From: Paul Stansell <paulstansell@gmail.com>
To: emacs-orgmode@gnu.org
Subject: [BUG] With R using ":var d=data" breaks ":colnames yes" [9.7-pre (release_9.6.10-881-g595a32]
Date: Wed, 6 Mar 2024 23:09:46 +0000 [thread overview]
Message-ID: <CAMJKaZwtXfTksqW7AY2HMb99FSv56PKzhRAr=-8n0MfRKwxHqg@mail.gmail.com> (raw)
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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
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org-table-dataline-regexp
org-table-any-border-regexp
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org-complex-heading-regexp calendar-mode-map t)
nil (setq imenu-create-index-function
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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*
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org-babel-tangle-uncomment-comments org-src-lang-modes
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nil
(add-hook 'change-major-mode-hook
#'org-babel-show-result-all 'append
'local)
)
org-babel-result-hide-spec org-babel-hide-all-hashes)
org-clock-persist 'history
org-odt-format-drawer-function '(closure
(hfy-user-sheet-assoc hfy-html-quote-regex
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(_name contents) contents)
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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-persist-after-read-hook '(org-element--cache-persist-after-read)
org-bibtex-headline-format-function 'org-bibtex-headline-format-default
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(_ contents) contents)
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"))
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org-export-with-drawers '("LATEX_DRAW")
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. t) (python . t)
(fortran . t) (sql . t) (ditaa . t) (dot . t)
(shell . t))
org-log-done 'time
org-highlight-latex-and-related '(latex)
org-ascii-format-drawer-function '(closure (t) (_name contents _width)
contents)
org-cycle-tab-first-hook '(org-babel-hide-result-toggle-maybe
org-babel-header-arg-expand)
org-agenda-loop-over-headlines-in-active-region nil
org-fontify-done-headline nil
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org-occur-hook '(org-first-headline-recenter)
org-log-into-drawer t
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org-cycle-optimize-window-after-visibility-change
org-cycle-display-inline-images)
org-todo-keywords '((sequence "TODO(t!)" "MAYBE(m!)" "STARTED(s!)"
"WAITING(w@/!)" "|"
"DONE(d)" "INFO(i!)" "CANCELLED(c@)" "UNFINISHED(u@)"
"ABANDONED(a@)")
)
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org-babel-speed-command-activate)
org-yank-image-file-name-function 'org-yank-image-autogen-filename
org-odt-format-inlinetask-function
'org-odt-format-inlinetask-default-function
org-fold-catch-invisible-edits 'error
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-export-before-parsing-hook '(org-attach-expand-links)
org-confirm-shell-link-function 'yes-or-no-p
org-link-parameters '(("attachment" :follow org-attach-follow :complete
org-attach-complete-link)
("eww" :follow org-eww-open :store
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("rmail" :follow org-rmail-open :store
org-rmail-store-link)
("mhe" :follow org-mhe-open :store
org-mhe-store-link)
("irc" :follow org-irc-visit :store
org-irc-store-link :export
org-irc-export)
("info" :follow org-info-open :export
org-info-export :store
org-info-store-link :insert-description
org-info-description-as-command)
("gnus" :follow org-gnus-open :store
org-gnus-store-link)
("docview" :follow org-docview-open :export
org-docview-export :store
org-docview-store-link)
("bibtex" :follow org-bibtex-open :store
org-bibtex-store-link)
("bbdb" :follow org-bbdb-open :export
org-bbdb-export :complete
org-bbdb-complete-link :store org-bbdb-store-link)
("w3m" :store org-w3m-store-link)
("doi" :follow org-link-doi-open :export
org-link-doi-export)
("id" :follow org-id-open :store
org-id-store-link-maybe)
("file+sys") ("file+emacs") ("shell" :follow
org-link--open-shell)
("news" :follow
(closure
((scheme . "news") (--dolist-tail--) org-ts-regexp
org-src-source-file-name org-outline-regexp-bol
org-inhibit-startup org-id-link-to-org-use-id
org-highlight-links
org-comment-string org-agenda-buffer-name
clean-buffer-list-kill-buffer-names t)
(url arg) (browse-url (concat scheme ":" url) arg))
)
("mailto" :follow
(closure
((scheme . "mailto") (--dolist-tail--)
org-ts-regexp
org-src-source-file-name org-outline-regexp-bol
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org-highlight-links
org-comment-string org-agenda-buffer-name
clean-buffer-list-kill-buffer-names t)
(url arg) (browse-url (concat scheme ":" url) arg))
)
("https" :follow
(closure
((scheme . "https") (--dolist-tail--) org-ts-regexp
org-src-source-file-name org-outline-regexp-bol
org-inhibit-startup org-id-link-to-org-use-id
org-highlight-links
org-comment-string org-agenda-buffer-name
clean-buffer-list-kill-buffer-names t)
(url arg) (browse-url (concat scheme ":" url) arg))
)
("http" :follow
(closure
((scheme . "http") (--dolist-tail--) org-ts-regexp
org-src-source-file-name org-outline-regexp-bol
org-inhibit-startup org-id-link-to-org-use-id
org-highlight-links
org-comment-string org-agenda-buffer-name
clean-buffer-list-kill-buffer-names t)
(url arg) (browse-url (concat scheme ":" url) arg))
)
("ftp" :follow
(closure
((scheme . "ftp") (--dolist-tail--) org-ts-regexp
org-src-source-file-name org-outline-regexp-bol
org-inhibit-startup org-id-link-to-org-use-id
org-highlight-links
org-comment-string org-agenda-buffer-name
clean-buffer-list-kill-buffer-names t)
(url arg) (browse-url (concat scheme ":" 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-latex-format-headline-function
'org-latex-format-headline-default-function
org-link-elisp-confirm-function 'yes-or-no-p
org-todo-keyword-faces '(("TODO" :foreground "light pink" :weight bold)
("MAYBE" :foreground "light pink" :weight bold)
("STARTED" :foreground "gold" :weight bold)
("DONE" :foreground "light green" :weight bold)
("WAITING" :foreground "gold" :weight bold)
("CANCELLED" :foreground "light green" :weight
bold)
("UNFINISHED" :foreground "light green" :weight
bold)
("ABANDONED" :foreground "light green" :weight
bold))
org-latex-format-inlinetask-function
'org-latex-format-inlinetask-default-function
org-html-format-drawer-function '(closure
(htmlize-buffer-places
org-html-format-table-no-css
htmlize-css-name-prefix
htmlize-output-type
htmlize-output-type
htmlize-css-name-prefix t)
(_name contents) contents)
org-clock-into-drawer "CLOCK"
org-clock-in-switch-to-state "STARTED"
org-html-format-headline-function
'org-html-format-headline-default-function
org-clock-out-remove-zero-time-clocks t
org-confirm-babel-evaluate nil
)
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next reply other threads:[~2024-03-06 23:10 UTC|newest]
Thread overview: 4+ messages / expand[flat|nested] mbox.gz Atom feed top
2024-03-06 23:09 Paul Stansell [this message]
2024-03-07 13:20 ` [BUG] With R using ":var d=data" breaks ":colnames yes" [9.7-pre (release_9.6.10-881-g595a32] Ihor Radchenko
2024-03-07 18:38 ` Paul Stansell
2024-03-07 19:05 ` Ihor Radchenko
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