* [BUG] tangle breaks fortran modules [9.7-pre (release_9.6.7-581-gd38ca5)]
@ 2023-09-04 1:59 Paul Stansell
2023-09-04 7:56 ` Ihor Radchenko
0 siblings, 1 reply; 6+ messages in thread
From: Paul Stansell @ 2023-09-04 1:59 UTC (permalink / raw)
To: emacs-orgmode
[-- Attachment #1.1: Type: text/plain, Size: 8258 bytes --]
Hello,
The attached file is an example of how tangle wraps the Fortran module in
program main
end program main
which prevents the code from compiling.
There are more instructions on how to reproduce the bug in the attached
bug.org file.
Paul
Emacs : GNU Emacs 28.2 (build 1, x86_64-pc-linux-gnu, GTK+ Version
3.24.37, cairo version 1.16.0)
of 2023-03-16, modified by Debian
Package: Org mode version 9.7-pre (release_9.6.7-581-gd38ca5 @
/home/ps/.emacs.d_Kubuntu-23.04/org-mode-git/lisp/)
current state:
==============
(setq
org-link-elisp-confirm-function 'yes-or-no-p
org-bibtex-headline-format-function 'org-bibtex-headline-format-default
org-log-done 'time
org-fontify-done-headline nil
org-log-into-drawer t
org-startup-folded t
org-persist-after-read-hook '(org-element--cache-persist-after-read)
org-format-latex-options '(:foreground "Yellow" :background default :scale
1.2
:html-foreground "Black" :html-background
"Transparent"
:html-scale 1.07 :matchers ("begin" "$1" "$"
"$$" "\\(" "\\["))
org-export-before-parsing-hook '(org-attach-expand-links)
org-cycle-tab-first-hook '(org-babel-hide-result-toggle-maybe
org-babel-header-arg-expand)
org-archive-hook '(org-attach-archive-delete-maybe)
org-file-apps '((auto-mode . emacs) ("\\.odt\\'" . "libreoffice %s")
("\\.docx\\'" . "libreoffice %s") ("\\.xlsx\\'" .
"libreoffice %s")
("\\.png\\'" . "xv %s") ("\\.jpg\\'" . "xv %s")
("\\.jpeg\\'" . "xv %s")
("\\.webp\\'" . "xv %s") ("\\.pdf\\'" . "okular \"%s\"")
("\\.xoj" . "xournal %s") ("\\.xopp" . "xournalpp %s"))
org-odt-format-inlinetask-function
'org-odt-format-inlinetask-default-function
org-ascii-format-drawer-function #[771 " \207" [] 4 "\n\n(fn NAME CONTENTS
WIDTH)"]
org-cycle-hook '(org-cycle-hide-archived-subtrees
org-cycle-show-empty-lines
org-cycle-optimize-window-after-visibility-change
org-cycle-display-inline-images)
org-persist-before-read-hook '(org-element--cache-persist-before-read)
org-mode-hook '(#[0 "\300\301\302\303\304$\207"
[add-hook change-major-mode-hook org-fold-show-all
append local] 5]
#[0 "\300\301\302\303\304$\207"
[add-hook change-major-mode-hook
org-babel-show-result-all append local]
5]
org-babel-result-hide-spec org-babel-hide-all-hashes)
org-babel-load-languages '((R . t) (emacs-lisp . t) (gnuplot . t) (octave
. t) (python . t)
(fortran . t) (sql . t) (ditaa . t) (dot . t)
(shell . t))
org-latex-format-drawer-function #[514 "\207" [] 3 "\n\n(fn _ CONTENTS)"]
org-latex-format-headline-function
'org-latex-format-headline-default-function
org-confirm-shell-link-function 'yes-or-no-p
org-adapt-indentation t
org-html-format-drawer-function #[514 "\207" [] 3 "\n\n(fn NAME CONTENTS)"]
outline-isearch-open-invisible-function 'outline-isearch-open-invisible
org-highlight-latex-and-related '(latex)
org-odt-format-headline-function 'org-odt-format-headline-default-function
org-agenda-before-write-hook '(org-agenda-add-entry-text)
org-babel-tangle-lang-exts '(("fortran" . "F90") ("python" . "py")
("emacs-lisp" . "el")
("elisp" . "el"))
org-src-mode-hook '(org-src-babel-configure-edit-buffer
org-src-mode-configure-edit-buffer)
org-confirm-elisp-link-function 'yes-or-no-p
org-clock-out-remove-zero-time-clocks t
org-hide-leading-stars t
org-todo-keywords '((sequence "TODO(t!)" "MAYBE(m!)" "STARTED(s!)"
"WAITING(w@/!)" "|"
"DONE(d)" "INFO(i!)" "CANCELLED(c@)" "UNFINISHED(u@)"
"ABANDONED(a@)")
)
org-id-link-to-org-use-id t
org-speed-command-hook '(org-speed-command-activate
org-babel-speed-command-activate)
org-html-format-inlinetask-function
'org-html-format-inlinetask-default-function
org-ascii-format-inlinetask-function 'org-ascii-format-inlinetask-default
org-odt-format-drawer-function #[514 "\207" [] 3 "\n\n(fn NAME CONTENTS)"]
org-confirm-babel-evaluate nil
org-fold-core-isearch-open-function 'org-fold--isearch-reveal
org-clock-in-switch-to-state "STARTED"
org-clock-persist 'history
org-latex-format-inlinetask-function
'org-latex-format-inlinetask-default-function
org-persist-before-write-hook '(org-element--cache-persist-before-write)
org-tab-first-hook '(org-babel-hide-result-toggle-maybe
org-babel-header-arg-expand)
org-link-shell-confirm-function 'yes-or-no-p
org-babel-pre-tangle-hook '(save-buffer)
org-clock-display-default-range 'untilnow
org-agenda-loop-over-headlines-in-active-region nil
org-todo-keyword-faces '(("TODO" :foreground "light pink" :weight bold)
("MAYBE" :foreground "light pink" :weight bold)
("STARTED" :foreground "gold" :weight bold)
("DONE" :foreground "light green" :weight bold)
("WAITING" :foreground "gold" :weight bold)
("CANCELLED" :foreground "light green" :weight
bold)
("UNFINISHED" :foreground "light green" :weight
bold)
("ABANDONED" :foreground "light green" :weight
bold))
org-occur-hook '(org-first-headline-recenter)
org-export-with-drawers '("LATEX_DRAW")
org-metadown-hook '(org-babel-pop-to-session-maybe)
org-link-parameters '(("attachment" :follow org-attach-follow :complete
org-attach-complete-link)
("eww" :follow org-eww-open :store
org-eww-store-link)
("rmail" :follow org-rmail-open :store
org-rmail-store-link)
("mhe" :follow org-mhe-open :store
org-mhe-store-link)
("irc" :follow org-irc-visit :store
org-irc-store-link :export
org-irc-export)
("info" :follow org-info-open :export
org-info-export :store
org-info-store-link :insert-description
org-info-description-as-command)
("gnus" :follow org-gnus-open :store
org-gnus-store-link)
("docview" :follow org-docview-open :export
org-docview-export :store
org-docview-store-link)
("bibtex" :follow org-bibtex-open :store
org-bibtex-store-link)
("bbdb" :follow org-bbdb-open :export
org-bbdb-export :complete
org-bbdb-complete-link :store org-bbdb-store-link)
("w3m" :store org-w3m-store-link)
("doi" :follow org-link-doi-open :export
org-link-doi-export)
("id" :follow org-id-open) ("file+sys")
("file+emacs")
("shell" :follow org-link--open-shell)
("news" :follow
#[514 "\301\300\302 Q \"\207" ["news" browse-url
":"] 6
"\n\n(fn URL ARG)"]
)
("mailto" :follow
#[514 "\301\300\302 Q \"\207" ["mailto" browse-url
":"] 6
"\n\n(fn URL ARG)"]
)
("https" :follow
#[514 "\301\300\302 Q \"\207" ["https" browse-url
":"] 6
"\n\n(fn URL ARG)"]
)
("http" :follow
#[514 "\301\300\302 Q \"\207" ["http" browse-url
":"] 6
"\n\n(fn URL ARG)"]
)
("ftp" :follow
#[514 "\301\300\302 Q \"\207" ["ftp" browse-url
":"] 6
"\n\n(fn URL ARG)"]
)
("help" :follow org-link--open-help :store
org-link--store-help)
("file" :complete org-link-complete-file)
("elisp" :follow org-link--open-elisp))
org-html-format-headline-function
'org-html-format-headline-default-function
org-metaup-hook '(org-babel-load-in-session-maybe)
org-clock-history-length 28
org-clock-into-drawer "CLOCK"
)
[-- Attachment #1.2: Type: text/html, Size: 11132 bytes --]
[-- Attachment #2: bug.org --]
[-- Type: text/org, Size: 1628 bytes --]
Run with
/usr/bin/emacs -Q -l init.el bug.org
One should be able to click on the following link
- elisp:org-babel-tangle
to tangle (export) the code blocks in this org file.
Then one should be able to execute the code block
- [[code_block_to_execute]]
by using C-c C-c in code block.
However, it does not work because the tangle stage wraps the fortran
module in
program main
end program main
which prevents the code from compiling.
#+BEGIN_SRC fortran :tangle circle.f90
MODULE Circle
implicit None
public :: area
contains
function area(r)
implicit none
real, intent(in) :: r
real :: area
area = 3.14159 * r**2
return
end function area
END MODULE Circle
#+END_SRC
#+BEGIN_SRC fortran :tangle main.f90
program main
use circle, only: area
implicit none
integer :: i
REAL, DIMENSION(5) :: R
R = (/1.0, 2.0, 3.0, 4.0, 5.0 /)
print *, "#+tblname: circle-area"
do i = 1, 5
print *, "|", R(i), "|", area(R(i)), "|"
end do
end program main
#+END_SRC
#+BEGIN_SRC makefile :tangle makefile-main
circle:
@gfortran -c circle.f90
main: circle
@gfortran -c main.f90
@gfortran circle.o main.o -o main
clean:
@rm -f *.o main
#+END_SRC
<<code_block_to_execute>>
#+BEGIN_SRC sh :results raw replace
make -f makefile-main clean main
./main
#+END_SRC
#+RESULTS:
#+tblname: circle-area
| 1.00000000 | 3.14159012 |
| 2.00000000 | 12.5663605 |
| 3.00000000 | 28.2743111 |
| 4.00000000 | 50.2654419 |
| 5.00000000 | 78.5397491 |
[-- Attachment #3: init.el --]
[-- Type: text/x-emacs-lisp, Size: 122 bytes --]
(org-babel-do-load-languages
'org-babel-load-languages
'((fortran . t)))
(setq org-confirm-babel-evaluate nil)
^ permalink raw reply [flat|nested] 6+ messages in thread
* Re: [BUG] tangle breaks fortran modules [9.7-pre (release_9.6.7-581-gd38ca5)]
2023-09-04 1:59 [BUG] tangle breaks fortran modules [9.7-pre (release_9.6.7-581-gd38ca5)] Paul Stansell
@ 2023-09-04 7:56 ` Ihor Radchenko
2023-09-04 10:07 ` Paul Stansell
0 siblings, 1 reply; 6+ messages in thread
From: Ihor Radchenko @ 2023-09-04 7:56 UTC (permalink / raw)
To: Paul Stansell; +Cc: emacs-orgmode
Paul Stansell <paulstansell@gmail.com> writes:
> The attached file is an example of how tangle wraps the Fortran module in
>
> program main
> end program main
>
> which prevents the code from compiling.
>
> There are more instructions on how to reproduce the bug in the attached
> bug.org file.
I opened the latest Org git repo, ran make repro, opened the file,
clicked on "tangle" link, moved to the linked source code, and executed
it. It worked.
So, I am unable to reproduce the problem on my system.
--
Ihor Radchenko // yantar92,
Org mode contributor,
Learn more about Org mode at <https://orgmode.org/>.
Support Org development at <https://liberapay.com/org-mode>,
or support my work at <https://liberapay.com/yantar92>
^ permalink raw reply [flat|nested] 6+ messages in thread
* Re: [BUG] tangle breaks fortran modules [9.7-pre (release_9.6.7-581-gd38ca5)]
2023-09-04 7:56 ` Ihor Radchenko
@ 2023-09-04 10:07 ` Paul Stansell
2023-09-05 9:33 ` Ihor Radchenko
0 siblings, 1 reply; 6+ messages in thread
From: Paul Stansell @ 2023-09-04 10:07 UTC (permalink / raw)
To: Ihor Radchenko; +Cc: emacs-orgmode
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>
> I opened the latest Org git repo, ran make repro, opened the file,
> clicked on "tangle" link, moved to the linked source code, and executed
> it. It worked.
>
> So, I am unable to reproduce the problem on my system.
>
Hello Ihor,
Thanks for investigating. Can you please post your tangled file named
circle.f90.
Mine looks like this
program main
MODULE Circle
implicit None
public :: area
contains
function area(r)
implicit none
real, intent(in) :: r
real :: area
area = 3.14159 * r**2
return
end function area
END MODULE Circle
end program main
which is broken because org/babel has added the first and last lines.
Thanks,
Paul
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^ permalink raw reply [flat|nested] 6+ messages in thread
* Re: [BUG] tangle breaks fortran modules [9.7-pre (release_9.6.7-581-gd38ca5)]
2023-09-04 10:07 ` Paul Stansell
@ 2023-09-05 9:33 ` Ihor Radchenko
2023-09-05 15:53 ` Paul Stansell
0 siblings, 1 reply; 6+ messages in thread
From: Ihor Radchenko @ 2023-09-05 9:33 UTC (permalink / raw)
To: Paul Stansell; +Cc: emacs-orgmode
Paul Stansell <paulstansell@gmail.com> writes:
>>
>> I opened the latest Org git repo, ran make repro, opened the file,
>> clicked on "tangle" link, moved to the linked source code, and executed
>> it. It worked.
>>
>> So, I am unable to reproduce the problem on my system.
>>
>
> Thanks for investigating. Can you please post your tangled file named
> circle.f90.
>
> Mine looks like this
>
> program main
Never mind my previous message. I forgot the provided init.el file,
which makes all the difference.
Confirmed.
By default, ob-fortran (and at least ob-C) wrap the src block body to
become a standalone function unless you put :main no header argument.
The default behaviour is mostly useful during execution, but not when
tangling.
I will need to think about the best way to approach this. A tentative
fix would be handling :main header argument only during block evaluation.
Meanwhile, you can set :main no as default header argument for fortran.
--
Ihor Radchenko // yantar92,
Org mode contributor,
Learn more about Org mode at <https://orgmode.org/>.
Support Org development at <https://liberapay.com/org-mode>,
or support my work at <https://liberapay.com/yantar92>
^ permalink raw reply [flat|nested] 6+ messages in thread
* Re: [BUG] tangle breaks fortran modules [9.7-pre (release_9.6.7-581-gd38ca5)]
2023-09-05 9:33 ` Ihor Radchenko
@ 2023-09-05 15:53 ` Paul Stansell
2023-09-05 15:58 ` Ihor Radchenko
0 siblings, 1 reply; 6+ messages in thread
From: Paul Stansell @ 2023-09-05 15:53 UTC (permalink / raw)
To: Ihor Radchenko; +Cc: emacs-orgmode
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>
> Meanwhile, you can set :main no as default header argument for fortran.
>
Thanks for taking another look. I was not aware of ":main no", but it's a
perfectly good fix for my problem.
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^ permalink raw reply [flat|nested] 6+ messages in thread
* Re: [BUG] tangle breaks fortran modules [9.7-pre (release_9.6.7-581-gd38ca5)]
2023-09-05 15:53 ` Paul Stansell
@ 2023-09-05 15:58 ` Ihor Radchenko
0 siblings, 0 replies; 6+ messages in thread
From: Ihor Radchenko @ 2023-09-05 15:58 UTC (permalink / raw)
To: Paul Stansell; +Cc: emacs-orgmode
Paul Stansell <paulstansell@gmail.com> writes:
> ... I was not aware of ":main no"
Yeah. We don't have any documentation for ob-fortran, unfortunately.
--
Ihor Radchenko // yantar92,
Org mode contributor,
Learn more about Org mode at <https://orgmode.org/>.
Support Org development at <https://liberapay.com/org-mode>,
or support my work at <https://liberapay.com/yantar92>
^ permalink raw reply [flat|nested] 6+ messages in thread
end of thread, other threads:[~2023-09-05 15:58 UTC | newest]
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-- links below jump to the message on this page --
2023-09-04 1:59 [BUG] tangle breaks fortran modules [9.7-pre (release_9.6.7-581-gd38ca5)] Paul Stansell
2023-09-04 7:56 ` Ihor Radchenko
2023-09-04 10:07 ` Paul Stansell
2023-09-05 9:33 ` Ihor Radchenko
2023-09-05 15:53 ` Paul Stansell
2023-09-05 15:58 ` Ihor Radchenko
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