Re: [O] org-babel C math.h issue

[Thierry Banel]

  
  
Seems good.
  I tested it.
  
  As a refinement, the associated documentation should be updated
  (but that is a separate patch).
  http://orgmode.org/worg/org-contrib/babel/languages/ob-doc-C.html
  
  Thierry
  
  Le 11/03/2016 20:14, Oz Ben-Ami a écrit :


  

  

  Thanks for the response.

  
  On my machine, I get the undefined references even with
  GCC 5 (gcc version 5.2.1 20151010 (Ubuntu
  5.2.1-22ubuntu2)), if I put -lm before the source file
  name. 
  

As far as a patch, I can try but this would be my first time
really playing with org-mode code. As far as I can see, I
would need to add the following lines in ob-C.el:
L133: (libs (cdr (assoc :libs params)))
 (libs (mapconcat 'identity
               (if (listp libs) libs (list libs)) " "))
L142: (format "%s -o %s %s %s %s" ;; (added %s)
L147: libs

  
  Am I missing anything?
  

Oz
  
  
On Fri, Mar 11, 2016 at 1:52 PM,
  Thierry Banel 
  wrote:
  To
summarize this thread:
It seems there was an issue long ago.
Version 5 of GCC magically fixed it.
But it is still here for older compilers.

-

To debug, execute the following piece of lisp code:

    (defadvice org-babel-eval (before xxx (cmd body))
      ""
      (message "org-babel-eval : %s" cmd))
    (ad-activate 'org-babel-eval)

The actual compilation command will be displayed in the
*Messages* buffer.

With your example, we get

   gcc -o /tmp/babel-8412zIw/C-bin-8412IZR -lm
/tmp/babel-8412zIw/C-src-84127OL.c

--

You are right, Oz, this can be fixed in line 147.
But :flags is intended for flags like -g or -O, which need
to appear
before the source file.

Probably we are missing an additional flag, which could be
named :libs
Then your example would be:

  #+BEGIN_SRC C :includes '( )
:libs -lm
  int i=9;
    printf("%d\n",(int)sqrt(i));
    #+END_SRC
  
--

Oz, do you think you would be able to provide a patch?
The way to contribute is documented here:
http://orgmode.org/worg/org-contribute.html#orgheadline1

Thanks for reporting.
Thierry
  

  

Le 06/03/2016 23:44, Oz Ben-Ami a écrit :
> Hi,
>
> I'm a new org user, and I'm sorry if I'm missing
something obvious.
> When executing a C code snippet with org-babel,
that contains a math
> function, I get the famous "undefined reference"
errors. I tried
> adding ":flags -lm", but that doesn't help. Looking
at the code, it
> seems the -lm flag is inserted in the wrong place,
before the source
> file. An easy change would be in line 147 of
ob-C.el version
> 8.3.4-634, moving "flags" to after the source file.
This seems to
> work, but I don't know if it would break anything
else.
>
> A minimal working example, attached, includes the
following snippet:
>
> #+BEGIN_SRC C :includes '(
) :flags -lm
> int i=9;
> printf("%d\n",(int)sqrt(i));
> #+END_SRC
>
> Note the issue disappears if constants are directly
used rather than
> variables, presumably because the function call is
optimized away
> entirely.
>
> Any thoughts are appreciated.
>
> Oz


  

  


  


  

Re: [O] org-babel C math.h issue

[Oz Ben-Ami]

Thanks for the response.

On my machine, I get the undefined references even with GCC 5 (gcc version
5.2.1 20151010 (Ubuntu 5.2.1-22ubuntu2)), if I put -lm before the source
file name.

As far as a patch, I can try but this would be my first time really playing
with org-mode code. As far as I can see, I would need to add the following
lines in ob-C.el:
L133: (libs (cdr (assoc :libs params)))
 (libs (mapconcat 'identity
   (if (listp libs) libs (list libs)) " "))
L142: (format "%s -o %s %s %s %s" ;; (added %s)
L147: libs

Am I missing anything?

Oz

On Fri, Mar 11, 2016 at 1:52 PM, Thierry Banel  wrote:

> To summarize this thread:
> It seems there was an issue long ago.
> Version 5 of GCC magically fixed it.
> But it is still here for older compilers.
>
> -
>
> To debug, execute the following piece of lisp code:
>
> (defadvice org-babel-eval (before xxx (cmd body))
>   ""
>   (message "org-babel-eval : %s" cmd))
> (ad-activate 'org-babel-eval)
>
> The actual compilation command will be displayed in the *Messages* buffer.
>
> With your example, we get
>
>gcc -o /tmp/babel-8412zIw/C-bin-8412IZR -lm
> /tmp/babel-8412zIw/C-src-84127OL.c
>
> --
>
> You are right, Oz, this can be fixed in line 147.
> But :flags is intended for flags like -g or -O, which need to appear
> before the source file.
>
> Probably we are missing an additional flag, which could be named :libs
> Then your example would be:
>
>   #+BEGIN_SRC C :includes '( ) :libs -lm
>   int i=9;
>   printf("%d\n",(int)sqrt(i));
>   #+END_SRC
>
> --
>
> Oz, do you think you would be able to provide a patch?
> The way to contribute is documented here:
> http://orgmode.org/worg/org-contribute.html#orgheadline1
>
> Thanks for reporting.
> Thierry
>
>
> Le 06/03/2016 23:44, Oz Ben-Ami a écrit :
> > Hi,
> >
> > I'm a new org user, and I'm sorry if I'm missing something obvious.
> > When executing a C code snippet with org-babel, that contains a math
> > function, I get the famous "undefined reference" errors. I tried
> > adding ":flags -lm", but that doesn't help. Looking at the code, it
> > seems the -lm flag is inserted in the wrong place, before the source
> > file. An easy change would be in line 147 of ob-C.el version
> > 8.3.4-634, moving "flags" to after the source file. This seems to
> > work, but I don't know if it would break anything else.
> >
> > A minimal working example, attached, includes the following snippet:
> >
> > #+BEGIN_SRC C :includes '( ) :flags -lm
> > int i=9;
> > printf("%d\n",(int)sqrt(i));
> > #+END_SRC
> >
> > Note the issue disappears if constants are directly used rather than
> > variables, presumably because the function call is optimized away
> > entirely.
> >
> > Any thoughts are appreciated.
> >
> > Oz
>
>
>

Re: [O] org-babel C math.h issue

[Thierry Banel]

To summarize this thread:
It seems there was an issue long ago.
Version 5 of GCC magically fixed it.
But it is still here for older compilers.

-

To debug, execute the following piece of lisp code:

(defadvice org-babel-eval (before xxx (cmd body))
  ""
  (message "org-babel-eval : %s" cmd))
(ad-activate 'org-babel-eval)

The actual compilation command will be displayed in the *Messages* buffer.

With your example, we get

   gcc -o /tmp/babel-8412zIw/C-bin-8412IZR -lm
/tmp/babel-8412zIw/C-src-84127OL.c

--

You are right, Oz, this can be fixed in line 147.
But :flags is intended for flags like -g or -O, which need to appear
before the source file.

Probably we are missing an additional flag, which could be named :libs
Then your example would be:

  #+BEGIN_SRC C :includes '( ) :libs -lm
  int i=9;
  printf("%d\n",(int)sqrt(i));
  #+END_SRC

--

Oz, do you think you would be able to provide a patch?
The way to contribute is documented here:
http://orgmode.org/worg/org-contribute.html#orgheadline1

Thanks for reporting.
Thierry


Le 06/03/2016 23:44, Oz Ben-Ami a écrit :
> Hi,
>
> I'm a new org user, and I'm sorry if I'm missing something obvious.
> When executing a C code snippet with org-babel, that contains a math
> function, I get the famous "undefined reference" errors. I tried
> adding ":flags -lm", but that doesn't help. Looking at the code, it
> seems the -lm flag is inserted in the wrong place, before the source
> file. An easy change would be in line 147 of ob-C.el version
> 8.3.4-634, moving "flags" to after the source file. This seems to
> work, but I don't know if it would break anything else.
>
> A minimal working example, attached, includes the following snippet:
>
> #+BEGIN_SRC C :includes '( ) :flags -lm
> int i=9;
> printf("%d\n",(int)sqrt(i));
> #+END_SRC
>
> Note the issue disappears if constants are directly used rather than
> variables, presumably because the function call is optimized away
> entirely.
>
> Any thoughts are appreciated.
>
> Oz

Re: [O] org-babel C math.h issue

[Nick Dokos]

Anssi Saari  writes:

> Nick Dokos  writes:
>
>> You can test that that's the case: put your program into a file, say foo.c, 
>> and
>> execute
>>
>>   gcc -o foo.out -lm foo.c
>>
>> Does that give you undefined references?
>
> Does for me. gcc --version says
> gcc (Ubuntu 4.8.4-2ubuntu1~14.04) 4.8.4
>
> So is it gcc that has changed then?
>

Possibly. I use

gcc (GCC) 5.3.1 20151207 (Red Hat 5.3.1-2)

on Fedora 22.

-- 
Nick

Re: [O] org-babel C math.h issue

[Anssi Saari]

Nick Dokos  writes:

> You can test that that's the case: put your program into a file, say foo.c, 
> and
> execute
>
>   gcc -o foo.out -lm foo.c
>
> Does that give you undefined references?

Does for me. gcc --version says
gcc (Ubuntu 4.8.4-2ubuntu1~14.04) 4.8.4

So is it gcc that has changed then?

Re: [O] org-babel C math.h issue

[Nick Dokos]

Oz Ben-Ami  writes:

> Hi,
>
> I'm a new org user, and I'm sorry if I'm missing something obvious. When 
> executing a C code snippet with
> org-babel, that contains a math function, I get the famous "undefined 
> reference" errors. I tried adding
> ":flags -lm", but that doesn't help. Looking at the code, it seems the -lm 
> flag is inserted in the wrong
> place, before the source file. An easy change would be in line 147 of ob-C.el 
> version 8.3.4-634, moving
> "flags" to after the source file. This seems to work, but I don't know if it 
> would break anything else.
>
> A minimal working example, attached, includes the following snippet:
>
> #+BEGIN_SRC C :includes '( ) :flags -lm
> int i=9;
> printf("%d\n",(int)sqrt(i));
> #+END_SRC
>
> Note the issue disappears if constants are directly used rather than 
> variables, presumably because the
> function call is optimized away entirely.
>
> Any thoughts are appreciated.
>

I can't reproduce it either (with fairly recent emacs and bleeding-edge
org-mode, but the code in question has not changed since 8.2.7 or so).

The command that is executed looks like this:

  gcc -o /tmp/babel-212464kj/C-bin-21246R6L -lm 
/tmp/babel-212464kj/C-src-21246EwF.c

and that should work fine for gcc: you don't need to have the -lm after the
source file.

You can test that that's the case: put your program into a file, say foo.c, and
execute

  gcc -o foo.out -lm foo.c

Does that give you undefined references?

--
Nick

Re: [O] org-babel C math.h issue

[John Kitchin]

I get the right answer on a Mac with org-mode version 8.2.10


Anssi Saari writes:

> Oz Ben-Ami  writes:
>
>> A minimal working example, attached, includes the following snippet:
>>
>> #+BEGIN_SRC C :includes '( ) :flags -lm
>> int i=9;
>> printf("%d\n",(int)sqrt(i));
>> #+END_SRC
>
> I get the same problem, Ubuntu 14.04.3 LTS, GNU Emacs 24.3.1, Org-mode
> version 8.2.10. So maybe it got fixed at some point since these versions
> are about two years old?


--
Professor John Kitchin
Doherty Hall A207F
Department of Chemical Engineering
Carnegie Mellon University
Pittsburgh, PA 15213
412-268-7803
@johnkitchin
http://kitchingroup.cheme.cmu.edu

Re: [O] org-babel C math.h issue

[Anssi Saari]

Oz Ben-Ami  writes:

> A minimal working example, attached, includes the following snippet:
>
> #+BEGIN_SRC C :includes '( ) :flags -lm
> int i=9;
> printf("%d\n",(int)sqrt(i));
> #+END_SRC

I get the same problem, Ubuntu 14.04.3 LTS, GNU Emacs 24.3.1, Org-mode
version 8.2.10. So maybe it got fixed at some point since these versions
are about two years old?

Re: [O] org-babel C math.h issue

[Nicolas Goaziou]

Hello,

Oz Ben-Ami  writes:

> A minimal working example, attached, includes the following snippet:
>
> #+BEGIN_SRC C :includes '( ) :flags -lm
> int i=9;
> printf("%d\n",(int)sqrt(i));
> #+END_SRC

FWIW, I get

  #+BEGIN_SRC C :includes '( ) :flags -lm
  int i=9;
  printf("%d\n",(int)sqrt(i));
  #+END_SRC

  #+RESULTS:
  : 3

without any error.


Regards,

-- 
Nicolas Goaziou

[O] org-babel C math.h issue

[Oz Ben-Ami]

Hi,

I'm a new org user, and I'm sorry if I'm missing something obvious. When
executing a C code snippet with org-babel, that contains a math function, I
get the famous "undefined reference" errors. I tried adding ":flags -lm",
but that doesn't help. Looking at the code, it seems the -lm flag is
inserted in the wrong place, before the source file. An easy change would
be in line 147 of ob-C.el version 8.3.4-634, moving "flags" to after the
source file. This seems to work, but I don't know if it would break
anything else.

A minimal working example, attached, includes the following snippet:

#+BEGIN_SRC C :includes '( ) :flags -lm
int i=9;
printf("%d\n",(int)sqrt(i));
#+END_SRC

Note the issue disappears if constants are directly used rather than
variables, presumably because the function call is optimized away entirely.

Any thoughts are appreciated.

Oz


testC.org
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