From: John Hendy <firstname.lastname@example.org> To: Jeremie Juste <email@example.com> Cc: Jack Kamm <firstname.lastname@example.org>, emacs-orgmode <email@example.com>, "Berry, Charles" <firstname.lastname@example.org>, Ilja Kocken <email@example.com>, Dylan Schwilk <firstname.lastname@example.org> Subject: Re: Help debugging R source code block output problem with :session Date: Wed, 12 Jan 2022 09:04:48 -0600 [thread overview] Message-ID: <CA+M2ft_sg=CQd7W_HjLzwEFVuK9pG_NGR15xop3OU0i2G3ccvA@mail.gmail.com> (raw) In-Reply-To: <email@example.com> [-- Attachment #1: Type: text/plain, Size: 2390 bytes --] On Wed, Jan 12, 2022 at 1:50 AM Jeremie Juste <firstname.lastname@example.org> wrote: > > Hello John, > > Many thanks for reporting. I'm short of time right now, but I'll take a closer look at the problem over > the weekend and keep you posted. Could you let me know which version of > org-mode you are currently using? Sure thing and thanks for the quick note! I use org from git and *thought* it used to report the most recent release tag, but I see: $ git log commit 7fa8173282f85c2ca03cc7f51f28f6adfb250610 (HEAD -> master, origin/master, origin/HEAD) Author: Ian Martins <email@example.com> Date: Sat Jan 16 15:52:21 2021 -0500 But Mx-version: Org mode version 9.4.4 (release_9.4.4-186-g7fa817.dirty @ /home/jwhendy/.elisp/org/lisp/) So perhaps it appends the git commit to the system version? Btw, it's dirty as I was able to apply Jack's patches (with some mods) successfully and am a happy camper. In case it's helpful, I attached the patches as I applied them (first -1, then -2) to this org-version. Nothing special, they are just Jack's patches with a couple sections removed (one change was already present, and I removed the adjustments to the testing file as they were failing). Thanks so much to all of you who contributed to that, as I'm so happy that I can at least continue on with my report at this point with good looking output! Many thanks, John > > Best regards, > Jeremie Juste > > > On Tuesday, 11 Jan 2022 at 17:36, John Hendy wrote: > > Greetings, > > > > Apologies for writing off-list, but I don't have the original thread > > anymore to reply to. I just pulled this group in directly from the > > email I found... I just got bitten by this as well and burned most of > > my afternoon trying to figure out what the issue was. > > > > Any further thoughts on a patch that could be finalized/applied? > > > > Is the one from the thread still the best from your continued experience? > > https://firstname.lastname@example.org/ > > > > This r/orgmode post was what finally got me to the existence of this > > as a previous issue (I'd just sent my own email to list as my > > searching did not find the above): > > https://www.reddit.com/r/orgmode/comments/pt3em4/source_block_modifying_format_of_results_r/ > > > > And it links to a patch as well: > > https://gist.github.com/gtuckerkellogg/e356d20497cfdc8e4fc683412e320e3e > > > > Many thanks, > > John [-- Attachment #2: ob-R-1.patch --] [-- Type: text/x-patch, Size: 1724 bytes --] diff --git a/lisp/ob-R.el b/lisp/ob-R.el index 5e9d35f58..b37e3965a 100644 --- a/lisp/ob-R.el +++ b/lisp/ob-R.el @@ -437,24 +439,23 @@ (defun org-babel-R-evaluate-session (org-babel-import-elisp-from-file tmp-file '(16))) column-names-p))) (output - (mapconcat - 'org-babel-chomp - (butlast - (delq nil - (mapcar - (lambda (line) (when (> (length line) 0) line)) - (mapcar - (lambda (line) ;; cleanup extra prompts left in output - (if (string-match - "^\\([>+.]\\([ ][>.+]\\)*[ ]\\)" - (car (split-string line "\n"))) - (substring line (match-end 1)) - line)) - (org-babel-comint-with-output (session org-babel-R-eoe-output) - (insert (mapconcat 'org-babel-chomp - (list body org-babel-R-eoe-indicator) - "\n")) - (inferior-ess-send-input)))))) "\n")))) + (let* ((tmp-file (org-babel-temp-file "R-"))) + (with-temp-file tmp-file + (insert (concat body "\n" org-babel-R-eoe-indicator))) + (with-current-buffer session + (let* ((process (get-buffer-process (current-buffer))) + (string-buffer "") + (comint-output-filter-functions + (cons (lambda (text) (setq string-buffer + (concat string-buffer text))) + comint-output-filter-functions))) + (ess-send-string + process (format "source('%s', print.eval=TRUE)" + (org-babel-process-file-name tmp-file 'noquote))) + (while (not (string-match (regexp-quote org-babel-R-eoe-output) + string-buffer)) + (accept-process-output process)) + (substring string-buffer 0 (match-beginning 0)))))))) (defun org-babel-R-process-value-result (result column-names-p) "R-specific processing of return value. [-- Attachment #3: ob-R-2.patch --] [-- Type: text/x-patch, Size: 1044 bytes --] diff --git a/lisp/ob-R.el b/lisp/ob-R.el index b37e3965a..5ddf0ebd1 100644 --- a/lisp/ob-R.el +++ b/lisp/ob-R.el @@ -441,7 +441,7 @@ (defun org-babel-R-evaluate-session (output (let* ((tmp-file (org-babel-temp-file "R-"))) (with-temp-file tmp-file - (insert (concat body "\n" org-babel-R-eoe-indicator))) + (insert body)) (with-current-buffer session (let* ((process (get-buffer-process (current-buffer))) (string-buffer "") @@ -450,8 +450,9 @@ (defun org-babel-R-evaluate-session (concat string-buffer text))) comint-output-filter-functions))) (ess-send-string - process (format "source('%s', print.eval=TRUE)" - (org-babel-process-file-name tmp-file 'noquote))) + process (format "tryCatch(source('%s', print.eval=TRUE), finally=print(%s))" + (org-babel-process-file-name tmp-file 'noquote) + org-babel-R-eoe-indicator)) (while (not (string-match (regexp-quote org-babel-R-eoe-output) string-buffer)) (accept-process-output process))
next prev parent reply other threads:[~2022-01-12 15:40 UTC|newest] Thread overview: 25+ messages / expand[flat|nested] mbox.gz Atom feed top 2022-01-11 23:36 John Hendy 2022-01-12 7:49 ` Jeremie Juste 2022-01-12 15:04 ` John Hendy [this message] -- strict thread matches above, loose matches on Subject: below -- 2020-08-28 20:11 Dylan Schwilk 2020-08-29 2:36 ` Jack Kamm 2020-08-29 4:07 ` Dylan Schwilk 2020-08-29 7:24 ` Jack Kamm 2020-08-29 20:35 ` Berry, Charles via General discussions about Org-mode. 2020-08-30 4:37 ` Dylan Schwilk 2020-08-30 15:08 ` Jack Kamm 2020-09-07 8:18 ` Jack Kamm 2020-09-07 8:45 ` Jack Kamm 2020-09-07 17:37 ` Berry, Charles via General discussions about Org-mode. 2020-09-07 20:07 ` Jack Kamm 2020-09-07 22:12 ` Berry, Charles via General discussions about Org-mode. 2020-09-08 1:06 ` Jack Kamm 2020-09-08 2:08 ` Berry, Charles via General discussions about Org-mode. 2020-09-08 14:51 ` Jack Kamm 2020-09-08 16:45 ` Berry, Charles via General discussions about Org-mode. 2020-09-08 17:41 ` Jack Kamm 2020-09-18 16:39 ` Dylan Schwilk 2020-10-28 13:13 ` Jack Kamm 2020-10-28 13:46 ` Jeremie Juste 2020-08-30 4:18 ` Dylan Schwilk 2021-05-03 8:53 ` Jeremie Juste
Reply instructions: You may reply publicly to this message via plain-text email using any one of the following methods: * Save the following mbox file, import it into your mail client, and reply-to-all from there: mbox Avoid top-posting and favor interleaved quoting: https://en.wikipedia.org/wiki/Posting_style#Interleaved_style List information: https://www.orgmode.org/ * Reply using the --to, --cc, and --in-reply-to switches of git-send-email(1): git send-email \ --in-reply-to='CA+M2ft_sg=CQd7W_HjLzwEFVuK9pG_NGR15xop3OU0i2G3ccvA@mail.gmail.com' \ --email@example.com \ --firstname.lastname@example.org \ --email@example.com \ --firstname.lastname@example.org \ --email@example.com \ --firstname.lastname@example.org \ --email@example.com \ --subject='Re: Help debugging R source code block output problem with :session' \ /path/to/YOUR_REPLY https://kernel.org/pub/software/scm/git/docs/git-send-email.html * If your mail client supports setting the In-Reply-To header via mailto: links, try the mailto: link
Code repositories for project(s) associated with this inbox: https://git.savannah.gnu.org/cgit/emacs/org-mode.git This is a public inbox, see mirroring instructions for how to clone and mirror all data and code used for this inbox; as well as URLs for read-only IMAP folder(s) and NNTP newsgroup(s).