* Bug: [babel] Order of definition of :var makes or breaks the results [8.2.5f (release_8.2.5f-545-g630096 @ /Users/rainerkrug/.emacs.d/org-mode/lisp/)]
@ 2014-01-21 14:17 Rainer M Krug
2014-01-22 19:55 ` Rainer M Krug
0 siblings, 1 reply; 2+ messages in thread
From: Rainer M Krug @ 2014-01-21 14:17 UTC (permalink / raw)
To: emacs-orgmode
Depending on the order in which variables are declared, the definitions
are correct or wrong.
In the example below, if DUMMY is declared first and SPECIES and
SPECIES2 are declared via :var+ there are missing rownames and / or
colnames as well as mixups (see below).
If DUMMY is declared *after the first* table (SPECIES) everything works
as expected.
I don't know if it is the same in other languages.
Example:
#+PROPERTY: rownames yes
#+PROPERTY: colnames yes
#+PROPERTY: var DUMMY="dummy"
* Species names and iespece codes
#+NAME: SPECIES
| | fullName | shortName | iespece | IFNName | color |
|---------+-----------------+-----------+---------+-----------------+-------|
| fagus | Fagus sylvatica | fagus | 3 | fagus_sylvatica | red |
| quercus | Quercus robur | quercus | 4 | quercus_robur | green |
#+PROPERTY: var+ SPECIES=SPECIES
* And some more
#+NAME: SPECIES2
| | fullName | shortName | iespece | IFNName | color |
|---------+---------------+-----------+---------+---------------+-------|
| no idea | ffff | | | | |
| quercus | Quercus robur | quercus | 4 | quercus_robur | green |
#+PROPERTY: var+ SPECIES2=SPECIES2
* The code
#+begin_src R :exports both :results output
SPECIES
#+end_src
#+RESULTS:
: fullName shortName iespece IFNName color
: no idea Fagus sylvatica fagus 3 fagus_sylvatica red
: quercus Quercus robur quercus 4 quercus_robur green
#+begin_src R :exports both :results output
SPECIES2
#+end_src
#+RESULTS:
: X X.1 X.2 X.3
: Quercus robur quercus 4 quercus_robur green
Remember to cover the basics, that is, what you expected to happen and
what in fact did happen. You don't know how to make a good report? See
http://orgmode.org/manual/Feedback.html#Feedback
Your bug report will be posted to the Org-mode mailing list.
------------------------------------------------------------------------
Emacs : GNU Emacs 24.3.1 (x86_64-apple-darwin13.0.0, NS apple-appkit-1265.00)
of 2013-12-13 on Rainers-MacBook-Pro-2.local
Package: Org-mode version 8.2.5f (release_8.2.5f-545-g630096 @ /Users/rainerkrug/.emacs.d/org-mode/lisp/)
current state:
==============
(setq
org-src-lang-modes '(("plantuml" . plantuml) ("ocaml" . tuareg) ("elisp" . emacs-lisp) ("ditaa" . artist) ("asymptote" . asy)
("dot" . fundamental) ("sqlite" . sql) ("calc" . fundamental) ("C" . c) ("cpp" . c++) ("C++" . c++)
("screen" . shell-script))
org-hide-leading-stars t
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-ellipsis "〖 ✎ 〗"
org-occur-hook '(org-first-headline-recenter)
org-src-tab-acts-natively t
org-metaup-hook '(org-babel-load-in-session-maybe)
org-html-format-drawer-function '(lambda (name contents) contents)
org-src-window-setup 'current-window
org-latex-format-inlinetask-function 'ignore
org-confirm-shell-link-function 'y-or-n-p
org-ascii-format-inlinetask-function 'org-ascii-format-inlinetask-default
org-latex-format-headline-function 'org-latex-format-headline-default-function
org-startup-indented t
org-after-todo-state-change-hook '(org-clock-out-if-current)
org-latex-format-drawer-function '(lambda (name contents) contents)
org-odt-format-headline-function 'ignore
org-from-is-user-regexp "\\<Rainer M Krug\\>"
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-ascii-format-drawer-function '(lambda (name contents width) contents)
org-odt-format-inlinetask-function 'ignore
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-plantuml-jar-path "/Users/rainerkrug/jar/plantuml.jar"
org-latex-packages-alist '(("" "color") ("" "listings"))
org-ctrl-k-protect-subtree "ask"
org-babel-tangle-lang-exts '(("latex" . "tex") ("emacs-lisp" . "el"))
org-confirm-elisp-link-function 'yes-or-no-p
org-metadown-hook '(org-babel-pop-to-session-maybe)
org-odt-format-drawer-function '(lambda (name contents) contents)
org-latex-listings t
org-show-siblings '((default) (isearch t) (bookmark-jump . t))
org-html-format-headline-function 'ignore
org-structure-template-alist '(("le" "#+end_src \n\n#+begin_src emacs-lisp" "<src lang=\"R\">\n\n</src>")
("lua" "#+begin_src lua \n ?\n#+end_src" "<src lang=\"lua\">\n\n</src>")
("r" "#+begin_src R ?\n\n#+end_src" "<src lang=\"R\">\n\n</src>")
("s" "#+BEGIN_SRC ?\n\n#+END_SRC" "<src lang=\"?\">\n\n</src>")
("e" "#+BEGIN_EXAMPLE\n?\n#+END_EXAMPLE" "<example>\n?\n</example>")
("q" "#+BEGIN_QUOTE\n?\n#+END_QUOTE" "<quote>\n?\n</quote>")
("v" "#+BEGIN_VERSE\n?\n#+END_VERSE" "<verse>\n?\n</verse>")
("V" "#+BEGIN_VERBATIM\n?\n#+END_VERBATIM" "<verbatim>\n?\n</verbatim>")
("c" "#+BEGIN_CENTER\n?\n#+END_CENTER" "<center>\n?\n</center>")
("l" "#+BEGIN_LaTeX\n?\n#+END_LaTeX" "<literal style=\"latex\">\n?\n</literal>")
("L" "#+LaTeX: " "<literal style=\"latex\">?</literal>")
("h" "#+BEGIN_HTML\n?\n#+END_HTML" "<literal style=\"html\">\n?\n</literal>")
("H" "#+HTML: " "<literal style=\"html\">?</literal>") ("a" "#+BEGIN_ASCII\n?\n#+END_ASCII" "")
("A" "#+ASCII: " "") ("i" "#+INDEX: ?" "#+INDEX: ?")
("I" "#+INCLUDE: %file ?" "<include file=%file markup=\"?\">"))
org-babel-load-languages '((R . t) (latex . t) (sh . t) (plantuml . t) (emacs-lisp . t))
org-src-preserve-indentation t
org-babel-post-tangle-hook '(org-babel-run-post-tangle-script org-babel-mark-file-as-tangled)
org-html-format-inlinetask-function 'ignore
org-agenda-files '("~/org")
org-clock-out-hook '(org-clock-remove-empty-clock-drawer)
org-confirm-babel-evaluate nil
)
--
Rainer M. Krug, PhD (Conservation Ecology, SUN), MSc (Conservation Biology, UCT), Dipl. Phys. (Germany)
Centre of Excellence for Invasion Biology
Stellenbosch University
South Africa
Tel : +33 - (0)9 53 10 27 44
Cell: +33 - (0)6 85 62 59 98
Fax : +33 - (0)9 58 10 27 44
Fax (D): +49 - (0)3 21 21 25 22 44
email: Rainer@krugs.de
Skype: RMkrug
^ permalink raw reply [flat|nested] 2+ messages in thread
* Re: Bug: [babel] Order of definition of :var makes or breaks the results [8.2.5f (release_8.2.5f-545-g630096 @ /Users/rainerkrug/.emacs.d/org-mode/lisp/)]
2014-01-21 14:17 Bug: [babel] Order of definition of :var makes or breaks the results [8.2.5f (release_8.2.5f-545-g630096 @ /Users/rainerkrug/.emacs.d/org-mode/lisp/)] Rainer M Krug
@ 2014-01-22 19:55 ` Rainer M Krug
0 siblings, 0 replies; 2+ messages in thread
From: Rainer M Krug @ 2014-01-22 19:55 UTC (permalink / raw)
To: emacs-orgmode
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA1
Any confirmation of this bug?
Rainer
On 01/21/14, 15:17 , Rainer M Krug wrote:
> Depending on the order in which variables are declared, the
> definitions are correct or wrong.
>
> In the example below, if DUMMY is declared first and SPECIES and
> SPECIES2 are declared via :var+ there are missing rownames and /
> or colnames as well as mixups (see below).
>
> If DUMMY is declared *after the first* table (SPECIES) everything
> works as expected.
>
> I don't know if it is the same in other languages.
>
> Example:
>
> #+PROPERTY: rownames yes #+PROPERTY: colnames yes #+PROPERTY: var
> DUMMY="dummy"
>
> * Species names and iespece codes #+NAME: SPECIES | |
> fullName | shortName | iespece | IFNName | color |
> |---------+-----------------+-----------+---------+-----------------+-------|
>
>
| fagus | Fagus sylvatica | fagus | 3 | fagus_sylvatica |
red |
> | quercus | Quercus robur | quercus | 4 | quercus_robur
> | green | #+PROPERTY: var+ SPECIES=SPECIES
>
>
> * And some more #+NAME: SPECIES2 | | fullName |
> shortName | iespece | IFNName | color |
> |---------+---------------+-----------+---------+---------------+-------|
>
>
| no idea | ffff | | | | |
> | quercus | Quercus robur | quercus | 4 | quercus_robur |
> green | #+PROPERTY: var+ SPECIES2=SPECIES2
>
>
> * The code #+begin_src R :exports both :results output SPECIES
> #+end_src
>
> #+RESULTS: : fullName shortName iespece
> IFNName color : no idea Fagus sylvatica fagus 3
> fagus_sylvatica red : quercus Quercus robur quercus 4
> quercus_robur green
>
>
> #+begin_src R :exports both :results output SPECIES2 #+end_src
>
> #+RESULTS: : X X.1 X.2 X.3 :
> Quercus robur quercus 4 quercus_robur green
>
>
>
> Remember to cover the basics, that is, what you expected to happen
> and what in fact did happen. You don't know how to make a good
> report? See
>
> http://orgmode.org/manual/Feedback.html#Feedback
>
> Your bug report will be posted to the Org-mode mailing list.
> ------------------------------------------------------------------------
>
>
>
>
> Emacs : GNU Emacs 24.3.1 (x86_64-apple-darwin13.0.0, NS
> apple-appkit-1265.00) of 2013-12-13 on Rainers-MacBook-Pro-2.local
> Package: Org-mode version 8.2.5f (release_8.2.5f-545-g630096 @
> /Users/rainerkrug/.emacs.d/org-mode/lisp/)
>
> current state: ============== (setq org-src-lang-modes
> '(("plantuml" . plantuml) ("ocaml" . tuareg) ("elisp" . emacs-lisp)
> ("ditaa" . artist) ("asymptote" . asy) ("dot" . fundamental)
> ("sqlite" . sql) ("calc" . fundamental) ("C" . c) ("cpp" . c++)
> ("C++" . c++) ("screen" . shell-script)) org-hide-leading-stars t
> 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-ellipsis "〖 ✎ 〗" org-occur-hook
> '(org-first-headline-recenter) org-src-tab-acts-natively t
> org-metaup-hook '(org-babel-load-in-session-maybe)
> org-html-format-drawer-function '(lambda (name contents) contents)
> org-src-window-setup 'current-window
> org-latex-format-inlinetask-function 'ignore
> org-confirm-shell-link-function 'y-or-n-p
> org-ascii-format-inlinetask-function
> 'org-ascii-format-inlinetask-default
> org-latex-format-headline-function
> 'org-latex-format-headline-default-function org-startup-indented t
> org-after-todo-state-change-hook '(org-clock-out-if-current)
> org-latex-format-drawer-function '(lambda (name contents)
> contents) org-odt-format-headline-function 'ignore
> org-from-is-user-regexp "\\<Rainer M Krug\\>" 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-ascii-format-drawer-function '(lambda (name contents width)
> contents) org-odt-format-inlinetask-function 'ignore
> 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-plantuml-jar-path
> "/Users/rainerkrug/jar/plantuml.jar" org-latex-packages-alist '((""
> "color") ("" "listings")) org-ctrl-k-protect-subtree "ask"
> org-babel-tangle-lang-exts '(("latex" . "tex") ("emacs-lisp" .
> "el")) org-confirm-elisp-link-function 'yes-or-no-p
> org-metadown-hook '(org-babel-pop-to-session-maybe)
> org-odt-format-drawer-function '(lambda (name contents) contents)
> org-latex-listings t org-show-siblings '((default) (isearch t)
> (bookmark-jump . t)) org-html-format-headline-function 'ignore
> org-structure-template-alist '(("le" "#+end_src \n\n#+begin_src
> emacs-lisp" "<src lang=\"R\">\n\n</src>") ("lua" "#+begin_src lua
> \n ?\n#+end_src" "<src lang=\"lua\">\n\n</src>") ("r" "#+begin_src
> R ?\n\n#+end_src" "<src lang=\"R\">\n\n</src>") ("s" "#+BEGIN_SRC
> ?\n\n#+END_SRC" "<src lang=\"?\">\n\n</src>") ("e"
> "#+BEGIN_EXAMPLE\n?\n#+END_EXAMPLE" "<example>\n?\n</example>")
> ("q" "#+BEGIN_QUOTE\n?\n#+END_QUOTE" "<quote>\n?\n</quote>") ("v"
> "#+BEGIN_VERSE\n?\n#+END_VERSE" "<verse>\n?\n</verse>") ("V"
> "#+BEGIN_VERBATIM\n?\n#+END_VERBATIM"
> "<verbatim>\n?\n</verbatim>") ("c"
> "#+BEGIN_CENTER\n?\n#+END_CENTER" "<center>\n?\n</center>") ("l"
> "#+BEGIN_LaTeX\n?\n#+END_LaTeX" "<literal
> style=\"latex\">\n?\n</literal>") ("L" "#+LaTeX: " "<literal
> style=\"latex\">?</literal>") ("h" "#+BEGIN_HTML\n?\n#+END_HTML"
> "<literal style=\"html\">\n?\n</literal>") ("H" "#+HTML: "
> "<literal style=\"html\">?</literal>") ("a"
> "#+BEGIN_ASCII\n?\n#+END_ASCII" "") ("A" "#+ASCII: " "") ("i"
> "#+INDEX: ?" "#+INDEX: ?") ("I" "#+INCLUDE: %file ?" "<include
> file=%file markup=\"?\">")) org-babel-load-languages '((R . t)
> (latex . t) (sh . t) (plantuml . t) (emacs-lisp . t))
> org-src-preserve-indentation t org-babel-post-tangle-hook
> '(org-babel-run-post-tangle-script org-babel-mark-file-as-tangled)
> org-html-format-inlinetask-function 'ignore org-agenda-files
> '("~/org") org-clock-out-hook
> '(org-clock-remove-empty-clock-drawer) org-confirm-babel-evaluate
> nil )
>
- --
Rainer M. Krug, PhD (Conservation Ecology, SUN), MSc (Conservation
Biology, UCT), Dipl. Phys. (Germany)
Centre of Excellence for Invasion Biology
Stellenbosch University
South Africa
Tel : +33 - (0)9 53 10 27 44
Cell: +33 - (0)6 85 62 59 98
Fax : +33 - (0)9 58 10 27 44
Fax (D): +49 - (0)3 21 21 25 22 44
email: Rainer@krugs.de
Skype: RMkrug
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^ permalink raw reply [flat|nested] 2+ messages in thread
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2014-01-21 14:17 Bug: [babel] Order of definition of :var makes or breaks the results [8.2.5f (release_8.2.5f-545-g630096 @ /Users/rainerkrug/.emacs.d/org-mode/lisp/)] Rainer M Krug
2014-01-22 19:55 ` Rainer M Krug
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