* 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
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