Citation leads to RStudio freeze #709

dragonattheend · 2022-04-21T23:14:26Z

dragonattheend
Apr 21, 2022

When I try to cite something my RStudio session becomes unusable. In particular, if I add a citation like [@example1900] and then remove the brackets (@example1900), I get this "Working..." message on top and cannot click any button.

I run an Archlinux based OS, so not sure if it is the reason for this bug and maybe everything is perfect on Mac and Win.

Answered by jjallaire

Apr 24, 2022

It looks to me like RStudio is looking for version of Pandoc that doesn't exist (at /home/dat/pandoc). I'm not sure why this would be -- do you have an RSTUDIO_PANDOC environment variable set? You might want to try removing that file to see if it clears things up.

Net: this is some sort of misconfiguration or environment conflict which is incredibly hard to debug speculatively.

View full answer

jjallaire · 2022-04-23T11:21:31Z

jjallaire
Apr 23, 2022
Maintainer

One thing that might help is to export a request log to see exactly where things are getting hung up (info on doing that here: https://support.rstudio.com/hc/en-us/articles/200488538-How-To-Export-a-Network-Request-Log-From-the-RStudio-IDE)

1 reply

dragonattheend Apr 23, 2022
Author

One thing that might help is to export a request log to see exactly where things are getting hung up (info on doing that here: https://support.rstudio.com/hc/en-us/articles/200488538-How-To-Export-a-Network-Request-Log-From-the-RStudio-IDE)

Another thing is that the time in log file is different from my system time (Sys.time()).

dragonattheend · 2022-04-23T19:15:52Z

dragonattheend
Apr 23, 2022
Author

There was a hunspell problem at first, I added .aff, .dic files, but still getting an error.

WARNING No memory control group found in /proc/self/cgroup; LOGGED FROM: std::string rstudio::core::system::{anonymous}::getMemoryCgroup() src/cpp/core/system/LinuxResources.cpp:335

ERROR CLIENT EXCEPTION (rsession-dat): TypeError: Cannot read property 'inside' of null;|||com/google/gwt/cell/client/AbstractEditableCell.java#41::viewDataMap||| ...

ERROR system error 2 (No such file or directory) [exe: /home/dat/pandoc]; OCCURRED AT rstudio::core::Error rstudio::core::system::ChildProcess::run() src/cpp/core/system/PosixChildProcess.cpp:819; LOGGED FROM: rstudio::core::Error rstudio::core::system::ChildProcess::run() src/cpp/core/system/PosixChildProcess.cpp:821

0 replies

jjallaire · 2022-04-24T00:38:31Z

jjallaire
Apr 24, 2022
Maintainer

It looks to me like RStudio is looking for version of Pandoc that doesn't exist (at /home/dat/pandoc). I'm not sure why this would be -- do you have an RSTUDIO_PANDOC environment variable set? You might want to try removing that file to see if it clears things up.

Net: this is some sort of misconfiguration or environment conflict which is incredibly hard to debug speculatively.

1 reply

dragonattheend Apr 24, 2022
Author

Thank you.
Turns out I had quarto removed, I reinstalled it, and still was getting the error, that the pandoc file was missing in usr/lib/quarto-cli/bin/, it was in usr/lib/quarto-cli/bin/tools/, so I copied it to usr/lib/quarto-cli/bin/ and it seems to work. Interestingly, I get a different location for Sys.getenv("RSTUDIO_PANDOC") [1] "/usr/lib/rstudio/bin/quarto/bin".

Thanks again.

jjallaire · 2022-04-24T10:46:27Z

jjallaire
Apr 24, 2022
Maintainer

Makes me think that there could be an Arch packaging issue related to a change we recently made (which was in fact moving pandoc from bin/ to /bin/tools !). It's possible that whomever packages RStudio for Arch needs to make a change to reflect this? @timtmok Could you follow up to see if this is the case?

0 replies

rgaiacs · 2022-04-26T03:18:37Z

rgaiacs
Apr 26, 2022

@jjallaire I don't think this is a Arch related issue. I updated RStudio and Quarto in my Ubuntu machine

$ sudo dpkg -i ~/Downloads/rstudio-2022.02.1-461-amd64.deb                                                                                                                                                                 
(Reading database ... 684683 files and directories currently installed.)                                                                                                                                                                                                                  
Preparing to unpack .../rstudio-2022.02.1-461-amd64.deb ...                                                                                                                                                                                                                               
Unpacking rstudio (2022.02.1+461) over (1.4.1106) ...                                                                                                                                                                                                                                     
Setting up rstudio (2022.02.1+461) ...                                                                                                                                                                                                                                                    
Processing triggers for mailcap (3.69ubuntu1) ...                                                                                                                                                                                                                                         
Processing triggers for desktop-file-utils (0.26-1ubuntu2) ...                                                                                                                                                                                                                            
Processing triggers for gnome-menus (3.36.0-1ubuntu1) ...                                                                                                                                                                                                                                 
Processing triggers for hicolor-icon-theme (0.17-2) ...                                                                                                                                                                                                                                   
Processing triggers for shared-mime-info (2.1-1) ...                                                                                                                                                                                                                                      
$ sudo dpkg -i ~/Downloads/quarto-0.9.309-linux-amd64.deb                                                                                                                                                                  
(Reading database ... 686253 files and directories currently installed.)                                                                                                                                                                                                                  
Preparing to unpack .../quarto-0.9.309-linux-amd64.deb ...
Unpacking quarto (0.9.309) over (0.9.238) ...
Setting up quarto (0.9.309) ...

and I'm having he same issue. I have

2022-04-26T02:58:18.518678Z [rsession-raniere] ERROR system error 2 (No such file or directory) [exe: /opt/quarto/bin/pandoc]; OCCURRED AT rstudio::core::Error rstudio::core::system::ChildProcess::run() src/cpp/core/system/PosixChildProcess.cpp:819; LOGGED FROM: rstudio::core::Error rstudio::core::system::ChildProcess::run() src/cpp/core/system/PosixChildProcess.cpp:821

in RStudio log. I checked the .deb from GitHub Releases and pandoc is in /opt/quarto/bin/tools/ instead of /opt/quarto/bin/pandoc.

0 replies

jjallaire · 2022-04-26T11:00:53Z

jjallaire
Apr 26, 2022
Maintainer

Right Pandoc is in /opt/quarto/bin/tools but the error message says that RStudio is looking for it at /opt/quarto/bin/pandoc. I think the Arch recipe for RStudio needs to be updated to work with the new location of Pandoc in more recent versions of Quarto.

6 replies

trap000d Apr 26, 2022

Well, I suppose it has to be addressed to RStudio upstream - see rstudio-2022.02.1-461/src/cpp/session/CMakeLists.txt - pandoc location is hardcoded:

if(QUARTO_ENABLED)
   set(RSTUDIO_DEPENDENCIES_PANDOC_DIR "${RSTUDIO_DEPENDENCIES_QUARTO_DIR}/bin")
elseif(EXISTS "${RSTUDIO_TOOLS_ROOT}/pandoc/${PANDOC_VERSION}")
   set(RSTUDIO_DEPENDENCIES_PANDOC_DIR "${RSTUDIO_TOOLS_ROOT}/pandoc/${PANDOC_VERSION}")
else()
   set(RSTUDIO_DEPENDENCIES_PANDOC_DIR "${RSTUDIO_DEPENDENCIES_DIR}/pandoc/${PANDOC_VERSION}")
endif()

UPD: It's fixed in RStudio master branch (rstudio/rstudio#10952). So I only need to backport changes.

jjallaire Apr 27, 2022
Maintainer

Okay, great. This does imply that users need to install new-ish versions of Quarto CLI (but that's essentially where the project is right now -- you pretty much need to be at HEAD). We will be releasing a stable version of Quarto (v1.0) around July.

trap000d Apr 27, 2022

Well, I've just pushed updates of 'rstudio-desktop' to AUR. Seems quarto works well (though I tested it with 'quarto-cli' package only). Unfortunately, all binary packages still have bug @dragonattheend reported.
RStudio developers have missed a place where pandoc is called.

diff -ur a/src/cpp/session/modules/quarto/SessionQuartoXRefs.cpp b/src/cpp/session/modules/quarto/SessionQuartoXRefs.cpp
--- a/src/cpp/session/modules/quarto/SessionQuartoXRefs.cpp     2022-04-27 22:28:07.480284489 +1200
+++ b/src/cpp/session/modules/quarto/SessionQuartoXRefs.cpp     2022-04-27 20:59:01.396159620 +1200
@@ -188,7 +188,7 @@
    core::system::ProcessResult result;

    error = module_context::runPandoc(
-      FilePath(config.bin_path).completeChildPath("pandoc").getAbsolutePath(),
+      FilePath(config.bin_path).completeChildPath("tools/pandoc").getAbsolutePath(),
       args,
       contents,
       options,

jjallaire Apr 27, 2022
Maintainer

This is actually fixed in the patch release of RStudio 2022.02. Here is the correct fix that should be backported to AUR (note it handles both possible locations for pandoc): https://github.com/rstudio/rstudio/blob/prairie-trillium/src/cpp/session/modules/quarto/SessionQuartoXRefs.cpp#L132-L151

There are a number of other fixes on the prairie-trillium branch (https://github.com/rstudio/rstudio/tree/prairie-trillium) that should also be backported.

trap000d Apr 28, 2022

Thanks, I've just spotted it v2022.02.2+485. Indeed it includes the fix.

P.S. I'm pretty sure it wasn't there yesterday, thought it's dated April 20, i.e. 7 days old. Let me guess, you hide releases until finish build and tests :)

jjallaire · 2022-04-28T00:45:37Z

jjallaire
Apr 28, 2022
Maintainer

Yes, you are right, the release just came out today (I thought it was already out!).

0 replies

Citation leads to RStudio freeze #709

Uh oh!

dragonattheend Apr 21, 2022

Replies: 7 comments · 8 replies

Uh oh!

jjallaire Apr 23, 2022 Maintainer

Uh oh!

dragonattheend Apr 23, 2022 Author

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dragonattheend Apr 23, 2022 Author

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jjallaire Apr 24, 2022 Maintainer

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dragonattheend Apr 24, 2022 Author

Uh oh!

jjallaire Apr 24, 2022 Maintainer

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rgaiacs Apr 26, 2022

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jjallaire Apr 26, 2022 Maintainer

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trap000d Apr 26, 2022

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jjallaire Apr 27, 2022 Maintainer

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trap000d Apr 27, 2022

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jjallaire Apr 27, 2022 Maintainer

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trap000d Apr 28, 2022

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jjallaire Apr 28, 2022 Maintainer

dragonattheend
Apr 21, 2022

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