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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
                   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
                   org-edit-src-content-indentation
org-babel-library-of-babel t)
                  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
                                   hfy-html-quote-map hfy-face-to-css
hfy-begin-span-handler
                                   hfy-end-span-handler archive-zip-extract
                                   nxml-auto-insert-xml-declaration-flag t)
                                  (_name contents) contents)
 org-archive-hook '(org-attach-archive-delete-maybe)
 org-persist-before-read-hook '(org-element--cache-persist-before-read)
 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
 org-adapt-indentation t
 org-latex-format-drawer-function '(closure
                                    (engrave-faces-latex-mathescape
                                     engrave-faces-current-preset-style
                                     engrave-faces-latex-output-style t)
                                    (_ 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"))
 org-tab-first-hook '(org-babel-hide-result-toggle-maybe
org-babel-header-arg-expand)
 org-export-with-drawers '("LATEX_DRAW")
 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-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
 org-fold-core-isearch-open-function 'org-fold--isearch-reveal
 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-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@)")
                     )
 org-speed-command-hook '(org-speed-command-activate
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
org-eww-store-link)
                       ("rmail" :follow org-rmail-open :store
org-rmail-store-link)
                       ("mhe" :follow org-mhe-open :store
org-mhe-store-link)
                       ("irc" :follow org-irc-visit :store
org-irc-store-link :export
                        org-irc-export)
                       ("info" :follow org-info-open :export
org-info-export :store
                        org-info-store-link :insert-description
                        org-info-description-as-command)
                       ("gnus" :follow org-gnus-open :store
org-gnus-store-link)
                       ("docview" :follow org-docview-open :export
org-docview-export :store
                        org-docview-store-link)
                       ("bibtex" :follow org-bibtex-open :store
org-bibtex-store-link)
                       ("bbdb" :follow org-bbdb-open :export
org-bbdb-export :complete
                        org-bbdb-complete-link :store org-bbdb-store-link)
                       ("w3m" :store org-w3m-store-link)
                       ("doi" :follow org-link-doi-open :export
org-link-doi-export)
                       ("id" :follow org-id-open :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
                          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))
                        )
                       ("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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             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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