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Wed, 6 Nov 2024 08:12:32 +0100 (CET) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=u-bordeaux.fr; s=2024020101; t=1730877152; h=from:from:reply-to:subject:subject:date:date:message-id:message-id: to:to:cc:mime-version:mime-version:content-type:content-type: content-transfer-encoding:content-transfer-encoding; bh=8TIw0U8PcseMAdCDfxZRztXKkYt2Zjc33CO9BqSB3KQ=; b=vIcmoApcKZ1eBYYqaqrRt7j8zPvg8QG6yC/KVW6vO/hV3HmnRyE2OT+X3FNeHe/LVYIVJA ebAW9pNRWvf4g30QQ+oyVYAyK2EmR06pxx3uE680CY9ITqp4Ac2DkJq1DW+ZVcNira5YFq bdvGWNu4Dz8WFtqGAktJkjh32OW9dls= Date: Wed, 6 Nov 2024 08:12:31 +0100 (CET) From: Frederic Santos To: emacs-orgmode@gnu.org Message-ID: <307177413.3351788.1730877151761.JavaMail.zimbra@u-bordeaux.fr> Subject: [BUG] Alignment issues with ob-R outputs [9.7.15 (9.7.15-a1df10 @ /home/fsantos/.emacs.d/elpa/org-9.7.15/)] MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable X-Originating-IP: [31.36.17.197] X-Mailer: Zimbra 10.0.9_GA_4654 (ZimbraWebClient - FF131 (Linux)/10.0.9_GA_4654) Thread-Index: OdukM04YNHkgyjZbam/O4Gv4x/dRYQ== Thread-Topic: Alignment issues with ob-R outputs [9.7.15 (9.7.15-a1df10 @ /home/fsantos/.emacs.d/elpa/org-9.7.15/)] X-AV-Checked: ClamAV using ClamSMTP Received-SPF: pass client-ip=147.210.215.83; envelope-from=frederic.santos@u-bordeaux.fr; helo=v-zimmta03.u-bordeaux.fr X-Spam_score_int: -43 X-Spam_score: -4.4 X-Spam_bar: ---- X-Spam_report: (-4.4 / 5.0 requ) BAYES_00=-1.9, DKIM_SIGNED=0.1, DKIM_VALID=-0.1, DKIM_VALID_AU=-0.1, DKIM_VALID_EF=-0.1, RCVD_IN_DNSWL_MED=-2.3, RCVD_IN_MSPIKE_H3=0.001, RCVD_IN_MSPIKE_WL=0.001, RCVD_IN_VALIDITY_CERTIFIED_BLOCKED=0.001, RCVD_IN_VALIDITY_RPBL_BLOCKED=0.001, SPF_HELO_NONE=0.001, SPF_PASS=-0.001 autolearn=ham autolearn_force=no X-Spam_action: no action X-BeenThere: emacs-orgmode@gnu.org X-Mailman-Version: 2.1.29 Precedence: list List-Id: "General discussions about Org-mode." List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: emacs-orgmode-bounces+larch=yhetil.org@gnu.org Sender: emacs-orgmode-bounces+larch=yhetil.org@gnu.org X-Migadu-Flow: FLOW_IN X-Migadu-Country: US X-Migadu-Spam-Score: 0.56 X-Spam-Score: 0.56 X-Migadu-Queue-Id: 7E429602E0 X-Migadu-Scanner: mx12.migadu.com X-TUID: hba9gqjqdAJM 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 =20 Min. :4.300 Min. :2.000 Min. :1.000 Min. :0.100 =20 1st Qu.:5.100 1st Qu.:2.800 1st Qu.:1.600 1st Qu.:0.300 =20 Median :5.800 Median :3.000 Median :4.350 Median :1.300 =20 Mean :5.843 Mean :3.057 Mean :3.758 Mean :1.199 =20 3rd Qu.:6.400 3rd Qu.:3.300 3rd Qu.:5.100 3rd Qu.:1.800 =20 Max. :7.900 Max. :4.400 Max. :6.900 Max. :2.500 =20 Species =20 setosa :50 =20 versicolor:50 =20 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 =20 Min. :4.300 Min. :2.000 Min. :1.000 Min. :0.100 =20 1st Qu.:5.100 1st Qu.:2.800 1st Qu.:1.600 1st Qu.:0.300 =20 Median :5.800 Median :3.000 Median :4.350 Median :1.300 =20 Mean :5.843 Mean :3.057 Mean :3.758 Mean :1.199 =20 3rd Qu.:6.400 3rd Qu.:3.300 3rd Qu.:5.100 3rd Qu.:1.800 =20 Max. :7.900 Max. :4.400 Max. :6.900 Max. :2.500 =20 Species =20 setosa :50 =20 versicolor:50 =20 virginica :50 #+end_example Thanks! Fr=C3=A9d=C3=A9ric 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/el= pa/org-9.7.15/) current state: =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D (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-he= ader-arg-expand) org-archive-hook '(org-attach-archive-delete-maybe) org-cite-follow-processor 'citar org-file-apps '(("\\.pdf\\'" . emacs) (auto-mode . emacs) (directory . ema= cs) ("\\.mm\\'" . default) ("\\.x?html?\\'" . default) ("\\.pdf\\'" . default)) org-log-reschedule 'note org-noter--pretty-print-location-for-title-hook '(org-noter-djvu--pretty-p= rint-location org-noter-nov--pretty-print-location org-noter-pdf--pretty-pr= int-location-for-title) org-odt-format-inlinetask-function 'org-odt-format-inlinetask-default-func= tion org-edit-src-content-indentation 0 org-ascii-format-drawer-function #[771 "=01\207" [] 4 "\n\n(fn NAME CONTEN= TS WIDTH)"] org-cycle-hook '(org-cycle-hide-archived-subtrees org-cycle-show-empty-lin= es org-cycle-optimize-window-after-visibility-change org-cycle-display-inline-images) org-latex-minted-langs '((SAS "sas") (R "r") (emacs-lisp "common-lisp") (c= c "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 o= l-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-pr= int-highlight) org-mode-hook '(tempel-setup-capf #[0 "\301\211=10\207" [imenu-create-inde= x-function org-imenu-get-tree] 2] org-fragtog-mode (lambda nil (local-set-key (kbd "C-u C-c C-x C-a") #'org-r= everse-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$\207" [add-hook change-major-mod= e-hook org-fold-show-all append local] 5] #[0 "\300\301\302\303\304$\207" [add-hook change-major-mod= e-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-locat= ion org-noter-nov--pretty-print-location org-noter-pdf--pretty-print-locati= on) 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-func= tion 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") ("eli= sp" . "el")) org-src-mode-hook '(org-src-babel-configure-edit-buffer org-src-mode-confi= gure-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)" "WAI= TING(w@)" "REVIEW(r)" "|" "DONE(d)" "CANCELED(c@)")) org--warnings nil org-roam-capture-new-node-hook '(orb--insert-captured-ref-h org-roam-captu= re--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 tab= le :session *julia* :exports both :colnames yes") ("jfig" . "src ess-julia :results output graphics fi= le :file FILENAME.png :session *julia* :exports both") ("j" . "src ess-julia :results output :sess= ion *julia* :exports both") ("einp" . "src ein-python :results output := session localhost :exports both") ("pfig" . "src python :results file :session :export= s both :var plot_filename=3D'FILENAME.png'\nimport matplotlib.pyplot as plt= \n\nplt.savefig(plot_filename)\nplot_filename") ("ip" . "src ipython :results output :sessi= on ip1 :exports both") ("p" . "src python :results output :session= :exports both") ("rtab" . "src R :results value table :coln= ames yes :rownames yes :session *R* :exports both") ("rfig" . "src R :results graphics file :file FILENA= ME.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-comman= d-activate) org-html-format-inlinetask-function 'org-html-format-inlinetask-default-fu= nction 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-enabl= e-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-no= ter-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-n= ov--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-locat= ion-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-a= rg-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-no= ter-nov--get-precise-info org-noter-pdf--doc-view-get-precise-inf= o 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-lin= k) ("rmail" :follow org-rmail-open :store org-rmail-sto= re-link) ("mhe" :follow org-mhe-open :store org-mhe-store-lin= k) ("irc" :follow org-irc-visit :store org-irc-store-li= nk :export org-irc-export) ("info" :follow org-info-open :export org-info-expor= t :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-docv= iew-export :store org-docview-store-link) ("bbdb" :follow org-bbdb-open :export org-bbdb-expor= t :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 or= g-attach-complete-link) ("id" :follow org-roam-id-open :store org-id-store-l= ink-maybe) ("file+sys") ("file+emacs") ("shell" :follow org-link--open-shell) ("news" :follow #[514 "\301\300\302=04Q=02\"\207" ["= news" browse-url ":"] 6 "\n\n(fn URL ARG)"]) ("mailto" :follow #[514 "\301\300\302=04Q=02\"\207" = ["mailto" browse-url ":"] 6 "\n\n(fn URL ARG)"]) ("https" :follow #[514 "\301\300\302=04Q=02\"\207" [= "https" browse-url ":"] 6 "\n\n(fn URL ARG)"]) ("http" :follow #[514 "\301\300\302=04Q=02\"\207" ["= http" browse-url ":"] 6 "\n\n(fn URL ARG)"]) ("ftp" :follow #[514 "\301\300\302=04Q=02\"\207" ["f= tp" 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-functi= on org-metaup-hook '(org-babel-load-in-session-maybe) org-noter-get-selected-text-hook '(org-noter-djvu--get-selected-text org-n= oter-nov--get-selected-text org-noter-pdf--get-selected-text) org-noter-create-session-from-document-hook '(org-noter--create-session-fr= om-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" . artis= t) ("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 )