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* Bug: org export rewrites the org buffer. if Emacs crashes during the export, the file gets corrupted [9.3.4 (9.3.4-5-ga0f3bb-elpa @ /home/lockywolf/.emacs.d/elpa/org-20200210/)]
@ 2020-05-28  9:38 Vladimir Nikishkin
  2020-05-28 12:01 ` Nicolas Goaziou
  0 siblings, 1 reply; 2+ messages in thread
From: Vladimir Nikishkin @ 2020-05-28  9:38 UTC (permalink / raw)
  To: emacs-orgmode



Remember to cover the basics, that is, what you expected to happen and
what in fact did happen.  You don't know how to make a good report?  See

     https://orgmode.org/manual/Feedback.html#Feedback

Your bug report will be posted to the Org mailing list.
------------------------------------------------------------------------

I have a very long org file, more than 70000 lines.

Exporting it is a naturally long process.
Additionally, some blocks are malformed, so the export process fails.
to debug them, I use toggle-debug-on-error

When I was debugging export today, I found that while exporting, org
destructively strips the header arguments from the blocks, such as
:exports, :results, :file.

It should be normally putting them back, I guess, but if
toggle-debug-on-error is on, and there are places where (debug) is
invoked or if emacs crashes (or is killed) during the export process,
the headers never go back.

Test file: https://gitlab.com/Lockywolf/chibi-sicp/-/blob/master/index.org

Emacs  : GNU Emacs 26.3 (build 1, x86_64-slackware-linux-gnu, GTK+ Version 3.24.12)
 of 2019-11-26
Package: Org mode version 9.3.4 (9.3.4-5-ga0f3bb-elpa @ /home/lockywolf/.emacs.d/elpa/org-20200210/)

current state:
==============
(setq
 org-src-mode-hook '((lambda nil (modify-syntax-entry 60 ".") (modify-syntax-entry 62 ".")
		      (setq geiser-autodoc--inhibit t))
		     org-src-babel-configure-edit-buffer org-src-mode-configure-edit-buffer)
 org-latex-listings t
 org-link-shell-confirm-function 'yes-or-no-p
 org-babel-after-execute-hook '((lambda nil
				 (if org-inline-image-overlays
				  (progn (org-redisplay-inline-images)))
				 )
				)
 org-metadown-hook '(org-babel-pop-to-session-maybe)
 org-export-with-sub-superscripts '{}
 org-clock-out-hook '(org-clock-remove-empty-clock-drawer)
 org-html-format-inlinetask-function 'org-html-format-inlinetask-default-function
 org-pretty-entities t
 org-odt-format-headline-function 'org-odt-format-headline-default-function
 org-link-descriptive nil
 org-latex-pdf-process '("latexmk  -lualatex -outdir=%o -f %f")
 org-agenda-files '("~/Personal_Planner/Planner.org" "~/Personal_Planner/lockywolf_net.org"
		    "~/Personal_Planner/cyberpunk_smarthome.org"
		    "~/Personal_Planner/notes.org"
		    "~/Personal_Planner/2020-04-28-hotkeys-to-remember.txt.org"
		    "~/DevLinux/chibi-sicp/index.org")
 org-ascii-format-inlinetask-function 'org-ascii-format-inlinetask-default
 org-modules '(org-habit ol-w3m ol-bbdb ol-bibtex ol-docview ol-gnus ol-info ol-irc ol-mhe
	       ol-rmail ol-eww)
 org-plantuml-jar-path "/usr/local/bin/plantuml.jar"
 org-mode-hook '(#[0 "\301\211\207" [imenu-create-index-function org-imenu-get-tree] 2]
		 turn-on-org-cdlatex org-tempo-setup
		 (lambda nil
		  (add-to-list (quote org-structure-template-alist)
		   (quote ("p" . "src plantuml :noweb no :exports both :file ")))
		  (add-to-list (quote org-structure-template-alist)
		   (quote ("SO" . "src scheme :exports both :results output")))
		  (add-to-list (quote org-structure-template-alist)
		   (quote ("SV" . "src scheme :exports both :results value")))
		  (add-to-list (quote org-structure-template-alist)
		   (quote ("SE" . "src scheme :exports code")))
		  (add-to-list (quote org-structure-template-alist)
		   (quote ("EL" . "src elisp :exports both :results output")))
		  (add-to-list (quote org-structure-template-alist)
		   (quote ("F" . "src f90 :exports both :results output")))
		  )
		 (lambda nil (modify-syntax-entry 60 ".") (modify-syntax-entry 62 "."))
		 (lambda nil (imenu-add-to-menubar "Imenu"))
		 #[0 "\300\301\302\303\304$\207"
		   [add-hook change-major-mode-hook org-show-all append local] 5]
		 #[0 "\300\301\302\303\304$\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-eldoc-load)
 org-odt-format-drawer-function #[514 "\207" [] 3 "\n\n(fn NAME CONTENTS)"]
 org-archive-hook '(org-attach-archive-delete-maybe)
 org-confirm-elisp-link-function 'yes-or-no-p
 org-agenda-before-write-hook '(org-agenda-add-entry-text)
 org-preview-latex-default-process 'imagemagick
 org-metaup-hook '(org-babel-load-in-session-maybe)
 org-bibtex-headline-format-function #[257 "\300\236A\207" [:title] 3 "\n\n(fn ENTRY)"]
 org-latex-format-drawer-function #[514 "\207" [] 3 "\n\n(fn _ CONTENTS)"]
 org-babel-pre-tangle-hook '(save-buffer)
 org-latex-compiler "lualatex"
 org-tab-first-hook '(org-babel-hide-result-toggle-maybe org-babel-header-arg-expand)
 org-babel-load-languages '((plantuml . t) (C . t) (scheme . t) (latex . t) (shell . t)
			    (fortran . t))
 org-log-done 'time
 org-link-abbrev-alist '(("bugzilla" . "http://10.1.2.9/bugzilla/show_bug.cgi?id=")
			 ("url-to-ja" .
			  "http://translate.google.fr/translate?sl=en&tl=ja&u=%h")
			 ("google" . "http://www.google.com/search?q=")
			 ("gmap" . "http://maps.google.com/maps?q=%s")
			 ("omap" . "http://nominatim.openstreetmap.org/search?q=%s&polygon=1")
			 ("ads" . "https://ui.adsabs.harvard.edu/search/q=%20author%3A\"%s\"")
			 ("note" .
			  "rtcite:~/GDrive_vladimir_nikishkin_AT_phystech_edu/BibTeX_Bibliography/bibliography-bib.org::#%s")
			 ("bib" .
			  "rtcite:~/GDrive_vladimir_nikishkin_AT_phystech_edu/BibTeX_Bibliography/bibliography-bib.bib::%s")
			 )
 org-startup-align-all-tables t
 org-ascii-format-drawer-function #[771 "\207" [] 4 "\n\n(fn NAME CONTENTS WIDTH)"]
 org-src-lang-modes '(("arduino" . arduino) ("redis" . redis) ("php" . php) ("C" . c)
		      ("C++" . c++) ("asymptote" . asy) ("bash" . sh) ("beamer" . latex)
		      ("calc" . fundamental) ("cpp" . c++) ("ditaa" . artist)
		      ("dot" . fundamental) ("elisp" . emacs-lisp) ("ocaml" . tuareg)
		      ("screen" . shell-script) ("shell" . sh) ("sqlite" . sql))
 org-catch-invisible-edits 'show
 org-occur-hook '(org-first-headline-recenter)
 org-log-into-drawer t
 org-edit-src-auto-save-idle-delay 15
 org-agenda-include-diary t
 org-structure-template-alist '(("F" . "src f90 :exports both :results output")
				("EL" . "src elisp :exports both :results output")
				("SE" . "src scheme :exports code")
				("SV" . "src scheme :exports both :results value")
				("SO" . "src scheme :exports both :results output")
				("p" . "src plantuml :noweb no :exports both :file ")
				("a" . "export ascii") ("c" . "center") ("C" . "comment")
				("e" . "example") ("E" . "export") ("h" . "export html")
				("l" . "export latex") ("q" . "quote") ("s" . "src")
				("v" . "verse"))
 org-cycle-hook '(org-cycle-hide-archived-subtrees org-cycle-show-empty-lines
		  org-optimize-window-after-visibility-change)
 org-edit-src-turn-on-auto-save t
 org-speed-command-hook '(org-speed-command-activate org-babel-speed-command-activate)
 org-hierarchical-todo-statistics nil
 org-preview-latex-process-alist '((dvipng :programs ("latex" "dvipng") :description
				    "dvi > png" :message
				    "you need to install the programs: latex and dvipng."
				    :image-input-type "dvi" :image-output-type "png"
				    :image-size-adjust (1.0 . 1.0) :latex-compiler
				    ("latex -interaction nonstopmode -output-directory %o %f")
				    :image-converter ("dvipng -D %D -T tight -o %O %f"))
				   (dvisvgm :programs ("latex" "dvisvgm") :description
				    "dvi > svg" :message
				    "you need to install the programs: latex and dvisvgm."
				    :image-input-type "dvi" :image-output-type "svg"
				    :image-size-adjust (1.7 . 1.5) :latex-compiler
				    ("latex -interaction nonstopmode -output-directory %o %f")
				    :image-converter ("dvisvgm %f -n -b min -c %S -o %O"))
				   (imagemagick :programs ("latex" "convert") :description
				    "pdf > png" :message
				    "you need to install the programs: latex and imagemagick."
				    :image-input-type "pdf" :image-output-type "png"
				    :image-size-adjust (1.0 . 1.0) :latex-compiler
				    ("lualatex -interaction nonstopmode -output-directory %o %f")
				    :image-converter
				    ("convert -density %D -trim -antialias %f -quality 100 %O")
				    )
				   )
 org-odt-format-inlinetask-function 'org-odt-format-inlinetask-default-function
 org-babel-tangle-lang-exts '(("fortran" . "F90") ("latex" . "tex") ("D" . "d")
			      ("C++" . "cpp") ("emacs-lisp" . "el") ("elisp" . "el"))
 org-format-latex-options '(:foreground default :background default :scale 3.0
			    :html-foreground "Black" :html-background "Transparent"
			    :html-scale 1.0 :matchers ("begin" "$1" "$" "$$" "\\(" "\\["))
 org-latex-listings-langs '((patch "bash") (shell "bash") (plantuml "MetaPost")
			    (elisp "elisp") (scheme "Lisp") (emacs-lisp "Lisp") (lisp "Lisp")
			    (clojure "Lisp") (c "C") (cc "C++") (fortran "fortran")
			    (perl "Perl") (cperl "Perl") (python "Python") (ruby "Ruby")
			    (html "HTML") (xml "XML") (tex "TeX") (latex "[LaTeX]TeX")
			    (shell-script "bash") (gnuplot "Gnuplot") (ocaml "Caml")
			    (caml "Caml") (sql "SQL") (sqlite "sql") (makefile "make")
			    (R "r"))
 org-confirm-shell-link-function 'yes-or-no-p
 org-link-parameters '(("attachment" :follow org-attach-open-link :export
			org-attach-export-link :complete org-attach-complete-link)
		       ("id" :follow org-id-open)
		       ("eww" :follow eww :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)
		       ("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)
		       ("rtcite" :follow org-bibtex-open :export my-rtcite-export-handler)
		       ("file+sys") ("file+emacs") ("shell" :follow org-link--open-shell)
		       (#1="news" :follow
			#[257 #2="\301\300\302Q!\207" [#1# browse-url #4=":"] 5 #5=
			  "\n\n(fn URL)"]
			)
		       (#3="mailto" :follow #[257 #2# [#3# browse-url #4#] 5 #5#])
		       (#6="https" :follow #[257 #2# [#6# browse-url #4#] 5 #5#])
		       (#7="http" :follow #[257 #2# [#7# browse-url #4#] 5 #5#])
		       (#8="ftp" :follow #[257 #2# [#8# browse-url #4#] 5 #5#])
		       ("help" :follow org-link--open-help)
		       ("file" :complete org-link-complete-file)
		       ("elisp" :follow org-link--open-elisp)
		       ("doi" :follow org-link--open-doi))
 org-latex-format-headline-function 'org-latex-format-headline-default-function
 org-agenda-start-with-follow-mode t
 org-link-elisp-confirm-function 'yes-or-no-p
 org-org-src-mode-hook '((lambda nil (modify-syntax-entry 60 ".")
			  (modify-syntax-entry 62 "."))
			 )
 org-latex-format-inlinetask-function 'org-latex-format-inlinetask-default-function
 org-tab-before-tab-emulation-hook '(org-tempo-complete-tag)
 org-html-format-drawer-function #[514 "\207" [] 3 "\n\n(fn NAME CONTENTS)"]
 org-latex-packages-alist '((#1="" "color") (#1# "listings"))
 org-image-actual-width nil
 org-html-use-infojs t
 org-latex-classes '(("acmart"
		      "\\documentclass[sigplan,anonymous,review,timestamp,natbib=false]{acmart}"
		      ("\\section{%s}" . "\\section*{%s}")
		      ("\\subsection{%s}" . "\\subsection*{%s}")
		      ("\\subsubsection{%s}" . "\\subsubsection*{%s}"))
		     ("article" "\\documentclass[11pt]{article}"
		      ("\\section{%s}" . "\\section*{%s}")
		      ("\\subsection{%s}" . "\\subsection*{%s}")
		      ("\\subsubsection{%s}" . "\\subsubsection*{%s}")
		      ("\\paragraph{%s}" . "\\paragraph*{%s}")
		      ("\\subparagraph{%s}" . "\\subparagraph*{%s}"))
		     ("report" "\\documentclass[11pt]{report}" ("\\part{%s}" . "\\part*{%s}")
		      ("\\chapter{%s}" . "\\chapter*{%s}")
		      ("\\section{%s}" . "\\section*{%s}")
		      ("\\subsection{%s}" . "\\subsection*{%s}")
		      ("\\subsubsection{%s}" . "\\subsubsection*{%s}"))
		     ("book" "\\documentclass[11pt]{book}" ("\\part{%s}" . "\\part*{%s}")
		      ("\\chapter{%s}" . "\\chapter*{%s}")
		      ("\\section{%s}" . "\\section*{%s}")
		      ("\\subsection{%s}" . "\\subsection*{%s}")
		      ("\\subsubsection{%s}" . "\\subsubsection*{%s}"))
		     )
 org-html-format-headline-function 'org-html-format-headline-default-function
 org-confirm-babel-evaluate 'my-org-confirm-babel-evaluate
 org-use-sub-superscripts '{}
 org-latex-listings-options '(("numbers" "left") ("frame" "single"))
 org-use-speed-commands t
 org-latex-bib-compiler "biber"
 org-default-notes-file "~/Personal_Planner/notes.org"
 )
-- 
--
Vladimir Nikishkin (MiEr, lockywolf)


^ permalink raw reply	[flat|nested] 2+ messages in thread

* Re: Bug: org export rewrites the org buffer. if Emacs crashes during the export, the file gets corrupted [9.3.4 (9.3.4-5-ga0f3bb-elpa @ /home/lockywolf/.emacs.d/elpa/org-20200210/)]
  2020-05-28  9:38 Bug: org export rewrites the org buffer. if Emacs crashes during the export, the file gets corrupted [9.3.4 (9.3.4-5-ga0f3bb-elpa @ /home/lockywolf/.emacs.d/elpa/org-20200210/)] Vladimir Nikishkin
@ 2020-05-28 12:01 ` Nicolas Goaziou
  0 siblings, 0 replies; 2+ messages in thread
From: Nicolas Goaziou @ 2020-05-28 12:01 UTC (permalink / raw)
  To: Vladimir Nikishkin; +Cc: emacs-orgmode

Hello,

Vladimir Nikishkin <lockywolf@gmail.com> writes:

> When I was debugging export today, I found that while exporting, org
> destructively strips the header arguments from the blocks, such as
> :exports, :results, :file.

Export process takes place in a copy of the original buffer. You were
probably looking at that copy. If you do think this was the genuine
buffer, please provide an ECM.

Also, removing some source code headers is a natural part of the process.

Regards,

-- 
Nicolas Goaziou


^ permalink raw reply	[flat|nested] 2+ messages in thread

end of thread, other threads:[~2020-05-28 12:01 UTC | newest]

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2020-05-28  9:38 Bug: org export rewrites the org buffer. if Emacs crashes during the export, the file gets corrupted [9.3.4 (9.3.4-5-ga0f3bb-elpa @ /home/lockywolf/.emacs.d/elpa/org-20200210/)] Vladimir Nikishkin
2020-05-28 12:01 ` Nicolas Goaziou

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