Re: Bug: ob-R.el breaks when :session is specified
Hi Charles, ob-R.el requires ess and the (require 'package) makes sure the ~/.emacs.d/elpa/ directory was added to the load path. But you were somewhat right already: the loaded ESS was years old and caused the issue. Thanks for your help! Christian On Sun, 2022-05-15 at 19:58 +, Berry, Charles wrote: > > Um... > > > On May 15, 2022, at 2:46 AM, Christian Heinrich > > wrote: > > > > I run > > > > emacs -q --load /tmp/init.el --file=/tmp/test.org > > > > with my /tmp/init.el being only > > > > > (require 'package) > > > (package-initialize) > > > (add-to-list 'load-path "~/.emacs.d/straight/repos/org/lisp/") > > > (require 'org) > > > > > > ;(require 'ess-site) > > The line above is commented out. So how do you load ess-site? > > > > > (org-babel-do-load-languages > > > 'org-babel-load-languages > > > '((R . t))) > > > > I hope this constitutes a minimal example for a config - please correct me > > if I'm wrong. > > > Just spitballing here: > > Have you tried instrumenting `org-babel-R-evaluate-session'? > > Maybe watching changes made to the session buffer on first evaluation and > comparing to subsequent > evals helps. > > HTH, > Chuck > signature.asc Description: This is a digitally signed message part
Re: Bug: ob-R.el breaks when :session is specified
Hi Jeremie,
thank you for providing this example!
The ess that was found in the load path was years old and once updated, all
issues were resolved. In
fact, my so-called minimum init still used (require 'package) and I didn't even
think about ESS
causing this trouble.
It's now a bit clearer how to build a real minimum init - thank you!
This is hence resolved.
Best regards
Christian
On Mon, 2022-05-16 at 00:21 +0200, Jeremie Juste wrote:
>
> Hello Christian
>
> On Sunday, 15 May 2022 at 20:06, Christian Heinrich wrote:
> > I just tested with
> >
> > Org mode version 9.5.3 (release_9.5.3-504-gcdbb1c @
> > /home/heinrich/.emacs.d/straight/repos/org/lisp/)
> >
> > using
> >
> > GNU Emacs 27.1 (build 1, x86_64-pc-linux-gnu, GTK+ Version 3.24.30, cairo
> > version 1.16.0) of
> > 2021-
> > 11-27, modified by Debian
>
>
> Many thanks for reporting back. I updated to gcdbb1c and it is still working
> fine.
>
> My minimum working example is the following. From the org-mode root directory,
>
> $ emacs -Q -L ./lisp -l org -l ~/ess-barebone.el
>
> where ~/ess-barebone.el is the following:
>
> #+begin_src elisp
> (add-to-list 'load-path "/home/djj/.emacs.d/elpa/ess-20220125.2207/")
> (require 'ess-r-mode)
>
> (org-babel-do-load-languages
> 'org-babel-load-languages
> '((R . t)))
>
> (setq org-confirm-babel-evaluate nil)
> #+end_src
>
> Note that I'm still using a rather old ess version. Could you please try
> with the above configuration? Note that I am using a rather old ess
> version but the I haven't experienced issues with the newer one.
>
> Best regards
> Jeremie
>
>
> > Hi Jeremie,
> >
> > I just tested with
> >
> > Org mode version 9.5.3 (release_9.5.3-504-gcdbb1c @
> > /home/heinrich/.emacs.d/straight/repos/org/lisp/)
> >
> > using
> >
> > GNU Emacs 27.1 (build 1, x86_64-pc-linux-gnu, GTK+ Version 3.24.30, cairo
> > version 1.16.0) of
> > 2021-
> > 11-27, modified by Debian
> >
> > I am on Debian Testing and that is the default emacs version.
> >
> > Using the unmodified org (git hash from above) I get the following messages
> > when executing a src
> > block with R:
> >
> > executing R code block...
> > Loading ‘ess-bugs-l’: unescaped character literals `?(', `?)' detected,
> > `?\(', `?\)'
> > expected!
> > Type C-h m for help on ESS version 15.09
> > ess-tracebug mode enabled
> > Quit
> > Package cl is deprecated
> >
> > Note that the "Quit" is me pressing Ctrl-g after a few seconds.
> >
> > Removing the commit in question makes the block return instantaneously:
> >
> > executing R code block...
> > Loading ‘ess-bugs-l’: unescaped character literals `?(', `?)' detected,
> > `?\(', `?\)'
> > expected!
> > Type C-h m for help on ESS version 15.09
> > ess-tracebug mode enabled
> > Code block evaluation complete.
> > Package cl is deprecated
> >
> > I anticipated that this would not be obvious, since this feature is used
> > too much to go
> > unnoticed for
> > two years - but I am clueless as to how I should continue with debugging...
> >
> > Thanks for your help!
> > Christian
> >
> > On Sun, 2022-05-15 at 16:16 +0200, Jeremie Juste wrote:
> > >
> > > Hello Christian,
> > >
> > > Thanks for reporting but I cannot reproduce the bug with the org and
> > > emacs version below.
> > >
> > > Org mode version 9.5.3 (release_9.5.3-467-g2bd34e @
> > > /home/djj/src/org-mode/lisp/)
> > > GNU Emacs 27.2 (build 1, x86_64-pc-linux-gnu, GTK+ Version 3.24.24) of
> > > 2022-01-16
> > >
> > > Can you please let me know which version of org-mode you are actually
> > > using?
> > >
> > > Ihor, many thanks for checking.
> > >
> > > Best regards,
> > > Jeremie
> > >
> > > On Sunday, 15 May 2022 at 16:08, Ihor Radchenko wrote:
> > > > Christian Heinrich writes:
> > > >
> > > > > I got back to an org file after upgrading to the latest release of
> > > > > org-mode and tried
> > > > > executing the
> > > > > contained R source blocks. Unfortunately, emacs got stuck in the
> > > > > execution and was
> > > > > blocked; I
> > > > > had to
> > > > > exit using C-g.
> > > > >
> > > > > Here's a minimal example src block that causes emacs to get stuck:
> > > > >
> > > > > #+begin_src R :results output :session *R* :exports both
> > > > > a <- 10
> > > > > a
> > > > > #+end_src
> > > > >
> > > > > R itself does start and the code is also executed correctly. However,
> > > > > the output from that
> > > > > session
> > > > > is apparently not returned to emacs or the buffer.
> > > >
> > > > I tried you example using Emacs >=26 and it works just fine.
> > > >
> > > > Best,
> > > > Ihor
>
signature.asc
Description: This is a digitally signed message part
Re: Bug: ob-R.el breaks when :session is specified
Hi Jeremie,
thank you for providing this example!
The ess that was found in the load path was years old and once updated, all
issues were resolved. In
fact, my so-called minimum init still used (require 'package) and I didn't even
think about ESS
causing this trouble.
It's now a bit clearer how to build a real minimum init - thank you!
This is hence resolved.
Best regards
Christian
On Mon, 2022-05-16 at 00:21 +0200, Jeremie Juste wrote:
>
> Hello Christian
>
> On Sunday, 15 May 2022 at 20:06, Christian Heinrich wrote:
> > I just tested with
> >
> > Org mode version 9.5.3 (release_9.5.3-504-gcdbb1c @
> > /home/heinrich/.emacs.d/straight/repos/org/lisp/)
> >
> > using
> >
> > GNU Emacs 27.1 (build 1, x86_64-pc-linux-gnu, GTK+ Version 3.24.30, cairo
> > version 1.16.0) of
> > 2021-
> > 11-27, modified by Debian
>
>
> Many thanks for reporting back. I updated to gcdbb1c and it is still working
> fine.
>
> My minimum working example is the following. From the org-mode root directory,
>
> $ emacs -Q -L ./lisp -l org -l ~/ess-barebone.el
>
> where ~/ess-barebone.el is the following:
>
> #+begin_src elisp
> (add-to-list 'load-path "/home/djj/.emacs.d/elpa/ess-20220125.2207/")
> (require 'ess-r-mode)
>
> (org-babel-do-load-languages
> 'org-babel-load-languages
> '((R . t)))
>
> (setq org-confirm-babel-evaluate nil)
> #+end_src
>
> Note that I'm still using a rather old ess version. Could you please try
> with the above configuration? Note that I am using a rather old ess
> version but the I haven't experienced issues with the newer one.
>
> Best regards
> Jeremie
>
>
> > Hi Jeremie,
> >
> > I just tested with
> >
> > Org mode version 9.5.3 (release_9.5.3-504-gcdbb1c @
> > /home/heinrich/.emacs.d/straight/repos/org/lisp/)
> >
> > using
> >
> > GNU Emacs 27.1 (build 1, x86_64-pc-linux-gnu, GTK+ Version 3.24.30, cairo
> > version 1.16.0) of
> > 2021-
> > 11-27, modified by Debian
> >
> > I am on Debian Testing and that is the default emacs version.
> >
> > Using the unmodified org (git hash from above) I get the following messages
> > when executing a src
> > block with R:
> >
> > executing R code block...
> > Loading ‘ess-bugs-l’: unescaped character literals `?(', `?)' detected,
> > `?\(', `?\)'
> > expected!
> > Type C-h m for help on ESS version 15.09
> > ess-tracebug mode enabled
> > Quit
> > Package cl is deprecated
> >
> > Note that the "Quit" is me pressing Ctrl-g after a few seconds.
> >
> > Removing the commit in question makes the block return instantaneously:
> >
> > executing R code block...
> > Loading ‘ess-bugs-l’: unescaped character literals `?(', `?)' detected,
> > `?\(', `?\)'
> > expected!
> > Type C-h m for help on ESS version 15.09
> > ess-tracebug mode enabled
> > Code block evaluation complete.
> > Package cl is deprecated
> >
> > I anticipated that this would not be obvious, since this feature is used
> > too much to go
> > unnoticed for
> > two years - but I am clueless as to how I should continue with debugging...
> >
> > Thanks for your help!
> > Christian
> >
> > On Sun, 2022-05-15 at 16:16 +0200, Jeremie Juste wrote:
> > >
> > > Hello Christian,
> > >
> > > Thanks for reporting but I cannot reproduce the bug with the org and
> > > emacs version below.
> > >
> > > Org mode version 9.5.3 (release_9.5.3-467-g2bd34e @
> > > /home/djj/src/org-mode/lisp/)
> > > GNU Emacs 27.2 (build 1, x86_64-pc-linux-gnu, GTK+ Version 3.24.24) of
> > > 2022-01-16
> > >
> > > Can you please let me know which version of org-mode you are actually
> > > using?
> > >
> > > Ihor, many thanks for checking.
> > >
> > > Best regards,
> > > Jeremie
> > >
> > > On Sunday, 15 May 2022 at 16:08, Ihor Radchenko wrote:
> > > > Christian Heinrich writes:
> > > >
> > > > > I got back to an org file after upgrading to the latest release of
> > > > > org-mode and tried
> > > > > executing the
> > > > > contained R source blocks. Unfortunately, emacs got stuck in the
> > > > > execution and was
> > > > > blocked; I
> > > > > had to
> > > > > exit using C-g.
> > > > >
> > > > > Here's a minimal example src block that causes emacs to get stuck:
> > > > >
> > > > > #+begin_src R :results output :session *R* :exports both
> > > > > a <- 10
> > > > > a
> > > > > #+end_src
> > > > >
> > > > > R itself does start and the code is also executed correctly. However,
> > > > > the output from that
> > > > > session
> > > > > is apparently not returned to emacs or the buffer.
> > > >
> > > > I tried you example using Emacs >=26 and it works just fine.
> > > >
> > > > Best,
> > > > Ihor
>
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Description: This is a digitally signed message part
Re: Bug: ob-R.el breaks when :session is specified
Hello Christian
On Sunday, 15 May 2022 at 20:06, Christian Heinrich wrote:
> I just tested with
>
> Org mode version 9.5.3 (release_9.5.3-504-gcdbb1c @
> /home/heinrich/.emacs.d/straight/repos/org/lisp/)
>
> using
>
> GNU Emacs 27.1 (build 1, x86_64-pc-linux-gnu, GTK+ Version 3.24.30, cairo
> version 1.16.0) of 2021-
> 11-27, modified by Debian
Many thanks for reporting back. I updated to gcdbb1c and it is still working
fine.
My minimum working example is the following. From the org-mode root directory,
$ emacs -Q -L ./lisp -l org -l ~/ess-barebone.el
where ~/ess-barebone.el is the following:
#+begin_src elisp
(add-to-list 'load-path "/home/djj/.emacs.d/elpa/ess-20220125.2207/")
(require 'ess-r-mode)
(org-babel-do-load-languages
'org-babel-load-languages
'((R . t)))
(setq org-confirm-babel-evaluate nil)
#+end_src
Note that I'm still using a rather old ess version. Could you please try
with the above configuration? Note that I am using a rather old ess
version but the I haven't experienced issues with the newer one.
Best regards
Jeremie
> Hi Jeremie,
>
> I just tested with
>
> Org mode version 9.5.3 (release_9.5.3-504-gcdbb1c @
> /home/heinrich/.emacs.d/straight/repos/org/lisp/)
>
> using
>
> GNU Emacs 27.1 (build 1, x86_64-pc-linux-gnu, GTK+ Version 3.24.30, cairo
> version 1.16.0) of 2021-
> 11-27, modified by Debian
>
> I am on Debian Testing and that is the default emacs version.
>
> Using the unmodified org (git hash from above) I get the following messages
> when executing a src
> block with R:
>
>executing R code block...
>Loading ‘ess-bugs-l’: unescaped character literals `?(', `?)' detected,
> `?\(', `?\)' expected!
>Type C-h m for help on ESS version 15.09
>ess-tracebug mode enabled
>Quit
>Package cl is deprecated
>
> Note that the "Quit" is me pressing Ctrl-g after a few seconds.
>
> Removing the commit in question makes the block return instantaneously:
>
>executing R code block...
>Loading ‘ess-bugs-l’: unescaped character literals `?(', `?)' detected,
> `?\(', `?\)' expected!
>Type C-h m for help on ESS version 15.09
>ess-tracebug mode enabled
>Code block evaluation complete.
>Package cl is deprecated
>
> I anticipated that this would not be obvious, since this feature is used too
> much to go unnoticed for
> two years - but I am clueless as to how I should continue with debugging...
>
> Thanks for your help!
> Christian
>
> On Sun, 2022-05-15 at 16:16 +0200, Jeremie Juste wrote:
>>
>> Hello Christian,
>>
>> Thanks for reporting but I cannot reproduce the bug with the org and
>> emacs version below.
>>
>> Org mode version 9.5.3 (release_9.5.3-467-g2bd34e @
>> /home/djj/src/org-mode/lisp/)
>> GNU Emacs 27.2 (build 1, x86_64-pc-linux-gnu, GTK+ Version 3.24.24) of
>> 2022-01-16
>>
>> Can you please let me know which version of org-mode you are actually
>> using?
>>
>> Ihor, many thanks for checking.
>>
>> Best regards,
>> Jeremie
>>
>> On Sunday, 15 May 2022 at 16:08, Ihor Radchenko wrote:
>> > Christian Heinrich writes:
>> >
>> > > I got back to an org file after upgrading to the latest release of
>> > > org-mode and tried
>> > > executing the
>> > > contained R source blocks. Unfortunately, emacs got stuck in the
>> > > execution and was blocked; I
>> > > had to
>> > > exit using C-g.
>> > >
>> > > Here's a minimal example src block that causes emacs to get stuck:
>> > >
>> > > #+begin_src R :results output :session *R* :exports both
>> > > a <- 10
>> > > a
>> > > #+end_src
>> > >
>> > > R itself does start and the code is also executed correctly. However,
>> > > the output from that
>> > > session
>> > > is apparently not returned to emacs or the buffer.
>> >
>> > I tried you example using Emacs >=26 and it works just fine.
>> >
>> > Best,
>> > Ihor
Re: Bug: ob-R.el breaks when :session is specified
Um... > On May 15, 2022, at 2:46 AM, Christian Heinrich > wrote: > > I run > > emacs -q --load /tmp/init.el --file=/tmp/test.org > > with my /tmp/init.el being only > >> (require 'package) >> (package-initialize) >> (add-to-list 'load-path "~/.emacs.d/straight/repos/org/lisp/") >> (require 'org) >> >> ;(require 'ess-site) The line above is commented out. So how do you load ess-site? >> (org-babel-do-load-languages >> 'org-babel-load-languages >>'((R . t))) > > I hope this constitutes a minimal example for a config - please correct me if > I'm wrong. Just spitballing here: Have you tried instrumenting `org-babel-R-evaluate-session'? Maybe watching changes made to the session buffer on first evaluation and comparing to subsequent evals helps. HTH, Chuck
Re: Bug: ob-R.el breaks when :session is specified
Hi Jeremie,
I just tested with
Org mode version 9.5.3 (release_9.5.3-504-gcdbb1c @
/home/heinrich/.emacs.d/straight/repos/org/lisp/)
using
GNU Emacs 27.1 (build 1, x86_64-pc-linux-gnu, GTK+ Version 3.24.30, cairo
version 1.16.0) of 2021-
11-27, modified by Debian
I am on Debian Testing and that is the default emacs version.
Using the unmodified org (git hash from above) I get the following messages
when executing a src
block with R:
executing R code block...
Loading ‘ess-bugs-l’: unescaped character literals `?(', `?)' detected,
`?\(', `?\)' expected!
Type C-h m for help on ESS version 15.09
ess-tracebug mode enabled
Quit
Package cl is deprecated
Note that the "Quit" is me pressing Ctrl-g after a few seconds.
Removing the commit in question makes the block return instantaneously:
executing R code block...
Loading ‘ess-bugs-l’: unescaped character literals `?(', `?)' detected,
`?\(', `?\)' expected!
Type C-h m for help on ESS version 15.09
ess-tracebug mode enabled
Code block evaluation complete.
Package cl is deprecated
I anticipated that this would not be obvious, since this feature is used too
much to go unnoticed for
two years - but I am clueless as to how I should continue with debugging...
Thanks for your help!
Christian
On Sun, 2022-05-15 at 16:16 +0200, Jeremie Juste wrote:
>
> Hello Christian,
>
> Thanks for reporting but I cannot reproduce the bug with the org and
> emacs version below.
>
> Org mode version 9.5.3 (release_9.5.3-467-g2bd34e @
> /home/djj/src/org-mode/lisp/)
> GNU Emacs 27.2 (build 1, x86_64-pc-linux-gnu, GTK+ Version 3.24.24) of
> 2022-01-16
>
> Can you please let me know which version of org-mode you are actually
> using?
>
> Ihor, many thanks for checking.
>
> Best regards,
> Jeremie
>
> On Sunday, 15 May 2022 at 16:08, Ihor Radchenko wrote:
> > Christian Heinrich writes:
> >
> > > I got back to an org file after upgrading to the latest release of
> > > org-mode and tried
> > > executing the
> > > contained R source blocks. Unfortunately, emacs got stuck in the
> > > execution and was blocked; I
> > > had to
> > > exit using C-g.
> > >
> > > Here's a minimal example src block that causes emacs to get stuck:
> > >
> > > #+begin_src R :results output :session *R* :exports both
> > > a <- 10
> > > a
> > > #+end_src
> > >
> > > R itself does start and the code is also executed correctly. However, the
> > > output from that
> > > session
> > > is apparently not returned to emacs or the buffer.
> >
> > I tried you example using Emacs >=26 and it works just fine.
> >
> > Best,
> > Ihor
signature.asc
Description: This is a digitally signed message part
Re: Bug: ob-R.el breaks when :session is specified
Hello Christian, Thanks for reporting but I cannot reproduce the bug with the org and emacs version below. Org mode version 9.5.3 (release_9.5.3-467-g2bd34e @ /home/djj/src/org-mode/lisp/) GNU Emacs 27.2 (build 1, x86_64-pc-linux-gnu, GTK+ Version 3.24.24) of 2022-01-16 Can you please let me know which version of org-mode you are actually using? Ihor, many thanks for checking. Best regards, Jeremie On Sunday, 15 May 2022 at 16:08, Ihor Radchenko wrote: > Christian Heinrich writes: > >> I got back to an org file after upgrading to the latest release of org-mode >> and tried executing the >> contained R source blocks. Unfortunately, emacs got stuck in the execution >> and was blocked; I had to >> exit using C-g. >> >> Here's a minimal example src block that causes emacs to get stuck: >> >> #+begin_src R :results output :session *R* :exports both >> a <- 10 >> a >> #+end_src >> >> R itself does start and the code is also executed correctly. However, the >> output from that session >> is apparently not returned to emacs or the buffer. > > I tried you example using Emacs >=26 and it works just fine. > > Best, > Ihor
Re: Bug: ob-R.el breaks when :session is specified
Hi, thanks, that's what I had expected since that patch has been around for a long time. I run emacs -q --load /tmp/init.el --file=/tmp/test.org with my /tmp/init.el being only > (require 'package) > (package-initialize) > (add-to-list 'load-path "~/.emacs.d/straight/repos/org/lisp/") > (require 'org) > > ;(require 'ess-site) > (org-babel-do-load-languages >'org-babel-load-languages > '((R . t))) I hope this constitutes a minimal example for a config - please correct me if I'm wrong. My test.org contains the source block I had already posted: #+begin_src R :results output :session *R* :exports both a <- 10 a #+end_src Any ideas how I could continue to debug this? If I just remove that patch, everything works flawlessly for me but I would like to figure out what causes the issues. Thanks! Christian On Sun, 2022-05-15 at 16:08 +0800, Ihor Radchenko wrote: > Christian Heinrich writes: > > > I got back to an org file after upgrading to the latest release of org-mode > > and tried executing > > the > > contained R source blocks. Unfortunately, emacs got stuck in the execution > > and was blocked; I > > had to > > exit using C-g. > > > > Here's a minimal example src block that causes emacs to get stuck: > > > > #+begin_src R :results output :session *R* :exports both > > a <- 10 > > a > > #+end_src > > > > R itself does start and the code is also executed correctly. However, the > > output from that > > session > > is apparently not returned to emacs or the buffer. > > I tried you example using Emacs >=26 and it works just fine. > > Best, > Ihor signature.asc Description: This is a digitally signed message part
Re: Bug: ob-R.el breaks when :session is specified
Christian Heinrich writes: > I got back to an org file after upgrading to the latest release of org-mode > and tried executing the > contained R source blocks. Unfortunately, emacs got stuck in the execution > and was blocked; I had to > exit using C-g. > > Here's a minimal example src block that causes emacs to get stuck: > > #+begin_src R :results output :session *R* :exports both > a <- 10 > a > #+end_src > > R itself does start and the code is also executed correctly. However, the > output from that session > is apparently not returned to emacs or the buffer. I tried you example using Emacs >=26 and it works just fine. Best, Ihor
Bug: ob-R.el breaks when :session is specified
Hi there, I got back to an org file after upgrading to the latest release of org-mode and tried executing the contained R source blocks. Unfortunately, emacs got stuck in the execution and was blocked; I had to exit using C-g. Here's a minimal example src block that causes emacs to get stuck: #+begin_src R :results output :session *R* :exports both a <- 10 a #+end_src R itself does start and the code is also executed correctly. However, the output from that session is apparently not returned to emacs or the buffer. When removing the :session argument it executes and returns as expected. When bisecting this issue, I found that this commit causes it: ac8c009e006197d2dad226dbe822d450aec23d23 lisp/ob-R.el: Fix session output with substrings matching prompts Reverting it fixes the issue for earlier release (9.5.3) as well as for the current main branch. The (with-current-buffer session ... ) somehow seems to break it for me, but I am unsure why no one else here seems to experience this as the commit is from 2020? Any suggestions? Thanks! Christian signature.asc Description: This is a digitally signed message part
