* 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
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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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