12:20:51 -0600

It's possible that the file is there but doesn't have the right permissions: it isn't executable. You could try

$ chmod a+x factor
$ ./factor 2006

and see if that works.

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Thanks for the suggestion - I tried it and got an error (see my edit please).

rmp251 gravatar imagermp251 ( 2012-10-09 16:48:13 -0600 )edit

answered 2012-10-10 07:55:51 -0600

Given the error message in

>./factor 2006
/usr/bin/env: sage -python: No such file or directory

It looks like "sage" can't be found, so I would guess that you haven't followed this direction from the tutorial:

In order to use this script, your SAGE_ROOT must be in your PATH.

I don't know how to do this using VirtualBox, but it might be this: find the directory SAGE_ROOT where sage is; say it's "/home/user/sage-5.3/". Then do

> export PATH=/home/user/sage-5.3/:$PATH

(There should be exactly one space in this line, between "export" and "PATH".) Then try

> ./factor 2006


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sage is in the path: > echo $PATH /home/sage/sage:/usr/local/bin:/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/sbin

rmp251 gravatar imagermp251 ( 2012-10-11 16:17:02 -0600 )edit

From the command line, what does "which sage" say?

John Palmieri gravatar imageJohn Palmieri ( 2012-10-12 04:32:13 -0600 )edit

~/sage/sage which I believe is the same thing as /home/sage/sage/sage

rmp251 gravatar imagermp251 ( 2012-10-12 04:47:48 -0600 )edit

What happens if you replace first line of "factor" with "/usr/bin/env python" and then do "sage -sh -c ./factor"?

John Palmieri gravatar imageJohn Palmieri ( 2012-10-12 05:20:02 -0600 )edit

That seems to work, although I can't seem to pass in a parameter to factor that way. Now when I just do ./factor 2006, for example, I get ImportError: No module named sage.all

rmp251 gravatar imagermp251 ( 2012-10-12 07:13:22 -0600 )edit

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Asked: 2012-10-09 09:52:29 -0600

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Last updated: Oct 12 '12