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* [BUG] Alignment issues with ob-R outputs [9.7.15 (9.7.15-a1df10 @ /home/fsantos/.emacs.d/elpa/org-9.7.15/)]
@ 2024-11-06  7:12 Frederic Santos
  2024-11-23 18:39 ` Ihor Radchenko
  0 siblings, 1 reply; 2+ messages in thread
From: Frederic Santos @ 2024-11-06  7:12 UTC (permalink / raw)
  To: emacs-orgmode

Hi,

I noted that, roughly since the first updates of the Org 9.7.x series,
ob-R.el produces outputs that have alignment issues in the first line of
the output, if and only if the code block includes several lines of
code.

For instance, here is a code block including two lines of R code. As you
can see, in the output, the first line has a wrong alignment of column
names (all spaces being removed before the first word, "Sepal.Length"):

#+begin_src R :results output :session *R* :exports both
data(iris)
summary(iris)
#+end_src

#+RESULTS:
#+begin_example
Sepal.Length    Sepal.Width     Petal.Length    Petal.Width   
 Min.   :4.300   Min.   :2.000   Min.   :1.000   Min.   :0.100  
 1st Qu.:5.100   1st Qu.:2.800   1st Qu.:1.600   1st Qu.:0.300  
 Median :5.800   Median :3.000   Median :4.350   Median :1.300  
 Mean   :5.843   Mean   :3.057   Mean   :3.758   Mean   :1.199  
 3rd Qu.:6.400   3rd Qu.:3.300   3rd Qu.:5.100   3rd Qu.:1.800  
 Max.   :7.900   Max.   :4.400   Max.   :6.900   Max.   :2.500  
       Species  
 setosa    :50  
 versicolor:50  
 virginica :50
#+end_example

However, the output is correct if the code block is composed of one
single line of R code:

#+begin_src R :results output :session *R* :exports both
summary(iris)
#+end_src

#+RESULTS:
#+begin_example
  Sepal.Length    Sepal.Width     Petal.Length    Petal.Width   
 Min.   :4.300   Min.   :2.000   Min.   :1.000   Min.   :0.100  
 1st Qu.:5.100   1st Qu.:2.800   1st Qu.:1.600   1st Qu.:0.300  
 Median :5.800   Median :3.000   Median :4.350   Median :1.300  
 Mean   :5.843   Mean   :3.057   Mean   :3.758   Mean   :1.199  
 3rd Qu.:6.400   3rd Qu.:3.300   3rd Qu.:5.100   3rd Qu.:1.800  
 Max.   :7.900   Max.   :4.400   Max.   :6.900   Max.   :2.500  
       Species  
 setosa    :50  
 versicolor:50  
 virginica :50
#+end_example

Thanks!
Frédéric

Emacs  : GNU Emacs 29.4 (build 1, x86_64-pc-linux-gnu, GTK+ Version 3.24.43, cairo version 1.18.0)
Package: Org mode version 9.7.15 (9.7.15-a1df10 @ /home/fsantos/.emacs.d/elpa/org-9.7.15/)

current state:
==============
(setq
 org-link-elisp-confirm-function 'yes-or-no-p
 org-cite-insert-processor 'citar
 org-reverse-datetree-find-function 'org-reverse-datetree--find-or-insert
 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-babel-after-execute-hook '(org-display-inline-images)
 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-cite-follow-processor 'citar
 org-file-apps '(("\\.pdf\\'" . emacs) (auto-mode . emacs) (directory . emacs) ("\\.mm\\'" . default) ("\\.x?html?\\'" . default)
                 ("\\.pdf\\'" . default))
 org-log-reschedule 'note
 org-noter--pretty-print-location-for-title-hook '(org-noter-djvu--pretty-print-location org-noter-nov--pretty-print-location
                                                   org-noter-pdf--pretty-print-location-for-title)
 org-odt-format-inlinetask-function 'org-odt-format-inlinetask-default-function
 org-edit-src-content-indentation 0
 org-ascii-format-drawer-function #[771 "\x01\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-latex-minted-langs '((SAS "sas") (R "r") (emacs-lisp "common-lisp") (cc "c++") (cperl "perl") (shell-script "bash")
                          (caml "ocaml"))
 org-persist-before-read-hook '(org-element--cache-persist-before-read)
 org-modules '(ol-doi ol-w3m ol-bbdb ol-bibtex ol-docview ol-gnus ol-info ol-irc ol-mhe ol-rmail ol-eww org-habit)
 org-habit-preceding-days 30
 org-yank-image-file-name-function 'org-yank-image-autogen-filename
 org-starter-alternative-find-function 'org-starter-sparse-tree-on-file
 org-noter--pretty-print-highlight-location-hook '(org-noter-pdf--pretty-print-highlight)
 org-mode-hook '(tempel-setup-capf #[0 "\301\211\x10\207" [imenu-create-index-function org-imenu-get-tree] 2] org-fragtog-mode
                 (lambda nil (local-set-key (kbd "C-u C-c C-x C-a") #'org-reverse-datetree-archive-subtree))
                 org-display-inline-images turn-on-visual-line-mode (lambda nil (electric-indent-local-mode -1)) org-tempo-setup
                 #[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 '((emacs-lisp . t) (latex . t) (org . t) (R . t) (shell . t))
 org-noter--pretty-print-location-hook '(org-noter-djvu--pretty-print-location org-noter-nov--pretty-print-location
                                         org-noter-pdf--pretty-print-location)
 org-latex-format-drawer-function #[514 "\207" [] 3 "\n\n(fn _ CONTENTS)"]
 org-roam-db-node-include-function #[0 "\300\207" [t] 1]
 org-latex-format-headline-function 'org-latex-format-headline-default-function
 org-confirm-shell-link-function 'yes-or-no-p
 org-reveal-start-hook '(org-decrypt-entry)
 org-adapt-indentation 'headline-data
 org-html-format-drawer-function #[514 "\207" [] 3 "\n\n(fn NAME CONTENTS)"]
 outline-isearch-open-invisible-function 'outline-isearch-open-invisible
 org-after-todo-statistics-hook '(org-summary-todo)
 org-sort-function 'string-collate-lessp
 org-odt-format-headline-function 'org-odt-format-headline-default-function
 org-roam-capture-preface-hook '(org-roam-capture--try-capture-to-ref-h)
 org-agenda-before-write-hook '(org-agenda-add-entry-text)
 org-capture-prepare-finalize-hook '(org-roam-capture--install-finalize-h)
 org-src-preserve-indentation t
 org-latex-packages-alist '(("" "color"))
 org-roam-preview-function 'org-roam-preview-default-function
 org-babel-tangle-lang-exts '(("latex" . "tex") ("emacs-lisp" . "el") ("elisp" . "el"))
 org-src-mode-hook '(org-src-babel-configure-edit-buffer org-src-mode-configure-edit-buffer)
 org-roam-db-autosync-mode t
 org-checkbox-statistics-hook '(fs/org-checkbox-auto-close)
 org-confirm-elisp-link-function 'yes-or-no-p
 org-latex-src-block-backend 'minted
 org-log-buffer-setup-hook '(org-roam-log--setup)
 org-cite-activate-processor 'citar
 org-todo-keywords '((sequence "TODO(t)" "IN-PROGRESS(p)" "SOMEDAY(s)" "WAITING(w@)" "REVIEW(r)" "|" "DONE(d)" "CANCELED(c@)"))
 org--warnings nil
 org-roam-capture-new-node-hook '(orb--insert-captured-ref-h org-roam-capture--insert-captured-ref-h)
 org-structure-template-alist '(("init" . "src emacs-lisp :tangle init.el") ("el" . "src emacs-lisp :results output")
                                ("o" . "src octave :results output :session :exports both")
                                ("jtab" . "src ess-julia :results value table :session *julia* :exports both :colnames yes")
                                ("jfig" .
                                 "src ess-julia :results output graphics file :file FILENAME.png :session *julia* :exports both")
                                ("j" . "src ess-julia :results output :session *julia* :exports both")
                                ("einp" . "src ein-python :results output :session localhost :exports both")
                                ("pfig" .
                                 "src python :results file :session :exports both :var plot_filename='FILENAME.png'\nimport matplotlib.pyplot as plt\n\nplt.savefig(plot_filename)\nplot_filename")
                                ("ip" . "src ipython :results output :session ip1 :exports both")
                                ("p" . "src python :results output :session :exports both")
                                ("rtab" . "src R :results value table :colnames yes :rownames yes :session *R* :exports both")
                                ("rfig" .
                                 "src R :results graphics file :file FILENAME.png :exports both :width 600 :height 400 :session *R*")
                                ("r" . "src R :results output :session *R* :exports both") ("a" . "export ascii") ("c" . "center")
                                ("C" . "comment") ("e" . "example") ("E" . "export") ("h" . "export html") ("l" . "export latex")
                                ("q" . "quote") ("s" . "src") ("v" . "verse"))
 org-blocker-hook '(org-block-todo-from-children-or-siblings-or-parent)
 org-noter--show-arrow-hook '(org-noter-pdf--show-arrow)
 org-pretty-entities 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-habit-today-glyph 46
 org-habit-following-days 0
 org-roam-bibtex-mode t
 org-journal-mode-hook '(turn-on-visual-line-mode org-journal-default-enable-encryption)
 org-odt-format-drawer-function #[514 "\207" [] 3 "\n\n(fn NAME CONTENTS)"]
 org-noter--add-highlight-hook '(org-noter-pdf--highlight-location)
 org-noter--get-current-view-hook '(org-noter-djvu--get-current-view org-noter-nov--get-current-view
                                    org-noter-pdf--get-current-view)
 org-enforce-todo-dependencies t
 org-noter-set-up-document-hook '(org-noter-djvu--setup-handler org-noter-nov--setup-handler org-noter-pdf--doc-view-setup-handler
                                  org-noter-pdf--pdf-view-setup-handler)
 org-confirm-babel-evaluate nil
 org-noter--get-containing-element-hook '(org-noter--get-containing-heading org-noter--get-containing-property-drawer)
 org-fold-core-isearch-open-function 'org-fold--isearch-reveal
 org-export-with-smart-quotes t
 org-cite-export-processors '((beamer natbib) (latex natbib) (html csl) (t basic))
 org-latex-caption-above nil
 org-latex-format-inlinetask-function 'org-latex-format-inlinetask-default-function
 org-noter--convert-to-location-cons-hook '(org-noter-pdf--convert-to-location-cons)
 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-journal-file-type 'monthly
 org-agenda-loop-over-headlines-in-active-region nil
 org-todo-keyword-faces '(("TODO" . "red3") ("IN-PROGRESS" . "DarkOrange2") ("SOMEDAY" . "blue") ("WAITING" . "gold2")
                          ("REVIEW" . "purple") ("CANCELED" . "thistle4") ("DONE" . "forest green"))
 org-noter--get-precise-info-hook '(org-noter-djvu--get-precise-info org-noter-nov--get-precise-info
                                    org-noter-pdf--doc-view-get-precise-info org-noter-pdf--pdf-view-get-precise-info)
 org-fold-reveal-start-hook '(org-decrypt-entry)
 org-noter--get-highlight-location-hook '(org-noter-pdf--get-highlight)
 org-occur-hook '(org-first-headline-recenter)
 org-capture-after-finalize-hook '(orb-make-notes-cache)
 org-roam-log-setup-hook '(org-roam--register-completion-functions-h)
 org-metadown-hook '(org-babel-pop-to-session-maybe)
 org-noter--doc-approx-location-hook '(org-noter-djvu--approx-location-cons org-noter-nov--approx-location-cons
                                       org-noter-pdf--approx-location-cons)
 org-roam-node-annotation-function 'org-roam-node-read--annotation
 org-link-parameters '(("mu4e" :follow mu4e-org-open :store mu4e-org-store-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)
                       ("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)
                       ("roam" :follow org-roam-link-follow-link) ("bibtex" :follow org-bibtex-open :store org-bibtex-store-link)
                       ("attachment" :follow org-attach-follow :complete org-attach-complete-link)
                       ("id" :follow org-roam-id-open :store org-id-store-link-maybe) ("file+sys") ("file+emacs")
                       ("shell" :follow org-link--open-shell)
                       ("news" :follow #[514 "\301\300\302\x04Q\x02\"\207" ["news" browse-url ":"] 6 "\n\n(fn URL ARG)"])
                       ("mailto" :follow #[514 "\301\300\302\x04Q\x02\"\207" ["mailto" browse-url ":"] 6 "\n\n(fn URL ARG)"])
                       ("https" :follow #[514 "\301\300\302\x04Q\x02\"\207" ["https" browse-url ":"] 6 "\n\n(fn URL ARG)"])
                       ("http" :follow #[514 "\301\300\302\x04Q\x02\"\207" ["http" browse-url ":"] 6 "\n\n(fn URL ARG)"])
                       ("ftp" :follow #[514 "\301\300\302\x04Q\x02\"\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-journal-prefix-key "C-c j "
 org-noter-get-buffer-file-name-hook '(org-noter-nov--get-buffer-file-name org-noter-pdf--get-buffer-file-name)
 org-html-format-headline-function 'org-html-format-headline-default-function
 org-metaup-hook '(org-babel-load-in-session-maybe)
 org-noter-get-selected-text-hook '(org-noter-djvu--get-selected-text org-noter-nov--get-selected-text
                                    org-noter-pdf--get-selected-text)
 org-noter-create-session-from-document-hook '(org-noter--create-session-from-document-file-default)
 org-latex-pdf-process '("latexmk -shell-escape -bibtex -f -pdf %f")
 org-habit-completed-glyph 10003
 org-tags-column 0
 org-src-lang-modes '(("beamer" . LaTeX) ("latex" . LaTeX) ("C" . c) ("C++" . c++) ("asymptote" . asy) ("beamer" . latex)
                      ("calc" . fundamental) ("cpp" . c++) ("ditaa" . artist) ("desktop" . conf-desktop) ("dot" . fundamental)
                      ("elisp" . emacs-lisp) ("ocaml" . tuareg) ("screen" . shell-script) ("sqlite" . sql) ("toml" . conf-toml)
                      ("shell" . sh) ("ash" . sh) ("sh" . sh) ("bash" . sh) ("jsh" . sh) ("bash2" . sh) ("dash" . sh)
                      ("dtksh" . sh) ("ksh" . sh) ("es" . sh) ("rc" . sh) ("itcsh" . sh) ("tcsh" . sh) ("jcsh" . sh) ("csh" . sh)
                      ("ksh88" . sh) ("oash" . sh) ("pdksh" . sh) ("mksh" . sh) ("posix" . sh) ("wksh" . sh) ("wsh" . sh)
                      ("zsh" . sh) ("rpm" . sh))
 org-tab-before-tab-emulation-hook '(org-tempo-complete-tag)
 org-archive-reversed-order t
 org-roam-indirect-buffer-hook '(org-roam--register-completion-functions-h)
 org-clock-into-drawer "CLOCKING"
 org-journal-file-format "%Y%m%d.org"
 org-noter-create-skeleton-functions '(org-noter-djvu--create-skeleton org-noter-nov--create-skeleton-epub
                                       org-noter-pdf--create-skeleton)
 org-archive-subtree-save-file-p t
 org-list-allow-alphabetical t
 )


^ permalink raw reply	[flat|nested] 2+ messages in thread
end of thread, other threads:[~2024-11-23 18:39 UTC | newest]

Thread overview: 2+ messages (download: mbox.gz follow: Atom feed
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2024-11-06  7:12 [BUG] Alignment issues with ob-R outputs [9.7.15 (9.7.15-a1df10 @ /home/fsantos/.emacs.d/elpa/org-9.7.15/)] Frederic Santos
2024-11-23 18:39 ` Ihor Radchenko

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