* org-babel C math.h issue
@ 2016-03-06 22:44 Oz Ben-Ami
2016-03-10 9:43 ` Nicolas Goaziou
` (3 more replies)
0 siblings, 4 replies; 13+ messages in thread
From: Oz Ben-Ami @ 2016-03-06 22:44 UTC (permalink / raw
To: emacs-orgmode
[-- Attachment #1.1: Type: text/plain, Size: 884 bytes --]
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 '(<math.h> <stdio.h>) :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
[-- Attachment #1.2: Type: text/html, Size: 1049 bytes --]
[-- Attachment #2: testC.org --]
[-- Type: application/octet-stream, Size: 267 bytes --]
#+BEGIN_SRC elisp
(custom-set-variables
'(org-babel-load-languages
(quote
((emacs-lisp . t)
(C . t)))))
#+END_SRC
#+RESULTS:
#+BEGIN_SRC C :includes '(<math.h> <stdio.h>) :flags -lm
int i=9;
printf("%d\n",(int)sqrt(pow(i,i)));
#+END_SRC
#+RESULTS:
^ permalink raw reply [flat|nested] 13+ messages in thread
* Re: org-babel C math.h issue
2016-03-06 22:44 org-babel C math.h issue Oz Ben-Ami
@ 2016-03-10 9:43 ` Nicolas Goaziou
2016-03-10 14:06 ` Anssi Saari
` (2 subsequent siblings)
3 siblings, 0 replies; 13+ messages in thread
From: Nicolas Goaziou @ 2016-03-10 9:43 UTC (permalink / raw
To: Oz Ben-Ami; +Cc: emacs-orgmode
Hello,
Oz Ben-Ami <ozzieba@gmail.com> writes:
> A minimal working example, attached, includes the following snippet:
>
> #+BEGIN_SRC C :includes '(<math.h> <stdio.h>) :flags -lm
> int i=9;
> printf("%d\n",(int)sqrt(i));
> #+END_SRC
FWIW, I get
#+BEGIN_SRC C :includes '(<math.h> <stdio.h>) :flags -lm
int i=9;
printf("%d\n",(int)sqrt(i));
#+END_SRC
#+RESULTS:
: 3
without any error.
Regards,
--
Nicolas Goaziou
^ permalink raw reply [flat|nested] 13+ messages in thread
* Re: org-babel C math.h issue
2016-03-06 22:44 org-babel C math.h issue Oz Ben-Ami
2016-03-10 9:43 ` Nicolas Goaziou
@ 2016-03-10 14:06 ` Anssi Saari
2016-03-10 15:20 ` John Kitchin
2016-03-10 21:19 ` Nick Dokos
2016-03-11 18:52 ` Thierry Banel
3 siblings, 1 reply; 13+ messages in thread
From: Anssi Saari @ 2016-03-10 14:06 UTC (permalink / raw
To: emacs-orgmode
Oz Ben-Ami <ozzieba@gmail.com> writes:
> A minimal working example, attached, includes the following snippet:
>
> #+BEGIN_SRC C :includes '(<math.h> <stdio.h>) :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?
^ permalink raw reply [flat|nested] 13+ messages in thread
* Re: org-babel C math.h issue
2016-03-10 14:06 ` Anssi Saari
@ 2016-03-10 15:20 ` John Kitchin
0 siblings, 0 replies; 13+ messages in thread
From: John Kitchin @ 2016-03-10 15:20 UTC (permalink / raw
To: Anssi Saari; +Cc: emacs-orgmode
I get the right answer on a Mac with org-mode version 8.2.10
Anssi Saari writes:
> Oz Ben-Ami <ozzieba@gmail.com> writes:
>
>> A minimal working example, attached, includes the following snippet:
>>
>> #+BEGIN_SRC C :includes '(<math.h> <stdio.h>) :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
^ permalink raw reply [flat|nested] 13+ messages in thread
* Re: org-babel C math.h issue
2016-03-06 22:44 org-babel C math.h issue Oz Ben-Ami
2016-03-10 9:43 ` Nicolas Goaziou
2016-03-10 14:06 ` Anssi Saari
@ 2016-03-10 21:19 ` Nick Dokos
2016-03-11 6:44 ` Anssi Saari
2016-03-11 18:52 ` Thierry Banel
3 siblings, 1 reply; 13+ messages in thread
From: Nick Dokos @ 2016-03-10 21:19 UTC (permalink / raw
To: emacs-orgmode
Oz Ben-Ami <ozzieba@gmail.com> 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 '(<math.h> <stdio.h>) :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
^ permalink raw reply [flat|nested] 13+ messages in thread
* Re: org-babel C math.h issue
2016-03-10 21:19 ` Nick Dokos
@ 2016-03-11 6:44 ` Anssi Saari
2016-03-11 15:36 ` Nick Dokos
0 siblings, 1 reply; 13+ messages in thread
From: Anssi Saari @ 2016-03-11 6:44 UTC (permalink / raw
To: emacs-orgmode
Nick Dokos <ndokos@gmail.com> 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?
^ permalink raw reply [flat|nested] 13+ messages in thread
* Re: org-babel C math.h issue
2016-03-11 6:44 ` Anssi Saari
@ 2016-03-11 15:36 ` Nick Dokos
0 siblings, 0 replies; 13+ messages in thread
From: Nick Dokos @ 2016-03-11 15:36 UTC (permalink / raw
To: emacs-orgmode
Anssi Saari <as@sci.fi> writes:
> Nick Dokos <ndokos@gmail.com> 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
^ permalink raw reply [flat|nested] 13+ messages in thread
* Re: org-babel C math.h issue
2016-03-06 22:44 org-babel C math.h issue Oz Ben-Ami
` (2 preceding siblings ...)
2016-03-10 21:19 ` Nick Dokos
@ 2016-03-11 18:52 ` Thierry Banel
2016-03-11 19:14 ` Oz Ben-Ami
3 siblings, 1 reply; 13+ messages in thread
From: Thierry Banel @ 2016-03-11 18:52 UTC (permalink / raw
To: emacs-orgmode
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 '(<math.h> <stdio.h>) :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 '(<math.h> <stdio.h>) :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
^ permalink raw reply [flat|nested] 13+ messages in thread
* Re: org-babel C math.h issue
2016-03-11 18:52 ` Thierry Banel
@ 2016-03-11 19:14 ` Oz Ben-Ami
2016-03-11 23:14 ` Thierry Banel
2016-03-20 14:03 ` [PATCH] " Thierry Banel
0 siblings, 2 replies; 13+ messages in thread
From: Oz Ben-Ami @ 2016-03-11 19:14 UTC (permalink / raw
To: Thierry Banel; +Cc: emacs-orgmode
[-- Attachment #1: Type: text/plain, Size: 3003 bytes --]
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 <tbanelwebmin@free.fr> 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 '(<math.h> <stdio.h>) :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 '(<math.h> <stdio.h>) :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
>
>
>
[-- Attachment #2: Type: text/html, Size: 4016 bytes --]
^ permalink raw reply [flat|nested] 13+ messages in thread
* Re: org-babel C math.h issue
2016-03-11 19:14 ` Oz Ben-Ami
@ 2016-03-11 23:14 ` Thierry Banel
2016-03-20 14:03 ` [PATCH] " Thierry Banel
1 sibling, 0 replies; 13+ messages in thread
From: Thierry Banel @ 2016-03-11 23:14 UTC (permalink / raw
To: emacs-orgmode
[-- Attachment #1: Type: text/html, Size: 6583 bytes --]
^ permalink raw reply [flat|nested] 13+ messages in thread
* Re: [PATCH] org-babel C math.h issue
2016-03-11 19:14 ` Oz Ben-Ami
2016-03-11 23:14 ` Thierry Banel
@ 2016-03-20 14:03 ` Thierry Banel
2016-03-25 23:42 ` Nicolas Goaziou
1 sibling, 1 reply; 13+ messages in thread
From: Thierry Banel @ 2016-03-20 14:03 UTC (permalink / raw
To: emacs-orgmode
[-- Attachment #1: Type: text/plain, Size: 765 bytes --]
Attached is Oz's patch adding optional :libs support to Babel C++
Thanks Oz.
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
>
[-- Attachment #2: 0001-Add-libs-to-babel-C.patch --]
[-- Type: text/x-diff, Size: 1543 bytes --]
From 69661d4406c51f678dad6f14aaa8f3447c398825 Mon Sep 17 00:00:00 2001
From: Thierry Banel <tbanelwebmin@free.fr>
Date: Sun, 20 Mar 2016 14:50:17 +0100
Subject: [PATCH] Add :libs to babel C++
* lisp/ob-C.el (org-babel-C-execute): add support for :libs header
parameter to specify libraries to link with.
---
lisp/ob-C.el | 12 ++++++++++--
1 file changed, 10 insertions(+), 2 deletions(-)
diff --git a/lisp/ob-C.el b/lisp/ob-C.el
index dd34b0b..d5855ab 100644
--- a/lisp/ob-C.el
+++ b/lisp/ob-C.el
@@ -130,6 +130,12 @@ or `org-babel-execute:C++' or `org-babel-execute:D'."
(flags (cdr (assoc :flags params)))
(flags (mapconcat 'identity
(if (listp flags) flags (list flags)) " "))
+ (libs (org-babel-read
+ (or (cdr (assoc :libs params))
+ (org-entry-get nil "libs" t))
+ nil))
+ (libs (mapconcat 'identity
+ (if (listp libs) libs (list libs)) " "))
(full-body
(case org-babel-c-variant
(c (org-babel-C-expand-C body params))
@@ -139,13 +145,15 @@ or `org-babel-execute:C++' or `org-babel-execute:D'."
(case org-babel-c-variant
((c cpp)
(org-babel-eval
- (format "%s -o %s %s %s"
+ (format "%s -o %s %s %s %s"
(case org-babel-c-variant
(c org-babel-C-compiler)
(cpp org-babel-C++-compiler))
(org-babel-process-file-name tmp-bin-file)
flags
- (org-babel-process-file-name tmp-src-file)) ""))
+ (org-babel-process-file-name tmp-src-file)
+ libs)
+ ""))
(d nil)) ;; no separate compilation for D
(let ((results
(org-babel-eval
--
2.1.4
^ permalink raw reply related [flat|nested] 13+ messages in thread
* Re: [PATCH] org-babel C math.h issue
2016-03-20 14:03 ` [PATCH] " Thierry Banel
@ 2016-03-25 23:42 ` Nicolas Goaziou
2016-03-26 17:08 ` Thierry Banel
0 siblings, 1 reply; 13+ messages in thread
From: Nicolas Goaziou @ 2016-03-25 23:42 UTC (permalink / raw
To: Thierry Banel; +Cc: emacs-orgmode
Hello,
Thierry Banel <tbanelwebmin@free.fr> writes:
> Attached is Oz's patch adding optional :libs support to Babel C++
Applied. Thank you.
Would you (or the OP) mind documenting the feature at
<http://orgmode.org/worg/org-contrib/babel/languages.html>?
Regards,
--
Nicolas Goaziou
^ permalink raw reply [flat|nested] 13+ messages in thread
* Re: [PATCH] org-babel C math.h issue
2016-03-25 23:42 ` Nicolas Goaziou
@ 2016-03-26 17:08 ` Thierry Banel
0 siblings, 0 replies; 13+ messages in thread
From: Thierry Banel @ 2016-03-26 17:08 UTC (permalink / raw
To: emacs-orgmode
Done.
Le 26/03/2016 00:42, Nicolas Goaziou a écrit :
> Applied. Thank you.
>
> Would you (or the OP) mind documenting the feature at
> <http://orgmode.org/worg/org-contrib/babel/languages.html>?
>
^ permalink raw reply [flat|nested] 13+ messages in thread
end of thread, other threads:[~2016-03-26 17:09 UTC | newest]
Thread overview: 13+ messages (download: mbox.gz follow: Atom feed
-- links below jump to the message on this page --
2016-03-06 22:44 org-babel C math.h issue Oz Ben-Ami
2016-03-10 9:43 ` Nicolas Goaziou
2016-03-10 14:06 ` Anssi Saari
2016-03-10 15:20 ` John Kitchin
2016-03-10 21:19 ` Nick Dokos
2016-03-11 6:44 ` Anssi Saari
2016-03-11 15:36 ` Nick Dokos
2016-03-11 18:52 ` Thierry Banel
2016-03-11 19:14 ` Oz Ben-Ami
2016-03-11 23:14 ` Thierry Banel
2016-03-20 14:03 ` [PATCH] " Thierry Banel
2016-03-25 23:42 ` Nicolas Goaziou
2016-03-26 17:08 ` Thierry Banel
Code repositories for project(s) associated with this external index
https://git.savannah.gnu.org/cgit/emacs.git
https://git.savannah.gnu.org/cgit/emacs/org-mode.git
This is an external index of several public inboxes,
see mirroring instructions on how to clone and mirror
all data and code used by this external index.