Re: [BUG] With R using ":var d=data" breaks ":colnames yes" [9.7-pre (release_9.6.10-881-g595a32]
Hi Ihor, Thanks for your advice, it helps a lot. Sorry for submitting something that wasn't a bug. Paul On Thu, 7 Mar 2024 at 13:16, Ihor Radchenko wrote: > Paul Stansell writes: > > > It seems that using ":var d=data" breaks ":colnames yes" in the header of > > an R code block. > > ... > > #+name: data > > |+| > > | x | y | > > |+| > > | 111.89 | 88.37 | > > | 392.12 | 297.33 | > > |+| > > It is expected. > :colnames yes implies: > > The ‘colnames’ header argument accepts ‘yes’, ‘no’, or ‘nil’ > values. The default value is ‘nil’: if an input table has column > names--because the second row is a horizontal rule--then Org > removes the column names, processes the table, puts back the column > names, and then writes the table to the results block. Using > ‘yes’, Org does the same to the first row, even if the initial > ^ > table does not contain any horizontal rule. When set to ‘no’, Org > does not pre-process column names at all. > > In your table, the first row is a horizontal line, so Org tries to parse > the first line as column names. And fails, of course. > > I guess that we can make `org-babel-get-colnames' smarter and make it > skip the leading hlines. > > -- > 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> >
[BUG] With R using ":var d=data" breaks ":colnames yes" [9.7-pre (release_9.6.10-881-g595a32]
Hello, It seems that using ":var d=data" breaks ":colnames yes" in the header of an R code block. In the example below the first code block uses ":colnames yes" and gives the correct output, the second code block uses ":var d=data" to read the data in the table (although it read the header as data), and the third code uses both ":colnames yes" and ":var d=data" but gives the error "Wrong type argument: sequencep, hline". Thanks, Paul # = Start example = #+name: data |+| | x | y | |+| | 111.89 | 88.37 | | 392.12 | 297.33 | |+| This code block works as expected. #+begin_src R --no-save --no-restore :colnames yes data.frame(x=1, y=2) #+end_src #+RESULTS: | x | y | |---+---| | 1 | 2 | This code block shows that the data in the table can be read (although the table header is read as data). #+begin_src R --no-save --no-restore :var d=data d #+end_src #+RESULTS: | x | y | | 111.89 | 88.37 | | 392.12 | 297.33 | However, using both ":colnames yes" and ":var d=data" together gives an error "Wrong type argument: sequencep, hline" #+begin_src R --no-save --no-restore :colnames yes :var d=data data.frame(x=1, y=2) #+end_src # = End example = Emacs : GNU Emacs 27.1 (build 1, x86_64-pc-linux-gnu, GTK+ Version 3.24.33, cairo version 1.16.0) of 2023-08-16, modified by Debian Package: Org mode version 9.7-pre (release_9.6.10-881-g595a32 @ /home/ps/.emacs.d_Kubuntu-23.04/org-mode-git/lisp/) current state: == (setq org-src-mode-hook '(org-src-babel-configure-edit-buffer org-src-mode-configure-edit-buffer) org-link-shell-confirm-function 'yes-or-no-p org-metadown-hook '(org-babel-pop-to-session-maybe) org-html-format-inlinetask-function 'org-html-format-inlinetask-default-function org-odt-format-headline-function 'org-odt-format-headline-default-function org-persist-before-write-hook '(org-element--cache-persist-before-write) org-ascii-format-inlinetask-function 'org-ascii-format-inlinetask-default org-startup-folded t org-id-link-to-org-use-id t org-mode-hook '((closure (org-agenda-skip-regexp org-fold-core-style org-table1-hline-regexp org-table-tab-recognizes-table\.el org-table-dataline-regexp org-table-any-border-regexp org-agenda-restriction-lock-overlay org-agenda-overriding-restriction org-agenda-diary-file org-complex-heading-regexp calendar-mode-map t) nil (setq imenu-create-index-function 'org-imenu-get-tree)) (closure (org--rds reftex-docstruct-symbol org-attach-method org--single-lines-list-is-paragraph org-element-greater-elements org-agenda-restrict-end org-agenda-restrict-begin org-agenda-restrict visual-fill-column-width org-clock-history org-agenda-current-date org-with-time org-defdecode org-def org-read-date-inactive org-ans2 org-ans1 org-columns-current-fmt-compiled org-clock-current-task org-clock-effort org-agenda-skip-function org-agenda-skip-comment-trees org-agenda-archives-mode org-end-time-was-given org-time-was-given org-log-note-extra org-log-note-purpose org-log-post-message org-last-inserted-timestamp org-last-changed-timestamp org-entry-property-inherited-from org-state org-agenda-headline-snapshot-before-repeat org-agenda-buffer-name org-agenda-start-on-weekday org-agenda-buffer-tmp-name org-priority-regexp org-mode-abbrev-table org-element-cache-persistent org-element-cache-version buffer-face-mode-face org-tbl-menu org-org-menu org-struct-menu org-entities org-last-state org-id-track-globally org-clock-start-time texmathp-why remember-data-file org-agenda-tags-todo-honor-ignore-options calc-embedded-open-mode calc-embedded-open-formula calc-embedded-close-formula align-mode-rules-list org-emphasis-alist org-emphasis-regexp-components org-export-registered-backends org-modules crm-separator org-babel-load-languages org-id-overriding-file-name org-indent-indentation-per-level org-element--timestamp-regexp org-element-cache-map-continue-from org-element-paragraph-separate org-agenda-buffer-name org-inlinetask-min-level t) nil (add-hook 'change-major-mode-hook 'org-fold-show-all 'append 'local)) (closure (org-src-window-setup *this* org-babel-confirm-evaluate-answer-no org-babel-tangle-uncomment-comments org-src-lang-modes
Bug: file names capitalised when using gnuplot [9.3 (release_9.3 @ /usr/share/emacs/27.1/lisp/org/)]
Hello,
A bug occurs when plotting data from an Org table using Gnuplot. An
example is given below. In the first code block the plot is produced as
expected, but in the second code block (where I have changed a lowercase
"c" to an uppercase "C") gnuplot tries to plot data from a
non-existent file name that consists of all uppercase letters.
Thanks,
Paul
# = Start example =
#+name: data
|+|
| x | y |
|+|
| 111.89 | 88.37 |
| 392.12 | 297.33 |
|+|
This code block works. It tries to read the data from
"/tmp/babel-stable-462/gnuplot--633772447824105179", which exists.
#+begin_src gnuplot :var c=data :results silent
reset session
plot "$c" u 1:2
#+end_src
This code block does not work. It tries to read the data from
"/TMP/BABEL-STABLE-462/GNUPLOT-2096937058546578295", which does not
exist.
#+begin_src gnuplot :var C=data :results silent
reset session
plot "$C" u 1:2
#+end_src
# = End example =
current state:
==
(setq
org-src-mode-hook '(org-src-babel-configure-edit-buffer
org-src-mode-configure-edit-buffer)
org-link-shell-confirm-function 'yes-or-no-p
org-metadown-hook '(org-babel-pop-to-session-maybe)
org-clock-out-hook '(org-clock-remove-empty-clock-drawer)
org-id-link-to-org-use-id t
org-mode-hook '(#[0 "\300\301\302\303\304$\207"
[add-hook change-major-mode-hook org-show-all append
local] 5]
#[0 "\300\301\302\303\304$\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-clock-persist 'history
org-archive-hook '(org-attach-archive-delete-maybe)
org-confirm-elisp-link-function 'yes-or-no-p
org-clock-history-length 28
org-agenda-before-write-hook '(org-agenda-add-entry-text)
org-metaup-hook '(org-babel-load-in-session-maybe)
org-bibtex-headline-format-function #[257 "\300 \236A\207" [:title] 3
"\n\n(fn ENTRY)"]
org-babel-pre-tangle-hook '(save-buffer)
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-tab-first-hook '(org-babel-hide-result-toggle-maybe
org-babel-header-arg-expand)
org-hide-leading-stars t
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-log-done 'time
org-highlight-latex-and-related '(latex)
org-occur-hook '(org-first-headline-recenter)
org-log-into-drawer t
org-cycle-hook '(org-cycle-hide-archived-subtrees
org-cycle-show-empty-lines
org-optimize-window-after-visibility-change)
org-todo-keywords '((sequence "TODO(t!)" "MAYBE(m!)" "STARTED(s!)"
"WAITING(w@/!)" "|"
"DONE(d)" "INFO(i!)" "CANCELLED(c@)" "UNFINISHED(u@)"
"ABANDONED(a@)")
)
org-speed-command-hook '(org-speed-command-activate
org-babel-speed-command-activate)
org-babel-tangle-lang-exts '(("fortran" . "F90") ("python" . "py")
("emacs-lisp" . "el")
("elisp" . "el"))
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-clock-display-default-range 'untilnow
org-confirm-shell-link-function 'yes-or-no-p
org-link-parameters '(("attachment" :follow org-attach-open-link :export
org-attach-export-link :complete
org-attach-complete-link)
("eww" :follow eww :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)
("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)
Re: [BUG] tmp [9.7-pre (release_9.6.10-881-g595a32 @ /home/ps/.emacs.d/org-mode-git/lisp/)]
Hello Ihor, Thanks very much for your clarification and advice. I didn't know about C- or `org-fold-catch-invisible-edits'. Setting (setq org-fold-catch-invisible-edits 'error) is very useful. Paul
[BUG] tmp [9.7-pre (release_9.6.10-881-g595a32 @ /home/ps/.emacs.d/org-mode-git/lisp/)]
Hello,
When using Org Mode version 9.7-pre (release_9.6.10-881-g595a32) the
following happens that doesn't happen when using Org Mode version 9.5.5
(release_9.5.5 @ /usr/share/emacs/28.2/lisp/org/)]:
When the cursor is at the end of a folded section, that is, immediately
after the ellipses, and return is pressed the folded section is made
visible (i.e., it is unfolded).
This is particularly problematic when adding a new section after the last
section in an org file. If the last section is folded it seems impossible
to get the cursor beyond the final ellipses so when adding a new section
below this one (using return or Alt-return) the previous section is
always opened. For sections that aren't the last one can put the cursor at
the start of the next section and press Alt-return to insert a new section
above it without unfolding any sections.
Kind regards,
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_9.6.10-881-g595a32 @
/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 'content
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 "\301\211 \207" [imenu-create-index-function
org-imenu-get-tree] 2]
#[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
Re: [BUG] Search leaves draws open [9.7-pre (release_9.6.10-835-gf3de4c @ ~/.emacs.d/org-mode-git/lisp/)]
> >> org-hide-drawer-all > >> > > > > I don't seem to have that command. I'm using Org mode > > release_9.6.10-835-gf3de4c. > > It was made into a command in > > https://git.savannah.gnu.org/cgit/emacs/org-mode.git/commit/?id=13353f1fa34f6f085ffbf142b380af7308f02981 I see, I found the command, it's called org-fold-hide-drawer-all (not org-hide-drawer-all). However, strangely, it doesn't close drawers that have been opened by the bug that causes drawers to remain open after the searching (eg, those opened by searching for "text" in the file I included in my bug report).
Re: [BUG] Search leaves draws open [9.7-pre (release_9.6.10-835-gf3de4c @ ~/.emacs.d/org-mode-git/lisp/)]
> > > In the meantime, is there a command that will close all drawers, even > those > > that are open in sections (headings) that are closed? I searched but > > didn't find anything. > > org-hide-drawer-all > I don't seem to have that command. I'm using Org mode release_9.6.10-835-gf3de4c. I grep for org-hide-drawer-all there is the following entry that seems to imply the command is obsolete: (define-obsolete-function-alias 'org-hide-drawer-all 'org-fold-hide-drawer-all "9.6") If I try to run the command using M-x org-hide-drawer-all I'm told "no match".
Re: [BUG] Search leaves draws open [9.7-pre (release_9.6.10-835-gf3de4c @ ~/.emacs.d/org-mode-git/lisp/)]
Hello Ihor, In the meantime, is there a command that will close all drawers, even those that are open in sections (headings) that are closed? I searched but didn't find anything. Thanks, Paul
[BUG] Search leaves draws open [9.7-pre (release_9.6.10-835-gf3de4c @ ~/.emacs.d/org-mode-git/lisp/)]
Hello,
Using Ctrl-S to search an org file leaves drawers open after the search.
For example, open the attached org file, search_bug.org, and, with the
cursor initially at the first line of the file, search for "text" with
- Ctrl-s text
This finds the first occurrence of "text" in "Subsection 1". Then press
Ctrl-a to go to the beginning of the line. At this point all the drawers
in "Subsection 1" are opened and left open. They are not closed by
Shift-tab visibility cycling.
This doesn't happen with Org mode version 9.5.5 (release_9.5.5).
Thanks,
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_9.6.10-835-gf3de4c @
~/.emacs.d/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-persist-after-read-hook '(org-element--cache-persist-after-read)
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-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-confirm-shell-link-function 'yes-or-no-p
outline-isearch-open-invisible-function 'outline-isearch-open-invisible
org-agenda-before-write-hook '(org-agenda-add-entry-text)
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-speed-command-hook '(org-speed-command-activate
org-babel-speed-command-activate)
org-persist-directory "/tmp/org-persist-Fs6tWx"
org-fold-core-isearch-open-function 'org-fold--isearch-reveal
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-agenda-loop-over-headlines-in-active-region nil
org-occur-hook '(org-first-headline-recenter)
org-metadown-hook '(org-babel-pop-to-session-maybe)
org-link-parameters '(("attachment" :follow org-attach-follow :complete
org-attach-complete-link)
("id" :follow org-id-open)
("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)
("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-metaup-hook '(org-babel-load-in-session-maybe)
)
--
Paul
#+STARTUP: content
* Section
** STARTED Subsection 1
:LOGBOOK:
- State "STARTED"from [2022-04-25 Mon 10:56]
:END:
:CLOCK:
CLOCK: [2023-01-29 Sun 19:10]--[2023-01-29 Sun 19:34] => 0:24
CLOCK: [2023-01-28 Sat 21:24]--[2023-01-28 Sat 21:53] => 0:29
CLOCK: [2022-04-26 Tue 15:48]--[2022-04-26 Tue 16:43] => 0:55
CLOCK: [2022-04-25 Mon 10:56]--[2022-04-25 Mon 11:36] => 0:40
:END:
text
** STARTED Subsection 2
:LOGBOOK:
- State
Re: Named columns in org tables [9.7-pre (release_9.6.9-797-g4d0f89]
Hello Bruno, > Could allowing column names on the LHS in my first example be put on a > todo list? > It seems to be on a todo list already as the following exists: - https://list.orgmode.org/877cqwbpa2@runbox.com Paul
Fwd: Named columns in org tables [9.7-pre (release_9.6.9-797-g4d0f89]
Hello Bruno,
It seems to me it's a bug in the documentation.
>
> Currently, column names are not allowed in the LHS (Left Hand Side) of
> the formula ('org-table-get-stored-formulas' assumes it). Although I'm
> not sure why.
>
However, the following, with the column name on the RHS, works
|---+++|
| | 3 | 4 ||
| ^ | c1 | c2 | c3 |
|---+++|
#+TBLFM: $c3 = $c1 + $c2
Could allowing column names on the LHS in my first example be put on a todo
list?
By the way, there is a small error in your example as your $3 should be $4.
Thanks,
Paul
Named columns in org tables [9.7-pre (release_9.6.9-797-g4d0f89]
Hello,
On this page https://orgmode.org/manual/Advanced-features.html
it says
- '!' :: The fields in this line define names for the columns, so that
you may refer to a column as '$Tot' instead of '$6'.
However, when I experimented with this I found that the first of the
following two tables works (i.e. the empty cells are filled in
correctly), but the second doesn't (the only difference is the
replacement of $4 with $c3 in the second table):
|---+++|
| ! | c1 | c2 | c3 |
| # | 1 | 2 ||
| # | 3 | 4 ||
|---+++|
#+TBLFM: $4 = $c1 + $c2
|---+++|
| ! | c1 | c2 | c3 |
| # | 1 | 2 ||
| # | 3 | 4 ||
|---+++|
#+TBLFM: $c3 = $c1 + $c2
Is this a bug?
Thanks,
Paul
===
Emacs : GNU Emacs 28.2 (build 1, x86_64-pc-linux-gnu, GTK+ Version
3.24.37, cairo version 1.16.0)
of 2023-03-16, modified by Debian
Package: Org mode version 9.7-pre (release_9.6.9-797-g4d0f89 @
~/.emacs.d/org-mode-git/lisp/)
current state:
==
(setq
org-link-elisp-confirm-function 'yes-or-no-p
org-bibtex-headline-format-function 'org-bibtex-headline-format-default
org-persist-after-read-hook '(org-element--cache-persist-after-read)
org-export-before-parsing-hook '(org-attach-expand-links)
org-cycle-tab-first-hook '(org-babel-hide-result-toggle-maybe
org-babel-header-arg-expand)
org-archive-hook '(org-attach-archive-delete-maybe)
org-cycle-hook '(org-cycle-hide-archived-subtrees
org-cycle-show-empty-lines
org-cycle-optimize-window-after-visibility-change
org-cycle-display-inline-images)
org-persist-before-read-hook '(org-element--cache-persist-before-read)
org-mode-hook '(#[0 "\300\301\302\303\304$\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-confirm-shell-link-function 'yes-or-no-p
outline-isearch-open-invisible-function 'outline-isearch-open-invisible
org-agenda-before-write-hook '(org-agenda-add-entry-text)
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-speed-command-hook '(org-speed-command-activate
org-babel-speed-command-activate)
org-persist-directory "/tmp/org-persist-Cls3dG"
org-fold-core-isearch-open-function 'org-fold--isearch-reveal
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-agenda-loop-over-headlines-in-active-region nil
org-occur-hook '(org-first-headline-recenter)
org-metadown-hook '(org-babel-pop-to-session-maybe)
org-link-parameters '(("attachment" :follow org-attach-follow :complete
org-attach-complete-link)
("id" :follow org-id-open)
("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)
("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-metaup-hook '(org-babel-load-in-session-maybe)
)
Re: [BUG] wrong-type-argument listp 4240 [9.7-pre (release_9.6.8-749-g4fe52f @ .emacs.d/org-mode-git/lisp/)]
> May you please add > > (setq org-element--cache-self-verify 'backtrace) > (setq org-element--cache-self-verify-frequency 1.0) > > to your config? > Yes, I'll do that, thanks.
Re: [BUG] wrong-type-argument listp 4240 [9.7-pre (release_9.6.8-749-g4fe52f @ .emacs.d/org-mode-git/lisp/)]
Hello Ihor, Please let us know if you keep seeing the error more than once. > > If you do, we will provide instructions how to get more debugging info, > so that we can figure out what exactly is going wrong. > Since I reported the first warning message in this thread, I've had about half a dozen similar (but not identical) ones when opening an org file. They are not repeatable though, in the sense that if I close the file and re-open it I don't see the warning a second time. The latest message is this: Warning (org-element-cache): org-element--cache: Org parser error in file.org::1687. Resetting. The error was: (error "Invalid search bound (wrong side of point)") Backtrace: nil Please report this to Org mode mailing list (M-x org-submit-bug-report). Disable showing Disable logging Paul
[BUG] wrong-type-argument listp 4240 [9.7-pre (release_9.6.8-749-g4fe52f @ .emacs.d/org-mode-git/lisp/)]
Hello,
I don't know what caused the following message when I opened an org file,
but I'm reporting it as requested by the message:
Warning (org-element-cache): org-element--cache: Org parser error in
tmp_train_notes.org::1. Resetting.
The error was: (wrong-type-argument listp 4240)
Backtrace:
nil
Please report this to Org mode mailing list (M-x org-submit-bug-report).
Disable showing Disable logging
When I opened the same file a second time there was no error message.
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_9.6.8-749-g4fe52f @
~/.emacs.d/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-src-preserve-indentation t
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-core--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
Re: [BUG] unexpected octave output from code blocks [9.7-pre (release_9.6.7-581-gd38ca5)]
> > Thanks for reporting! > Fixed, on main. > https://git.savannah.gnu.org/cgit/emacs/org-mode.git/commit/?id=13e4ee737 Great work, thanks!
[BUG] unexpected octave output from code blocks [9.7-pre (release_9.6.7-581-gd38ca5)]
Hello, The attached org file gives examples of outputs from octave code blocks that are unexpected and inconsistent. The attached bug.org file should be opened with emacs -Q -l init.el bug.org The problems only occur when the ":session" header is used. 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/) (org-babel-do-load-languages 'org-babel-load-languages '((octave . t))) (setq org-confirm-babel-evaluate nil) Run with /usr/bin/emacs -Q -l init.el bug.org Then execute the code blocks by using C-c C-c in code block. Unexpected output (as it includes a blank line ": " and "octave >") #+begin_src octave :session oct1 :results output x = 1; x = 1; x = 1 #+end_src #+RESULTS: : : octave> x = 1 Unexpected output (as it does not include ": x = 1") #+begin_src octave :session oct2 :results output x = 1; x = 1 x = 1; #+end_src #+RESULTS: By comparison, these code block give expected results #+begin_src octave :session oct3 :results output x = 1 x = 1 x = 1 #+end_src #+RESULTS: : x = 1 : x = 1 : x = 1 #+begin_src octave :session oct4 :results output x = 1; x = 1 x = 1 #+end_src #+RESULTS: : : x = 1 : x = 1 Also, if the ":session" headers are removed the all the code blocks give the expected results, for example, #+begin_src octave :results output x = 1; x = 1; x = 1 #+end_src #+RESULTS: : x = 1
Re: [BUG] tangle breaks fortran modules [9.7-pre (release_9.6.7-581-gd38ca5)]
> > 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.
Re: [BUG] tangle breaks fortran modules [9.7-pre (release_9.6.7-581-gd38ca5)]
> > 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
[BUG] tangle breaks fortran modules [9.7-pre (release_9.6.7-581-gd38ca5)]
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)
Re: [BUG] org-export-data: Unable to resolve link [9.7-pre (release_9.6.7-579-gde9f89)]
On Sat, 29 Jul 2023 at 09:30, Ihor Radchenko wrote > > Thanks for reporting! > Fixed, on main. > https://git.savannah.gnu.org/cgit/emacs/org-mode.git/commit/?id=d38ca5923 It's working fine now. Thanks very much for your quick response!
[BUG] org-export-data: Unable to resolve link [9.7-pre (release_9.6.7-579-gde9f89)]
In org version 9.3, the gnuplot code block below successfully plots the data
in Table1 (which includes a local hyperlink in the last column).
#+name: Table1
| x | y | notes |
|---++|
| 0 | 0 | [[note_1]] |
| 1 | 1 ||
| 2 | 4 ||
<>: a note
#+begin_src gnuplot :var d=Table1 :results silent
plot [][] d u 1:2 w lp
#+end_src
However, trying the same in the newer org versions 9.3 or 9.7-pre gives the
error:
Unable to resolve link: "note_1"
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_9.6.7-579-gde9f89 @
/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-persist-after-read-hook '(org-element--cache-persist-after-read)
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-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 '((gnuplot . 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-html-format-drawer-function #[514 "\207" [] 3 "\n\n(fn NAME CONTENTS)"]
outline-isearch-open-invisible-function 'outline-isearch-open-invisible
org-odt-format-headline-function 'org-odt-format-headline-default-function
org-agenda-before-write-hook '(org-agenda-add-entry-text)
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-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-fold-core-isearch-open-function 'org-fold--isearch-reveal
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-agenda-loop-over-headlines-in-active-region nil
org-occur-hook '(org-first-headline-recenter)
org-metadown-hook '(org-babel-pop-to-session-maybe)
org-link-parameters '(("attachment" :follow org-attach-follow :complete
org-attach-complete-link)
("id" :follow org-id-open)
("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)
("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
Re: [O] Bug: Clock times not summed correctly between years [9.0.9 (9.0.9-82-gb862c2-elpa @ ~/.emacs.d/elpa/org/)]
I see that the exact same "bug" was reported at the start of 2016 by David Bremner. Personally, I feel that fewer people would be confused by this if the default value was set to "untilnow". I also realised that the full list of values that I can use for org-clock-display-default-range is described in org-clock.el. By the way, you guys are brilliant and I thank you for your work on org mode (which I'd struggle to live without now that I'm so dependent on it).
Re: [O] Bug: Clock times not summed correctly between years [9.0.9 (9.0.9-82-gb862c2-elpa @ ~/.emacs.d/elpa/org/)]
Hello Nicolas, Thanks for that tip, I was totally unaware of that option (it doesn't seem to be mentioned in the user documentation, eg, it's not mentioned on https://orgmode.org/manual/Clocking-commands.html). I do wonder why the default range should be set at the current year and not simply over the full range of clocked times in a heading. Kind regards, Paul On 7 January 2018 at 00:32, Nicolas Goaziou <m...@nicolasgoaziou.fr> wrote: > Hello, > > Paul Stansell <paulstans...@gmail.com> writes: > > > The sum of the clock time seems to be summing just times in the current > > year. In the example below typing C-c C-x C-d in the "Example" section > > displays "1:00" instead of "2:00" on the heading line. The clocktable > > computes the sum correctly as "2:00". > > See `org-clock-display-default-range'. > > Regards, > > -- > Nicolas Goaziou >
[O] Bug: Clock times not summed correctly between years [9.0.9 (9.0.9-82-gb862c2-elpa @ ~/.emacs.d/elpa/org/)]
Hello,
The sum of the clock time seems to be summing just times in the current
year. In the example below typing C-c C-x C-d in the "Example" section
displays "1:00" instead of "2:00" on the heading line. The clocktable
computes the sum correctly as "2:00".
Thanks
# Start Example
#+BEGIN: clocktable :maxlevel 2 :scope file
#+CAPTION: Clock summary at [2018-01-06 Sat 21:57]
| Headline | Time |
|--+|
| *Total time* | *2:00* |
|--+|
| Example | 2:00 |
#+END:
* DONE Example
:END:
:CLOCK:
CLOCK: [2018-01-06 Sat 20:00]--[2018-01-06 Sat 20:30] => 0:30
CLOCK: [2018-01-06 Sat 19:30]--[2018-01-06 Sat 20:00] => 0:30
CLOCK: [2017-01-06 Fri 20:00]--[2017-01-06 Fri 20:30] => 0:30
CLOCK: [2017-01-06 Fri 19:30]--[2017-01-06 Fri 20:00] => 0:30
:END:
# End Example --
Emacs : GNU Emacs 24.5.1 (x86_64-redhat-linux-gnu, GTK+ Version 2.24.23)
of 2015-08-26 on localhost.localdomain
Package: Org mode version 9.0.9 (9.0.9-82-gb862c2-elpa @ ~/.emacs.d/elpa/org/)
current state:
==
(setq
org-tab-first-hook '(org-babel-hide-result-toggle-maybe
org-babel-header-arg-expand)
org-speed-command-hook '(org-speed-command-default-hook
org-babel-speed-command-hook)
org-occur-hook '(org-first-headline-recenter)
org-metaup-hook '(org-babel-load-in-session-maybe)
org-confirm-shell-link-function 'yes-or-no-p
org-after-todo-state-change-hook '(org-clock-out-if-current)
org-src-mode-hook '(org-src-babel-configure-edit-buffer
org-src-mode-configure-edit-buffer)
org-agenda-before-write-hook '(org-agenda-add-entry-text)
org-babel-pre-tangle-hook '(save-buffer)
org-mode-hook '(#[0 "\300\301\302\303\304$\207"
[add-hook change-major-mode-hook org-show-block-all append local] 5
"\n\n(fn)"]
#[0 "\300\301\302\303\304$\207"
[add-hook change-major-mode-hook org-babel-show-result-all
append local] 5
"\n\n(fn)"]
org-babel-result-hide-spec org-babel-hide-all-hashes)
org-archive-hook '(org-attach-archive-delete-maybe)
org-cycle-hook '(org-cycle-hide-archived-subtrees org-cycle-hide-drawers
org-cycle-show-empty-lines
org-optimize-window-after-visibility-change)
org-confirm-elisp-link-function 'yes-or-no-p
org-metadown-hook '(org-babel-pop-to-session-maybe)
org-link-parameters '(("id" :follow org-id-open)
("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)
("info" :follow org-info-open :export org-info-export :store
org-info-store-link)
("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) ("file+sys") ("file+emacs")
("doi" :follow org--open-doi-link)
("elisp" :follow org--open-elisp-link)
("file" :complete org-file-complete-link)
("ftp" :follow (lambda (path) (browse-url (concat "ftp:" path
("help" :follow org--open-help-link)
("http" :follow (lambda (path) (browse-url (concat
"http:" path
("https" :follow (lambda (path) (browse-url (concat
"https:" path
("mailto" :follow (lambda (path) (browse-url (concat
"mailto:; path
("message" :follow
(lambda (path) (browse-url (concat "message:" path
("news" :follow (lambda (path) (browse-url (concat
"news:; path
("shell" :follow org--open-shell-link))
org-clock-out-hook '(org-clock-remove-empty-clock-drawer)
)
[O] Bug: python code block single import line [9.0.9 (release_9.0.9-754-g940c90)]
Hello,
When executing the python code block
#+begin_src python :session python1
import numpy as np
#+end_src
I get this error in my python buffer
Python 3.5.1 |Anaconda 2.5.0 (64-bit)| (default, Dec 7 2015, 11:16:01)
[GCC 4.4.7 20120313 (Red Hat 4.4.7-1)] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> >>> >>> import numpy as np
>>>
open('/tmp/babel-5320QCO/python-5320y31', 'w').write(str(_))
'org_babel_python_eoe'
>>> >>> Traceback (most recent call last):
File "", line 1, in
NameError: name '_' is not defined
>>> >>> >>> 'org_babel_python_eoe'
>>>
However, the following code block does not give an error:
#+begin_src python :session python2
import numpy as np
1
#+end_src
Thanks,
Paul
Emacs : GNU Emacs 24.5.1 (x86_64-redhat-linux-gnu, GTK+ Version 2.24.23)
of 2015-08-26 on localhost.localdomain
Package: Org mode version 9.0.9 (release_9.0.9-754-g940c90)
current state:
==
(setq
org-tab-first-hook '(org-babel-hide-result-toggle-maybe
org-babel-header-arg-expand)
org-speed-command-hook '(org-speed-command-activate
org-babel-speed-command-activate)
org-occur-hook '(org-first-headline-recenter)
org-metaup-hook '(org-babel-load-in-session-maybe)
org-confirm-shell-link-function 'yes-or-no-p
org-after-todo-state-change-hook '(org-clock-out-if-current)
org-src-mode-hook '(org-src-babel-configure-edit-buffer
org-src-mode-configure-edit-buffer)
org-agenda-before-write-hook '(org-agenda-add-entry-text)
org-babel-pre-tangle-hook '(save-buffer)
org-mode-hook '(#[0 "\300\301\302\303\304$\207"
[add-hook change-major-mode-hook org-show-block-all append
local] 5
"\n\n(fn)"]
#[0 "\300\301\302\303\304$\207"
[add-hook change-major-mode-hook org-babel-show-result-all
append local] 5
"\n\n(fn)"]
org-babel-result-hide-spec org-babel-hide-all-hashes)
org-bibtex-headline-format-function #[257 "\300 \236A\207" [:title] 3
"\n\n(fn ENTRY)"]
org-archive-hook '(org-attach-archive-delete-maybe)
org-cycle-hook '(org-cycle-hide-archived-subtrees org-cycle-hide-drawers
org-cycle-show-empty-lines
org-optimize-window-after-visibility-change)
org-babel-tangle-lang-exts '(("python" . "py") ("emacs-lisp" . "el")
("elisp" . "el"))
org-confirm-elisp-link-function 'yes-or-no-p
org-metadown-hook '(org-babel-pop-to-session-maybe)
org-link-parameters '(("id" :follow org-id-open)
("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)
("info" :follow org-info-open :export org-info-export :store
org-info-store-link)
("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) ("file+sys") ("file+emacs")
("doi" :follow org--open-doi-link)
("elisp" :follow org--open-elisp-link)
("file" :complete org-file-complete-link)
("ftp" :follow (lambda (path) (browse-url (concat "ftp:"
path
("help" :follow org--open-help-link)
("http" :follow (lambda (path) (browse-url (concat "http:"
path
("https" :follow (lambda (path) (browse-url (concat "https:"
path
("mailto" :follow (lambda (path) (browse-url (concat "mailto:;
path
("news" :follow (lambda (path) (browse-url (concat "news:;
path
("shell" :follow org--open-shell-link))
org-babel-load-languages '((python . t))
org-clock-out-hook '(org-clock-remove-empty-clock-drawer)
)
[O] Bug: Explicit <6> table column width [9.0.9 (release_9.0.9-754-g940c90)]
Hello,
I think there might be a something wrong when explicitly setting a width
of a table column.
For example, for this table
|---+--|
| | <6> |
| 1 | one |
| 2 | This is a long chunk of text |
| 3 | three|
|---+--|
when I press in the table the view changes to
|---+--|
| | <6> |
| 1 | one |
| 2 | This i |
| 3 | three|
|---+--|
and when I press C-c the view toggles between
|---+|
| | <6>|
| 1 | one|
| 2 | This is a long chunk of text |
| 3 | three |
|---+|
and
|---+--|
| | <6> |
| 1 | one |
| 2 | This is a long chunk of text |
| 3 | three|
|---+--|
Based on previous versions of org mode, I expect to see
|---+|
| | <6>|
| 1 | one|
| 2 | This=> |
| 3 | three |
|---+|
and
|---+--|
| | <6> |
| 1 | one |
| 2 | This is a long chunk of text |
| 3 | three|
|---+--|
Thanks,
Paul
Emacs : GNU Emacs 24.5.1 (x86_64-redhat-linux-gnu, GTK+ Version 2.24.23)
of 2015-08-26 on localhost.localdomain
Package: Org mode version 9.0.9 (release_9.0.9-754-g940c90)
current state:
==
(setq
org-tab-first-hook '(org-babel-hide-result-toggle-maybe
org-babel-header-arg-expand)
org-speed-command-hook '(org-speed-command-activate
org-babel-speed-command-activate)
org-occur-hook '(org-first-headline-recenter)
org-metaup-hook '(org-babel-load-in-session-maybe)
org-confirm-shell-link-function 'yes-or-no-p
org-after-todo-state-change-hook '(org-clock-out-if-current)
org-src-mode-hook '(org-src-babel-configure-edit-buffer
org-src-mode-configure-edit-buffer)
org-agenda-before-write-hook '(org-agenda-add-entry-text)
org-babel-pre-tangle-hook '(save-buffer)
org-mode-hook '(#[0 "\300\301\302\303\304$\207"
[add-hook change-major-mode-hook org-show-block-all append
local] 5
"\n\n(fn)"]
#[0 "\300\301\302\303\304$\207"
[add-hook change-major-mode-hook org-babel-show-result-all
append local] 5
"\n\n(fn)"]
org-babel-result-hide-spec org-babel-hide-all-hashes)
org-bibtex-headline-format-function #[257 "\300 \236A\207" [:title] 3
"\n\n(fn ENTRY)"]
org-archive-hook '(org-attach-archive-delete-maybe)
org-cycle-hook '(org-cycle-hide-archived-subtrees org-cycle-hide-drawers
org-cycle-show-empty-lines
org-optimize-window-after-visibility-change)
org-confirm-elisp-link-function 'yes-or-no-p
org-metadown-hook '(org-babel-pop-to-session-maybe)
org-link-parameters '(("id" :follow org-id-open)
("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)
("info" :follow org-info-open :export org-info-export :store
org-info-store-link)
("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) ("file+sys") ("file+emacs")
("doi" :follow org--open-doi-link)
("elisp" :follow org--open-elisp-link)
("file" :complete org-file-complete-link)
("ftp" :follow (lambda (path) (browse-url (concat "ftp:"
path
("help" :follow org--open-help-link)
("http" :follow (lambda (path) (browse-url (concat "http:"
path
("https" :follow (lambda (path) (browse-url (concat "https:"
path
("mailto" :follow (lambda (path) (browse-url (concat "mailto:;
path
("news" :follow (lambda (path) (browse-url (concat "news:;
path
("shell" :follow org--open-shell-link))
org-clock-out-hook '(org-clock-remove-empty-clock-drawer)
)
[O] Bug: Latex math mode not set in footnotes [9.0.9 (9.0.9-68-g492420-elpa @ /Home/ps/.emacs.d/elpa/org/)]
Hello,
Latex math mode is not set in a footnote when exporting an org file to
tex or pdf. Below and attached is a simple example.
Thanks
---cut here--
* Example
When exporting to pdf math $\hat{x}$ is okay in the main text but
not in this footnote.[fn:footnote_1: Math $\hat{x}$.]
---cut here--
Emacs : GNU Emacs 24.5.1 (x86_64-redhat-linux-gnu, GTK+ Version 2.24.23)
of 2015-08-26 on localhost.localdomain
Package: Org mode version 9.0.9 (9.0.9-68-g492420-elpa @
/Home/ps/.emacs.d/elpa/org/)
current state:
==
(setq
org-tab-first-hook '(org-babel-hide-result-toggle-maybe
org-babel-header-arg-expand)
org-speed-command-hook '(org-speed-command-default-hook
org-babel-speed-command-hook)
org-occur-hook '(org-first-headline-recenter)
org-metaup-hook '(org-babel-load-in-session-maybe)
org-confirm-shell-link-function 'yes-or-no-p
org-after-todo-state-change-hook '(org-clock-out-if-current)
org-src-mode-hook '(org-src-babel-configure-edit-buffer
org-src-mode-configure-edit-buffer)
org-agenda-before-write-hook '(org-agenda-add-entry-text)
org-babel-pre-tangle-hook '(save-buffer)
org-mode-hook '(#[0 "\300\301\302\303\304$\207"
[add-hook change-major-mode-hook org-show-block-all append local] 5
"\n\n(fn)"]
#[0 "\300\301\302\303\304$\207"
[add-hook change-major-mode-hook org-babel-show-result-all
append local] 5
"\n\n(fn)"]
org-babel-result-hide-spec org-babel-hide-all-hashes)
org-archive-hook '(org-attach-archive-delete-maybe)
org-cycle-hook '(org-cycle-hide-archived-subtrees org-cycle-hide-drawers
org-cycle-show-empty-lines
org-optimize-window-after-visibility-change)
org-confirm-elisp-link-function 'yes-or-no-p
org-metadown-hook '(org-babel-pop-to-session-maybe)
org-link-parameters '(("id" :follow org-id-open)
("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)
("info" :follow org-info-open :export org-info-export :store
org-info-store-link)
("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) ("file+sys") ("file+emacs")
("doi" :follow org--open-doi-link)
("elisp" :follow org--open-elisp-link)
("file" :complete org-file-complete-link)
("ftp" :follow (lambda (path) (browse-url (concat "ftp:" path
("help" :follow org--open-help-link)
("http" :follow (lambda (path) (browse-url (concat
"http:" path
("https" :follow (lambda (path) (browse-url (concat
"https:" path
("mailto" :follow (lambda (path) (browse-url (concat
"mailto:; path
("message" :follow
(lambda (path) (browse-url (concat "message:" path
("news" :follow (lambda (path) (browse-url (concat
"news:; path
("shell" :follow org--open-shell-link))
org-clock-out-hook '(org-clock-remove-empty-clock-drawer)
)
bug.org
Description: Lotus Organizer
[O] Bug: org-id-link-to-org-use-id causes double tangle output [8.2.10 (8.2.10-elpa @ ~/.emacs.d/elpa/org/)]
With the following org file: * Section #+begin_src R :tangle file.R x - 1 #+end_src and (setq org-id-link-to-org-use-id t) the first time tangling is done with C-c C-v t the ID property is added automatically and twice the expected output is written to file.R, that is, x - 1 x - 1 Subsequent tangling with C-c C-v t produces, as expected, a single copy of the output to file.R. Emacs : GNU Emacs 24.2.1 (x86_64-unknown-linux-gnu, GTK+ Version 2.18.9) of 2012-09-21 on CRMDA020L Package: Org-mode version 8.2.10 (8.2.10-elpa @ /Home/ps/.emacs.d/elpa/org/) current state: == (setq org-tab-first-hook '(org-hide-block-toggle-maybe org-src-native-tab-command-maybe org-babel-hide-result-toggle-maybe org-babel-header-arg-expand) org-speed-command-hook '(org-speed-command-default-hook org-babel-speed-command-hook) org-occur-hook '(org-first-headline-recenter) org-metaup-hook '(org-babel-load-in-session-maybe) org-confirm-shell-link-function 'yes-or-no-p org-id-link-to-org-use-id t org-after-todo-state-change-hook '(org-clock-out-if-current) org-src-mode-hook '(org-src-babel-configure-edit-buffer org-src-mode-configure-edit-buffer) org-agenda-before-write-hook '(org-agenda-add-entry-text) org-babel-pre-tangle-hook '(save-buffer) org-mode-hook '(#[nil \300\301\302\303\304$\207 [org-add-hook change-major-mode-hook org-show-block-all append local] 5] #[nil \300\301\302\303\304$\207 [org-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-ctrl-c-ctrl-c-hook '(org-babel-hash-at-point org-babel-execute-safely-maybe) org-cycle-hook '(org-cycle-hide-archived-subtrees org-cycle-hide-drawers org-cycle-hide-inline-tasks org-cycle-show-empty-lines org-optimize-window-after-visibility-change) org-confirm-elisp-link-function 'yes-or-no-p org-metadown-hook '(org-babel-pop-to-session-maybe) org-clock-out-hook '(org-clock-remove-empty-clock-drawer) )
Re: [O] Bug: org-catch-invisible-edits [8.2.5h (8.2.5h-30-gdd810b-elpa @ ~/.emacs.d/elpa/org/)]
Hi Bastien, Thanks for that info on org-catch-invisible-edits. It wasn't clear to me as the documentation implies that it helps when you inadvertently edit an invisible part of the buffer, but it seems that the edits have to be results of key presses (not yanks or replaces, etc). I'm not sure how useful I would find the function. I'd like a way to stop any edits (including yanks etc.) on invisible parts of a buffer. I experimented with org-catch-invisible-edits by typing and deleting characters in folded sections of a simple org file. It seem to work well if the insertions or deletions occur at one hidden level down. In this case it opens the folded section and shows the edit after a short delay. But if I edit or delete two hidden sections down it doesn't seem to work properly as it only open the first hidden section and so the edit, which is another level down, is not shown. For example, for the org file below, editing the line level 2 when both Section 1 and Section 2 are folded (hidden) causes only Section 1 to be unfolded with Section 2 still folded inside it. Thus, the edits are not visible. * section 1 level 1 ** section 2 level 2 Kind regards, Paul On 13 March 2014 14:24, Bastien b...@gnu.org wrote: Hi Paul, Paul Stansell paulstans...@gmail.com writes: Today I came across org-catch-invisible-edits, but I'm struggling to get it to work. Since I've never had it working it's possible that I'm misunderstanding it or doing something wrong, or maybe it's broken. In my .emacs file I put (setq org-catch-invisible-edits 'show) but both 'M-x query-replace' and 'M-x replace-string' still replace hidden strings in folded sections of an org file. The name of the option is a bit misleading: your setup will catch *insertions* not editions. To put it simply, it's only active when inserting a character, not when using general-purpose editing commands like replace-string. I'm not sure it's worth using another name, though. -- Bastien
Re: [O] Bug:
Yes, it's fixed now, thanks.
[O] Bug: org-catch-invisible-edits [8.2.5h (8.2.5h-30-gdd810b-elpa @ ~/.emacs.d/elpa/org/)]
Hi, Today I came across org-catch-invisible-edits, but I'm struggling to get it to work. Since I've never had it working it's possible that I'm misunderstanding it or doing something wrong, or maybe it's broken. In my .emacs file I put (setq org-catch-invisible-edits 'show) but both 'M-x query-replace' and 'M-x replace-string' still replace hidden strings in folded sections of an org file. Thanks, Paul current state: == (setq org-tab-first-hook '(org-hide-block-toggle-maybe org-src-native-tab-command-maybe org-babel-hide-result-toggle-maybe org-babel-header-arg-expand) org-speed-command-hook '(org-speed-command-default-hook org-babel-speed-command-hook) org-occur-hook '(org-first-headline-recenter) org-metaup-hook '(org-babel-load-in-session-maybe) org-confirm-shell-link-function 'yes-or-no-p org-after-todo-state-change-hook '(org-clock-out-if-current) org-src-mode-hook '(org-src-babel-configure-edit-buffer org-src-mode-configure-edit-buffer) org-agenda-before-write-hook '(org-agenda-add-entry-text) org-babel-pre-tangle-hook '(save-buffer) org-mode-hook '(#[nil \300\301\302\303\304$\207 [org-add-hook change-major-mode-hook org-show-block-all append local] 5] #[nil \300\301\302\303\304$\207 [org-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-ctrl-c-ctrl-c-hook '(org-babel-hash-at-point org-babel-execute-safely-maybe) org-cycle-hook '(org-cycle-hide-archived-subtrees org-cycle-hide-drawers org-cycle-hide-inline-tasks org-cycle-show-empty-lines org-optimize-window-after-visibility-change) org-catch-invisible-edits 'show org-confirm-elisp-link-function 'yes-or-no-p org-metadown-hook '(org-babel-pop-to-session-maybe) org-clock-out-hook '(org-clock-remove-empty-clock-drawer) )
[O] Bug: #+STARTUP: content shows text as well as headlines [8.2.5h (8.2.5h-elpa @ ~/.emacs.d/elpa/org/)
Hi, Opening an org file containing the line #+STARTUP: content shows the text and headlines. This STARTUP line used to cause an org file to open showing just the section headlines (like a contents page). According to the documentation at http://orgmode.org/manual/In_002dbuffer-settings.html, it still should. I've attached a simple org file as an example. Thanks, Paul Your bug report will be posted to the Org-mode mailing list. Emacs : GNU Emacs 24.2.1 (x86_64-unknown-linux-gnu, GTK+ Version 2.18.9) of 2012-09-21 on CRMDA020L Package: Org-mode version 8.2.5h (8.2.5h-elpa @ /Home/ps/.emacs.d/elpa/org/) current state: == (setq org-tab-first-hook '(org-hide-block-toggle-maybe org-src-native-tab-command-maybe org-babel-hide-result-toggle-maybe org-babel-header-arg-expand) org-speed-command-hook '(org-speed-command-default-hook org-babel-speed-command-hook) org-occur-hook '(org-first-headline-recenter) org-metaup-hook '(org-babel-load-in-session-maybe) org-confirm-shell-link-function 'yes-or-no-p org-after-todo-state-change-hook '(org-clock-out-if-current) org-src-mode-hook '(org-src-babel-configure-edit-buffer org-src-mode-configure-edit-buffer) org-agenda-before-write-hook '(org-agenda-add-entry-text) org-babel-pre-tangle-hook '(save-buffer) org-mode-hook '(#[nil \300\301\302\303\304$\207 [org-add-hook change-major-mode-hook org-show-block-all append local] 5] #[nil \300\301\302\303\304$\207 [org-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-ctrl-c-ctrl-c-hook '(org-babel-hash-at-point org-babel-execute-safely-maybe) org-cycle-hook '(org-cycle-hide-archived-subtrees org-cycle-hide-drawers org-cycle-hide-inline-tasks org-cycle-show-empty-lines org-optimize-window-after-visibility-change) org-confirm-elisp-link-function 'yes-or-no-p org-metadown-hook '(org-babel-pop-to-session-maybe) org-clock-out-hook '(org-clock-remove-empty-clock-drawer) ) * First header Some text ** First subheader Some more text * Second header Some text ** Second subheader Some more text #+STARTUP: content ; all headlines ;#+STARTUP: showall ; no folding of any entries
Re: [O] using gnuplot's splot and every commands on org-mode table data
I agree that it is easier and more clear to include set datafile missing... in the body of a gnuplot code block. I *do* think that the :missing header argument has value specifically as a way to replace missing values in the original table data. I've changed the behavior of the :missing header argument so that it *only* replaces missing values in table data and does not add a set datafile missing... line to the code block. If I understand you correctly I think that sounds like a good solution. As I understand it, your recent changes mean that if the :missing header is not used the table data will be exported as is, ie, with no changes, replacements or additions to any of the characters in the table cells; however, if the ':missing ?' header is used any empty table cells will be exported as ? (with no quotes) and one needs to explicitly add set datafile missing ? to the code block. In fact, it's not actually necessary to add this line to the code block as gnuplot will treat the non-parsible ? string as missing data without the line. Regards, Paul
Re: [O] using gnuplot's splot and every commands on org-mode table data
Hi Eric, Currently the :missing header argument for gnuplot code blocks does two things. It adds the set datafile missing... line to the code block body *and* it binds `*org-babel-gnuplot-missing*' to the value of the :missing header argument when the datafile is written, so empty table cells are replaced with the value of the :missing header argument. Thanks for the explanation. The reason you're not getting a blank line is because it is replaced with three missing values, in this case ? ? ?. Do you think this behavior should be changed or split between two header arguments? I think the :missing header should not replace empty fields in an org table by the missing character as blank lines have a special meaning in gnuplot. To fully use the versatility of gnuplot one needs blank lines and missing values. The set datafile missing command sets a specific character string to be treated as a missing value. The character string can even be a number, eg. set datafile missing -1. It says under gnuplot's help missing that: There is no default character for `missing`, but in many cases any non-parsible string of characters found where a numerical value is expected will be treated as missing data. My view is that for the purposes of exporting org tables for plotting with gnuplot all blank entries in the org table (fields and whole lines) should be exported as blanks, and all characters (letters or numerical digits etc.) should be exported exactly as they appear in the table (without any additional surrounding quotes being added). Maybe I'm missing the point of the :missing header, but I find it easier and clearer to include the datafile missing command in the gnuplot code block. I don't really see a need for the :missing header. Maybe the need stems from wanting to be able to use different plotting packages to plot the same org table data, but it's not clear to me. Kind regards, Paul
Re: [O] using gnuplot's splot and every commands on org-mode table data
Hi Eric, There appears to be a slight bug in the way gnuplot handles blocked data with missing entries. An example is provided in the org script at then end of this note. In the code block gnuplot_1 the use of ':missing ?' seems to cause the exported data file to lack the blanks lines that are essential for the plot. The plot from this code block is incorrect. In gnuplot_2 ':missing' is not used, but instead 'set datafile missing ?' is set explicitly in the gnuplot code block. The plot from this code block is correct. Surely gnuplot_1 should produce exactly the same plot as gnuplot_2. Kind regards, Paul Exported data file does not include blank lines. #+name: gnuplot_1 #+begin_src gnuplot :var d=block_data_missing :missing ? :results silent set ticslevel 0 splot d index 0 u 1:2:3 w lp pt 6 ps 5, d index 1 u 1:2:3 w lp pt 6 ps 5 #+end_src Exported data file includes blank lines. #+name: gnuplot_2 #+begin_src gnuplot :var d=block_data_missing :results silent set datafile missing ? set ticslevel 0 splot d index 0 u 1:2:3 w lp pt 6 ps 5, d index 1 u 1:2:3 w lp pt 6 ps 5 #+end_src #+name: block_data_missing | 1 | 1 | 2 | | 1 | 2 | 5 | | 1 | 3 | 10 | | | || | 2 | 1 | 5 | | 2 | 2 | 10 | | 2 | 3 | 13 | | | || | 3 | 1 | 10 | | 3 | 2 | ? | | 3 | 3 | 18 | | | || | | || | 1 | 1 | 12 | | 1 | 2 | 15 | | 1 | 3 | 20 | | | || | 2 | 1 | 15 | | 2 | 2 | 18 | | 2 | 3 | 23 | | | || | 3 | 1 | ? | | 3 | 2 | 23 | | 3 | 3 | 28 |
Re: [O] using gnuplot's splot and every commands on org-mode table data
Dear Eric, Recently you made some nice changes to the way gnuplot plots surface data from org tables. Your changes are present on git://orgmode.org/org-mode.git, but I switched to using ELPA recently and I've just noticed that your changes are not yet present on http://orgmode.org/elpa/. Do you know if it's just because the latter lags the former by 3 months or more? As far as I can tell, I'm using the following versions: From git: org-version: 8.0.7 (release_8.0.7-406-g4b7490) From ELPA: Org-mode version 8.0.7 (8.0.7-7-g9e5104-elpa (org-20130826) Kind regards, Paul On 17 May 2013 22:33, Paul Stansell paulstans...@gmail.com wrote: Hi Eric, That's seems perfect now; I can't see any other issues. Thanks! Kind regards, Paul
Re: [O] elpa's copy of org-version.el
Pierre Téchoueyres pierre.techoueyres at free.fr writes: Ok I've found *my* mistake : Melpa provides an org-mode from GIT too. Look like this version is buggy. Thanks for your help with this, but I'm still not entirely sure what I should do. Are you saying that when I install org via elpa I should _not_ install this one: org 20130720 installed Outline-based notes management and organizer [git] because it's from git? Should I be looking for an org installation from github? I can't see one in my package list. Should I uninstall my broken org, disable melpa to try again to install org from elpa? Thanks
Re: [O] elpa's copy of org-version.el
Yes, that is helpful. Thanks very much!
[O] elpa's copy of org-version.el
Hello, If I install org from elpa the file org-version.el is missing and I get the following: M-x org-version Org-mode version N/A (N/A !!check installation!! @ /Home/ps/.emacs.d/elpa/org-20130715.1743/) and M-x locate-library org-version No library org-version in search path However, the following give the expected results: M-x locate-library org Library is file ~/.emacs.d/elpa/org-20130715.1743/org.elc M-x locate-library org-install Library is file ~/.emacs.d/elpa/org-20130715.1743/org-install.el If I install org from git://orgmode.org/org-mode.git it includes the file org-version.el and all of the above commands work okay, eg, M-x locate-library org-version Library is file ~/local/emacs/site-lisp/org-git/org-version.el Is something wrong here? Thanks, Paul
[O] Help with babel and gnuplot
Hello, I hesitate to ask this question as I feel I should be able to work it out myself, but I don't seem to be able to. I'm trying to get gnuplot working via babel. I'm using Emacs 24.2.1 and I have Org-mode release_8.0.6-329-g0c233a installed in ~/org-mode. I'm running /usr/bin/emacs -Q -l minimal-org.el test.org where minimal-org.el contains just (setq debug-on-error t debug-on-signal nil debug-on-quit nil) (add-to-list 'load-path (expand-file-name ~/org-mode/lisp)) (org-babel-do-load-languages 'org-babel-load-languages '((gnuplot . t))) and test.org contains just #+begin_src gnuplot :results silent plot x #+end_src When I press C-c C-c inside the source block I get Debugger entered--Lisp error: (file-error Cannot open load file gnuplot) require(gnuplot) org-babel-execute:gnuplot(plot x ... org-babel-execute-src-block(nil) org-babel-execute-src-block-maybe() org-babel-execute-maybe() org-babel-execute-safely-maybe() run-hook-with-args-until-success(org-babel-execute-safely-maybe) org-ctrl-c-ctrl-c(nil) call-interactively(org-ctrl-c-ctrl-c nil nil) I've been assuming it's a path issue, but ~/org-mode/lisp/ob-gnuplot.elc is present and I have gnuplot installed in /usr/bin/gnuplot. Any advice would be greatly appreciated. Kind regards, Paul
Re: [O] Help with babel and gnuplot
Hi Eric, Thanks for your quick reply and helpful pointer! I got it to work. Paul On 12 July 2013 20:05, Eric Schulte schulte.e...@gmail.com wrote: You need to install gnuplot.el, which looks like it can be installed with ELPA. Cheers, Paul Stansell paulstans...@gmail.com writes: Hello, I hesitate to ask this question as I feel I should be able to work it out myself, but I don't seem to be able to. I'm trying to get gnuplot working via babel. I'm using Emacs 24.2.1 and I have Org-mode release_8.0.6-329-g0c233a installed in ~/org-mode. I'm running /usr/bin/emacs -Q -l minimal-org.el test.org where minimal-org.el contains just (setq debug-on-error t debug-on-signal nil debug-on-quit nil) (add-to-list 'load-path (expand-file-name ~/org-mode/lisp)) (org-babel-do-load-languages 'org-babel-load-languages '((gnuplot . t))) and test.org contains just #+begin_src gnuplot :results silent plot x #+end_src When I press C-c C-c inside the source block I get Debugger entered--Lisp error: (file-error Cannot open load file gnuplot) require(gnuplot) org-babel-execute:gnuplot(plot x ... org-babel-execute-src-block(nil) org-babel-execute-src-block-maybe() org-babel-execute-maybe() org-babel-execute-safely-maybe() run-hook-with-args-until-success(org-babel-execute-safely-maybe) org-ctrl-c-ctrl-c(nil) call-interactively(org-ctrl-c-ctrl-c nil nil) I've been assuming it's a path issue, but ~/org-mode/lisp/ob-gnuplot.elc is present and I have gnuplot installed in /usr/bin/gnuplot. Any advice would be greatly appreciated. Kind regards, Paul -- Eric Schulte http://cs.unm.edu/~eschulte
Re: [O] fill paragraph: math and latex environments
Nicolas,
Thanks for your reply.
If we allow \[...\] constructs to be an element, they cannot be
recognized as such within paragraphs. So
Some text \[1+1\] and some other text
will not be recognized anymore, even though any latex editing mode
supports it. Again, I think it's not worth loosing it.
Also, using \begin{...}...\end{...} environments is not really an issue
with editing facilities in Emacs (e.g., yasnippets).
I'm sorry, but I don't fully understand your explanation as I don't
know what you mean by an element in this context?
Also, am I missing something about the latex? Do you want to be able
to use display style maths inside a sentence (ie. avoid placing the
maths on a new line but have it formatted in display style)? That
would seem strange as that's not what it's for. I don't, therefore,
see why anyone would want to write
Some text \[1+1\] and some other text
as in the resulting processed document it will look like
Some text
1+1
and some other text
I think one should instead write
Some text \(1+1\) and some other text
or
Some text $1+1$ and some other text
which, in the processed document, will look like
Some text 1+1 and some other text
If someone wants a display maths equation they could write it in their
org file as
Some text
\[
1+1
\]
and some other text
so that the look of the org file resembles more closely that of the
processed document.
Also, using \begin{...}...\end{...} environments is not really an issue
with editing facilities in Emacs (e.g., yasnippets).
I agree with you there. It's not a big deal type, but I do think
\[
1+1
\[
looks a lot nicer and cleaner in the org file than
\begin{displaymath}
1+1
\end{displaymath}
Kind regards,
Paul
[O] Very minor bug in undo applied to org table
Hello, This seems like a very minor bug, but I thought I'd report it anyway in case it has wider ramifications that I'm unaware of. Create an org file with the following lines: | 1 | #+TBLFM: $1=2 Open it and type C-c C-c on the TBLFM line. This replaces the '1' in the table with a '2'. Now type C-_ (for undo). Not only does the '2' revert to a '1', but a second line reading '#+TBLFM: $1=2' is inserted directly under the first. An second C-_ removes this second TBLFM line. Regards, Paul PS. I'm using Emacs 24.2.1 and Org-mode release_8.0.3-331-gf7e6f1 and I tested with the minimal org-mode set-up from http://orgmode.org/manual/Feedback.html.
[O] Incorrect sum of times in table
Hello, I noticed a case where the sum of two times in a table does not give the correct answer. To see this, create an org file with the following lines: | 0:00:31 | | 0:00:30 | |-| | | Open it and type C-+ C-y in the empty cell of the table. The answer inserted is 0:01:00 instead of 0:01:01. Regards, Paul PS. I'm using Emacs 24.2.1 and Org-mode release_8.0.3-331-gf7e6f1 and I tested with the minimal org-mode set-up from http://orgmode.org/manual/Feedback.html.
[O] Help with babel and gnuplot
Hello, I hesitate to ask this question as I feel I should be able to work it out myself, but I don't seem to be able to. I'm trying to get gnuplot working through babel. I'm using Emacs 24.2.1 and I have Org-mode release_8.0.3-331-gf7e6f1 installed in ~/org-mode. I'm running /usr/bin/emacs -Q -l minimal-org.el test.org where minimal-org.el contains just (setq debug-on-error t debug-on-signal nil debug-on-quit nil) (add-to-list 'load-path (expand-file-name ~/org-mode/lisp)) (org-babel-do-load-languages 'org-babel-load-languages '((gnuplot . t))) and test.org contains just #+begin_src gnuplot :results silent plot x #+end_src When I press C-c C-c inside the source block I get Debugger entered--Lisp error: (file-error Cannot open load file gnuplot) require(gnuplot) org-babel-execute:gnuplot(plot x ... org-babel-execute-src-block(nil) org-babel-execute-src-block-maybe() org-babel-execute-maybe() org-babel-execute-safely-maybe() run-hook-with-args-until-success(org-babel-execute-safely-maybe) org-ctrl-c-ctrl-c(nil) call-interactively(org-ctrl-c-ctrl-c nil nil) I've been assuming it's a path issue, but ~/org-mode/lisp/ob-gnuplot.elc is present and I have gnuplot installed in /usr/bin/gnuplot. Also, other languages (eg. python) work okay through babel. Any advice would be greatly appreciated. Kind regards, Paul
Re: [O] fill paragraph: math and latex environments
Nicolas Goaziou n.goaziou at gmail.com writes:
Hello,
azw at fastmail.fm (Albert Z. Wang) writes:
Thanks for the clarification! Is there an easy way to have them be
treated as full-fledged environments? I usually prefer to use the above
for unnumbered display equations since it reduces visual clutter and
looks closer to the intent.
No, there's no easy way.
Making \[...\] an element would mean that \[...\] cannot exist anymore
within a paragraph. I'm not sure it's worth it.
Also, I think it's good, in this case, to have both an inlined and
a non-inlined version for the same thing.
Regards,
Hi Nicolas,
I hope you don't mind me giving my view on this so long after the initial
posts, but I been trying, without success, to get fill-paragraph to
recognise \[...\] as boundaries to it's function.
You say in your post
Making \[...\] an element would mean that \[...\] cannot exist anymore
within a paragraph. I'm not sure it's worth it.
Also, I think it's good, in this case, to have both an inlined and
a non-inlined version for the same thing.
In Lamport's book on Latex he explains that \[...\] is for display style
maths, that is, for maths that is not inside a paragraph but presented on
it's own line. Inside a paragraph one should use $...$ or \(...\) as they
are for inline equations (and Latex treats them the same). For display
style maths Latex uses
\begin{displaymath}
...
\end{displaymath}
and, for less typing,
\[
...
\]
and both are treated the same, ie., both produce the exact same output in
the processed latex document.
This being the case, my wish would be to see org mode treat
\[
...
\]
the same as
\begin{displaymath}
...
\end{displaymath}
and not fill past it's boundaries.
Kind regards,
Paul
Re: [O] #+ATTR_LaTeX no longer honoured
here's the line you're looking for: #+ATTR_LaTeX: :width 5cm :options angle=90 Thanks very much, that does what I want. Also, regarding the manual being up-to-date or not, I took my instructions from the page at http://orgmode.org/manual/Images-in-LaTeX-export.html which does seem out of date as it says one should use #+ATTR_LaTeX: width=5cm,angle=90 Regards, Paul
[O] #+ATTR_LaTeX no longer honoured
Hello,
I've noticed that #+ATTR_LaTeX seems to be no longer honoured (I'm
using release_8.0.3-133-ga5872)
This is demonstrated for the attached org file. It's the exact
example from http://orgmode.org/manual/Images-in-LaTeX-export.html.
I expect the exported latex file (C-c C-e l l) to contain something like
\includegraphics[width=5cm,angle=90]{./dummy.png}
but I instead it contains
\includegraphics[width=.9\linewidth]{./dummy.png}
Thanks,
Paul
PS. I'm using Emacs 24.2.1 and I tested with the minimal org-mode
set-up from http://orgmode.org/manual/Feedback.html.
attr_latex.org
Description: Binary data
Re: [O] using gnuplot's splot and every commands on org-mode table data
Hi Eric, Thanks for your work on this. I've tried your latest changes and I think they're a big improvement. I've attached another org-mode file for you to try. It illustrates the use of double blank lines in the first table (called block_data) to inform gnuplot that there're two separate data sets in the single data file. The first code block (gnuplot_1) plots these two data sets as red and green surfaces. It's really nice that gnuplot can now be used in this way from within org-mode. One slight drawback, however, is that there still doesn't seem to be a way to specify missing values in the org table in the way they're frequently used by gnuplot. An illustration of what I mean by this is given in the table block_data_missing in the attached org file. You'll see that I've inserted two '?' characters for missing z-values. If you execute the second and third code blocks (gnuplot_2 and gnuplot_3) you'll see that neither give the desired result. If the block_data_missing table were exported exactly as it is except for the removal of the '|' characters and set datafile missing '?' were specified in the gnuplot script this would enable gnuplot to plot the red and green surfaces with the missing values. To see this try executing the last code block (gnuplot_4) which plots the data which is first cleaned by the shell command you suggested in a previous post. This would also remove the need to have the :missing header argument. Kind regards, Paul gnuplot2.org Description: Binary data
Re: [O] using gnuplot's splot and every commands on org-mode table data
Hi Eric, That's seems perfect now; I can't see any other issues. Thanks! Kind regards, Paul
Re: [O] unexpected appearance of x^2 in pdf file
Hi Nicolas, Thanks for fixing that last problem, that's great! I've also come across a couple of other unexpected results exporting other latex equations to pdf. Examples are given in the attached org file. Both are quite trivial with easy work-arounds. In both cases, because the embedded png equations (displayed by C-c C-x C-l) are formatted correctly, the problem in the exported pdf file might go unnoticed. Regards, Paul equation_line_breaks.org Description: Binary data
Re: [O] unexpected appearance of x^2 in pdf file
Nicolas,
\[ x = y
+1 \]
\[ x = y
+ 1 \]
This is to be expected. In the second case, the second line defines
a list item, which has precedence over any LaTeX snippet.
Okay, I realised it was switching to the itemise environment, but I
didn't know it took precedence over the latex environment.
\[ x = \begin{array}{cc}
y u \\
z v
\end{array} \]
\[ x =
\begin{array}{cc}
y u \\
z v
\end{array} \]
I think this is because of a limitation on the number of lines a LaTeX
snippet can span across (IIRC, 3 is the maximum).
Maybe, but I see the same problem with the following two line example
\[ x =
\begin{array}{cc} z v \end{array} \]
In both cases, I suggest to use LaTeX environments instead:
\begin{equation*}
x = y
+ 1
\end{equation*}
Yes, I tried that, but as I understand it I need to
\usepackage{amsmath} to access the latex equation* environment. But
then I get an error about Command \iint already defined. I tried
the solution described at
http://www.tex.ac.uk/cgi-bin/texfaq2html?label=alreadydef, but it
didn't work for me.
Anyway, never mind, these are all quite trivial points.
Thanks very much for your help,
Paul
[O] unexpected appearance of x^2 in pdf file
Dear list,
I may be under a misapprehension, but I expected the pdf output
(created by C-c C-e l p) from the attached org file to show similar
results for both lines. Instead, however, the simple
x^2
outside of the verbatim environment puts the caret above the 2 even
though I have set
#+OPTIONS: ^:nil
This seems to be because org-mode exports x^2 as x\^2 in the tex file.
I think exporting it as x\^{}2 would give a better result. Is there
another way to get the appearance I'm looking for without using the
verbatim environment?
Thanks for your advice,
Paul
PS. I'm using Emacs 24.2.1 with Org mode 8.0.2.
caret_symbol.org
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Re: [O] using gnuplot's splot and every commands on org-mode table data
Hi Eric, It seems to be the first hline that causes the problem. For example, if the table data in splot.org is replaced by #+name: data || x | |+---| | r1 | 1 | it gets exported correctly as x r1 1 by both the shell and gnuplot commands. However, if the data is replace by #+name: data |+---| || x | | r1 | 1 | it still gets exported correctly by the shell command but the gnuplot command exports it as hline ( x) (r1 1) Thanks for your help with this, Paul Very weird, This does look like a bug to me. Can you isolate where the value of data in your example is first assigned the wrong value? Thanks for reporting. I will save your example for when I next have development time. Best,
Re: [O] using gnuplot's splot and every commands on org-mode table data
Hi Eric, In your last example are you illustrating the case of a data file with missing data? Replacing s with blank space in your example doesn't really break the plot, it's just that gnuplot interprets the first column of data as 1 2 3 16 6 7 4 9 and the second as 2 4 8 16 8 4 2 Gnuplot has a specific setting for handling missing values. It's common in gnuplot to use '?' to signify a missing value (type help missing at the gnuplot prompt). If, in your last example, you replace the missing values with '?' (without the quotes) and then type in gnuplot set datafile missing ? and then plot the data with plot data.txt u 0:1, '' u 0:2 you'll see that gnuplot handles it properly. Putting '?' in the blanks cells of the org mode table in your last attachment and plotting from within org mode gives a temporary data file containing '?', which gnuplot also handles correctly as it must recognise ? (with the quotes) as being a missing value. But org mode's behaviour of inserting in blank cells (instead of actual blanks) does break the use of every in gnuplot which is required by splot when plotting surfaces from data files (unless the data files are in matrix format). Also, inserting breaks the use of gnuplot's index which expects two blank lines to separate data sets in a single file, but I've never used this facility. I noticed that org mode writes table values of 'nan' and 'NaN' without the double quotes, but, for example, 'MaM' is written with double quotes, (as ''MaM') in the temporary data file. Also, I think it's generally better to remove the double quotes from around all strings exported by org mode for plotting by gnuplot as they're generally not needed (exceptions are strings which contain spaces which can be quoted so they are treated as a single entity by gnuplot). For example, there is a gnuplot demonstration script called datastrings.dem which plots data from a file called ctg-y2.dat. This data file has unquoted month names in the first column that are plotted as labels on the x-axis. Paul
Re: [O] using gnuplot's splot and every commands on org-mode table data
Eric, What you suggest is indeed a good solution, so thank you very much for that! I think it would still be nice, however, if someday the blank lines in the org table would be exported as blank lines in the temporary text file instead of as (which seems to be the root of the problem). Kind regards, Paul Hi Paul, While I can't claim to fully follow your gnuplot examples, i would recommend using an intervening shell code block to parse the Org-mode table data into something that gnuplot will ingest. If I understand your use case correctly, then something like the following should work. If you really wanted to be fancy, gnuplot will let you specify shell transformations as part of the plotting command which would allow you to forego the intermediate code block. -- Eric Schulte http://cs.unm.edu/~eschulte
Re: [O] using gnuplot's splot and every commands on org-mode table data
Hi Eric, If I change your example org file a little by adding row and column names to the table as in the attached file I get the following behaviour that I don't understand: if I execute C-c on the shell function the file /tmp/data.gnuplot has the format that gnuplot can plot; however, if I execute C-c on the gnuplot function the form of /tmp/data.gnuplot is mangled with and () so it can no longer be plotted by the gnuplot command. Can you shed any light on this? Thanks, Paul splot.org Description: Binary data
Re: [O] using gnuplot's splot and every commands on org-mode table data
Hi Eric, My view is that the removal of ''s will always be preferable for gnuplot as it uses what it calls datablocks which are delimited by blank lines (see, for example, http://gnuplot.sourceforge.net/docs_4.2/node121.html and http://gnuplot.sourceforge.net/docs_4.2/node61.html). Paul
[O] using gnuplot's splot and every commands on org-mode table data
Hello everyone, I'd be grateful if someone would offer me advice on using gnuplot's splot and every commands when plotting data from a table within org-mode. As far as I can tell, these gnuplot commands do not work properly because org-mode exports empty fields in tables as and gnuplot's every and splot commands expect the data file to be formatted as a datablock with blank lines marking the boundaries between datablocks. (For the definition of a datablock, type help glossary at the gnuplot prompt.) I'm using org-mode version 8.0.2 and emacs version 24.2.1 on a Fedora-18 system To illustrate my point, consider a blocked datafile called block.dat containing the following: 1 1 2 1 2 5 1 3 10 2 1 5 2 2 8 2 3 13 3 1 10 3 2 13 3 3 18 For this file the gnuplot command #+begin_src gnuplot :var d=block.dat :results silent plot $d u 2:3 ev :::0::0, u 2:3 ev :::1::1, u 2:3 ev :::2::2 #+end_src shows three separate lines of different colours as gnuplot recognises the datafile as blocked data. Also, the following command produces a surface plot #+begin_src gnuplot :var d=block.dat :results silent splot $d u 1:2:3 #+end_src However, if I put the same data in the table below #+tblname: data | 1 | 1 | 2 | | 1 | 2 | 5 | | 1 | 3 | 10 | | | || | 2 | 1 | 5 | | 2 | 2 | 8 | | 2 | 3 | 13 | | | || | 3 | 1 | 10 | | 3 | 2 | 13 | | 3 | 3 | 18 | and use the following plot command #+begin_src gnuplot :var d=data :results silent plot $d u 2:3 ev :::0::0, u 2:3 ev :::1::1, u 2:3 ev :::2::2 #+end_src the result is a plot of a single line of the same colour as gnuplot joins all of the points in the data file. This seems to be because org-mode exports the table as x y z 1 1 2 1 2 5 1 3 10 2 1 5 2 2 8 2 3 13 3 1 10 3 2 13 3 3 18 and gnuplot does not recognise this as a blocked data file because it contains no blank lines. The same problem occurs for #+begin_src gnuplot :var d=data :results silent splot $d u 1:2:3 #+end_src which does not produce a gridded surface plot. Thanks for your help, Paul
[O] Bug: Scheduled item appears in diary [7.8.03]
Hello, I think I've found a bug in org-mode 7.8.03. To reproduce do the following. Start emacs with the attached files bug.el and schedule_in_agenda.org using emacs --no-init-file --load bug.el schedule_in_agenda.org View the agenda by typing C-c a a As far as I understand the documentation, item 1b should not appear in the diary part of the agenda. All other items seem to be behaving correctly. Kind regards, Paul Stansell Output from M-x emacs-version RET Emacs : GNU Emacs 23.1.1 (i386-redhat-linux-gnu, GTK+ Version 2.18.9) of 2010-06-03 on xb-01.phx2.fedoraproject.org Package: Org-mode version 7.8.03 current state: == (setq org-export-latex-after-initial-vars-hook '(org-beamer-after-initial-vars) org-speed-command-hook '(org-speed-command-default-hook org-babel-speed-command-hook) org-agenda-files '(schedule_in_agenda.org) org-metaup-hook '(org-babel-load-in-session-maybe) org-after-todo-state-change-hook '(org-clock-out-if-current) org-export-latex-format-toc-function 'org-export-latex-format-toc-default org-tab-first-hook '(org-hide-block-toggle-maybe org-src-native-tab-command-maybe) org-src-mode-hook '(org-src-babel-configure-edit-buffer org-src-mode-configure-edit-buffer) org-confirm-shell-link-function 'yes-or-no-p org-export-first-hook '(org-beamer-initialize-open-trackers) org-agenda-before-write-hook '(org-agenda-add-entry-text) org-blank-before-new-entry nil org-babel-pre-tangle-hook '(save-buffer) org-cycle-hook '(org-cycle-hide-archived-subtrees org-cycle-hide-drawers org-cycle-show-empty-lines org-optimize-window-after-visibility-change) org-export-preprocess-before-normalizing-links-hook '(org-remove-file-link-modifiers) org-mode-hook '(#[nil \300\301\302\303\304$\207 [org-add-hook change-major-mode-hook org-show-block-all append local] 5] org-babel-hide-all-hashes) org-ctrl-c-ctrl-c-hook '(org-babel-hash-at-point org-babel-execute-safely-maybe) org-confirm-elisp-link-function 'yes-or-no-p org-export-interblocks '((lob org-babel-exp-lob-one-liners) (src org-babel-exp-inline-src-blocks)) org-clock-out-hook '(org-clock-remove-empty-clock-drawer) org-occur-hook '(org-first-headline-recenter) org-export-preprocess-before-selecting-backend-code-hook '(org-beamer-select-beamer-code) org-export-latex-final-hook '(org-beamer-amend-header org-beamer-fix-toc org-beamer-auto-fragile-frames org-beamer-place-default-actions-for-lists) org-metadown-hook '(org-babel-pop-to-session-maybe) org-export-blocks '((src org-babel-exp-src-block nil) (comment org-export-blocks-format-comment t) (ditaa org-export-blocks-format-ditaa nil) (dot org-export-blocks-format-dot nil)) ) (add-to-list 'load-path ~/local/share/emacs/site-lisp/org) (require 'org-install) (global-set-key \C-ca 'org-agenda) (setq org-agenda-files (quote ( schedule_in_agenda.org ) ) ) schedule_in_agenda.org Description: Lotus Organizer
[O] Bug: spreadsheet [7.7]
Hello, I think I have found a bug in the spreadsheet of orgmode. To reproduce the bug do the following: Edit this file with emacs orgmode. Place the cursor in the small table below and type C-c } to toggle on the display a labelled grid giving the cell references. Change the c=1 in the CONSTANTS line to c=2 and refresh this line with C-c C-c. Put the cursor on the TBLFM line and refresh this line with C-c C-c. An I*1 appears above the table which should not appear and can't be removed with the usual emacs commands. |---| | 1 | |---| #+TBLFM: $1=$c #+CONSTANTS: c=1 Emacs : GNU Emacs 23.1.1 (i386-redhat-linux-gnu, GTK+ Version 2.18.9) of 2010-06-03 on xb-01.phx2.fedoraproject.org Package: Org-mode version 7.7 current state: == (setq org-export-latex-after-initial-vars-hook '(org-beamer-after-initial-vars) org-speed-command-hook '(org-speed-command-default-hook org-babel-speed-command-hook) org-metaup-hook '(org-babel-load-in-session-maybe) org-after-todo-state-change-hook '(org-clock-out-if-current) org-export-blocks-postblock-hook '(org-exp-res/src-name-cleanup) org-export-latex-format-toc-function 'org-export-latex-format-toc-default org-tab-first-hook '(org-hide-block-toggle-maybe org-src-native-tab-command-maybe org-babel-hide-result-toggle-maybe) org-src-mode-hook '(org-src-babel-configure-edit-buffer org-src-mode-configure-edit-buffer) org-confirm-shell-link-function 'yes-or-no-p org-export-first-hook '(org-beamer-initialize-open-trackers) org-agenda-before-write-hook '(org-agenda-add-entry-text) org-babel-pre-tangle-hook '(save-buffer) org-cycle-hook '(org-cycle-hide-archived-subtrees org-cycle-hide-drawers org-cycle-show-empty-lines org-optimize-window-after-visibility-change) org-export-preprocess-before-normalizing-links-hook '(org-remove-file-link-modifiers) org-mode-hook '(#[nil \300\301\302\303\304$\207 [org-add-hook change-major-mode-hook org-show-block-all append local] 5] #[nil \300\301\302\303\304$\207 [org-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-ctrl-c-ctrl-c-hook '(org-babel-hash-at-point org-babel-execute-safely-maybe) org-confirm-elisp-link-function 'yes-or-no-p org-export-interblocks '((lob org-babel-exp-lob-one-liners) (src org-babel-exp-inline-src-blocks)) org-clock-out-hook '(org-clock-remove-empty-clock-drawer) org-occur-hook '(org-first-headline-recenter) org-export-preprocess-before-selecting-backend-code-hook '(org-beamer-select-beamer-code) org-export-latex-final-hook '(org-beamer-amend-header org-beamer-fix-toc org-beamer-auto-fragile-frames org-beamer-place-default-actions-for-lists) org-metadown-hook '(org-babel-pop-to-session-maybe) org-export-blocks '((src org-babel-exp-src-block nil) (comment org-export-blocks-format-comment t) (ditaa org-export-blocks-format-ditaa nil) (dot org-export-blocks-format-dot nil)) )
[O] Bug: incorrect indentation of DEADLINE [7.7]
Hello, I think I have found a very minor bug in the current org mode. The is a bug present when using: Org-mode version 7.7 with GNU Emacs 23.1.1 (i386-redhat-linux-gnu, GTK+ Version 2.18.9) of 2010-06-03 on xb-01.phx2.fedoraproject.org To reproduce the bug do: Start emacs on this email file with emacs --no-init-file --load bug.el bug.org Place the cursor on the TODO line below and press tab to expand the entry. Type C-c C-t The DEALINE line is in indented by 1 space when it should not be. Note that the presence of (setq org-log-done t) in bug.el causes the indentation, without this line there is no unwanted indentation. Thanks for your help! Emacs : GNU Emacs 23.1.1 (i386-redhat-linux-gnu, GTK+ Version 2.18.9) of 2010-06-03 on xb-01.phx2.fedoraproject.org Package: Org-mode version 7.7 current state: == (setq org-log-done 'time org-export-latex-after-initial-vars-hook '(org-beamer-after-initial-vars) org-speed-command-hook '(org-speed-command-default-hook org-babel-speed-command-hook) org-metaup-hook '(org-babel-load-in-session-maybe) org-after-todo-state-change-hook '(org-clock-out-if-current) org-export-blocks-postblock-hook '(org-exp-res/src-name-cleanup) org-export-latex-format-toc-function 'org-export-latex-format-toc-default org-tab-first-hook '(org-hide-block-toggle-maybe org-src-native-tab-command-maybe org-babel-hide-result-toggle-maybe) org-src-mode-hook '(org-src-babel-configure-edit-buffer org-src-mode-configure-edit-buffer) org-confirm-shell-link-function 'yes-or-no-p org-export-first-hook '(org-beamer-initialize-open-trackers) org-agenda-before-write-hook '(org-agenda-add-entry-text) org-babel-pre-tangle-hook '(save-buffer) org-cycle-hook '(org-cycle-hide-archived-subtrees org-cycle-hide-drawers org-cycle-show-empty-lines org-optimize-window-after-visibility-change) org-export-preprocess-before-normalizing-links-hook '(org-remove-file-link-modifiers) org-mode-hook '(#[nil \300\301\302\303\304$\207 [org-add-hook change-major-mode-hook org-show-block-all append local] 5] #[nil \300\301\302\303\304$\207 [org-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-ctrl-c-ctrl-c-hook '(org-babel-hash-at-point org-babel-execute-safely-maybe) org-confirm-elisp-link-function 'yes-or-no-p org-export-interblocks '((lob org-babel-exp-lob-one-liners) (src org-babel-exp-inline-src-blocks)) org-clock-out-hook '(org-clock-remove-empty-clock-drawer) org-occur-hook '(org-first-headline-recenter) org-export-preprocess-before-selecting-backend-code-hook '(org-beamer-select-beamer-code) org-export-latex-final-hook '(org-beamer-amend-header org-beamer-fix-toc org-beamer-auto-fragile-frames org-beamer-place-default-actions-for-lists) org-metadown-hook '(org-babel-pop-to-session-maybe) org-export-blocks '((src org-babel-exp-src-block nil) (comment org-export-blocks-format-comment t) (ditaa org-export-blocks-format-ditaa nil) (dot org-export-blocks-format-dot nil)) ) (add-to-list 'load-path ~/local/share/emacs/site-lisp/org) (require 'org-install) (add-to-list 'auto-mode-alist '(\\.org$ . org-mode)) ;; The presence of this line causes the indent bug. (setq org-log-done t) bug.org Description: Lotus Organizer
[Orgmode] Bug: Schedule in agenda gives wrong overdue days [7.4]
Dear Sirs, For an org file containing just the two following lines: * TODO Water plants at work SCHEDULED: 2010-12-27 Mon .+1w creating an agenda with C-c a a on 2011-01-06 displays the following three lines: Day-agenda (W01): Thursday6 January 2011 org_mode_bug:Sched. 4x: TODO Water plants at work I expected is for the schedule overdue days to be 11x instead of 4x. I've attached relevant files to reproduce this result with something like emacs --no-init-file --load bug.el bug.org Kind regards, Paul Stansell Emacs : GNU Emacs 23.1.1 (i386-redhat-linux-gnu, GTK+ Version 2.18.9) of 2010-06-03 on xb-01.phx2.fedoraproject.org Package: Org-mode version 7.4 current state: == (setq org-log-done 'time org-export-latex-after-initial-vars-hook '(org-beamer-after-initial-vars) org-speed-command-hook '(org-speed-command-default-hook org-babel-speed-command-hook) org-agenda-files '(~/org/org_mode_bug/org_mode_bug.org) org-metaup-hook '(org-babel-load-in-session-maybe) org-after-todo-state-change-hook '(org-clock-out-if-current) org-export-blocks-postblock-hook '(org-exp-res/src-name-cleanup) org-export-latex-format-toc-function 'org-export-latex-format-toc-default org-tab-first-hook '(org-hide-block-toggle-maybe org-src-native-tab-command-maybe org-babel-hide-result-toggle-maybe) org-src-mode-hook '(org-src-babel-configure-edit-buffer org-src-mode-configure-edit-buffer) org-confirm-shell-link-function 'yes-or-no-p org-export-first-hook '(org-beamer-initialize-open-trackers) org-agenda-before-write-hook '(org-agenda-add-entry-text) org-babel-pre-tangle-hook '(save-buffer) org-cycle-hook '(org-cycle-hide-archived-subtrees org-cycle-hide-drawers org-cycle-show-empty-lines org-optimize-window-after-visibility-change) org-export-preprocess-before-normalizing-links-hook '(org-remove-file-link-modifiers) org-mode-hook '(#[nil \300\301\302\303\304$\207 [org-add-hook change-major-mode-hook org-show-block-all append local] 5] #[nil \300\301\302\303\304$\207 [org-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-ctrl-c-ctrl-c-hook '(org-babel-hash-at-point org-babel-execute-safely-maybe) org-confirm-elisp-link-function 'yes-or-no-p org-export-interblocks '((lob org-babel-exp-lob-one-liners) (src org-babel-exp-inline-src-blocks)) org-occur-hook '(org-first-headline-recenter) org-export-preprocess-before-selecting-backend-code-hook '(org-beamer-select-beamer-code) org-export-latex-final-hook '(org-beamer-amend-header org-beamer-fix-toc org-beamer-auto-fragile-frames org-beamer-place-default-actions-for-lists) org-metadown-hook '(org-babel-pop-to-session-maybe) org-export-blocks '((src org-babel-exp-src-blocks nil) (comment org-export-blocks-format-comment t) (ditaa org-export-blocks-format-ditaa nil) (dot org-export-blocks-format-dot nil)) ) ;; emacs --no-init-file --load bug.el bug.org (add-to-list 'load-path ~/local/share/emacs/site-lisp) (require 'org-install) (add-to-list 'auto-mode-alist '(\\.org$ . org-mode)) (define-key global-map \C-cl 'org-store-link) (define-key global-map \C-ca 'org-agenda) (setq org-log-done t) (setq org-agenda-files (list ~/org/org_mode_bug/bug.org)) bug.org Description: Lotus Organizer ___ Emacs-orgmode mailing list Please use `Reply All' to send replies to the list. Emacs-orgmode@gnu.org http://lists.gnu.org/mailman/listinfo/emacs-orgmode
