Add check for the LibR.so that rsession believes it's using #9893

cm421 · 2021-09-27T22:46:37Z

Intent

Addresses https://github.com/rstudio/rstudio-pro/issues/2477 by adding a check on the libR.so that rsession believes it is running. If there are issues with loading that shared object, generate an error.

Note that this does not fix the problem. Instead it creates an error that can be used to find and fix the cause of the problem, which is a system environment issue

Approach

The linked issue describes the problem in detail, but essentially while linux is loading the rsession binary, if there's an issue with libR.so, it may load a different libR.so without rsession's knowledge. To address this, we check for issues manually once rsession is fully loaded by calling dload() with RTLD_NOLOAD. Any issues Linux had with loading the shared object will become apparent with that call, and the error can then be forwarded on to an error.

This is linux-only code; Windows and MacOS won't perform this check.

Automated Tests

There are no unit tests included. Integration tests will require:

A linux environment with at least 2 R installations
- One system R install
- One custom R install
Ability to "disable" the custom R version's libR.so before the test by chmoding out permissions so it can't be opened, and then restoring the permissions after the test is done

The test should include

Start an rsession with the default system R install
- No error should be generated
Switch R version to the broken custom version
- Error should be generated

QA Notes

None, see testing section above for how to reproduce/test

Checklist

If this PR adds a new feature, or fixes a bug in a previously released version, it includes an entry in NEWS.md
If this PR adds or changes UI, the updated UI meets accessibility standards
A reviewer is assigned to this PR (if unsure who to assign, check Area Owners list)
This PR passes all local unit tests

MariaSemple

Elegant solution! Very excited to see this improve for users.

MariaSemple · 2021-09-28T17:42:20Z

src/cpp/core/system/PosixLibraryLoader.cpp

+ * Verify that we can load a library (without actually loading it)
+ * by passing RTLD_NOLOAD to dlopen
+ */
+Error verifyLibrary(const std::string& libPath, void** ppLib)


Since you never use ppLib, I don't think you should call it here. You're also never closing the handle on success, but I'm not sure if that matters.

MariaSemple · 2021-09-28T17:42:32Z

src/cpp/core/system/PosixLibraryLoader.cpp

+                          -1,
+                          "Attempt to verify library failed",
+                          ErrorLocation());
+      error.addProperty("lib-path", libPath);


Suggested change

error.addProperty("lib-path", libPath);

error.addProperty("path", libPath);

MariaSemple · 2021-09-28T17:43:40Z

src/cpp/session/SessionMain.cpp

+   if (!ensureLibRSoValid())
+     LOG_ERROR_MESSAGE(s_libRSoWarning +
+                       ". Linux may have loaded a different libR.so than requested."
+                       " R_HOME: " + rsession::module_context::rHomeDir() +
+                       ", R Version: " + rsession::module_context::rVersion());
+


Rather than use a static which isn't thread safe, we should log this error message from within the ensureLibRSoValid() method.

Additionally, should we exit here? Or at the very list emit a similar error to the R Console so that the user can be informed? IIRC, this error message will only go to our log files, and a big problem with this behaviour is that the user is unware that they're using the wrong version of R. We should probably include a note about contacting your system administrator if the versions don't match.

Add warning to user's console Update warning text Clean up verifyLibrary() prototype

MariaSemple

LGTM!

abalter · 2023-05-31T20:56:26Z

Is this really fixed? Especially if R is installed in a non-default location, problems with libR.so are rampant.

#7868

#13184

#12508

https://community.rstudio.com/t/r-shared-library-usr-local-lib-r-lib-libr-so-not-found-if-this-is-a-custom-build-of-r-was-it-built-with-the-enable-r-shlib-option/126418

https://community.rstudio.com/t/r-shared-library-usr-local-lib64-r-lib-libr-so-not-found/131446/8

https://stackoverflow.com/questions/76102591/how-to-change-r-version-in-rstudio-inside-a-conda-environment-in-ubuntu

https://support.posit.co/hc/en-us/articles/200488508-RStudio-Desktop-IDE-Will-Not-Start

abalter · 2023-10-10T04:48:41Z

This is really not fixed. I'm still having the same problem. I've tried setting the path to R and R libraries in all of the places the docs say. For instance, /etc/rstudio/rsession-profile and /etc/rstudio/rserver.conf. I've made sure that root is using the same R as I am.

error while loading shared libraries: libR.so - R Admins - Posit Community
https://community.rstudio.com/t/error-while-loading-shared-libraries-libr-so/101389/13

r - RStudio Server (community) can't find libR.so even though it is in path - Stack Overflow
https://stackoverflow.com/questions/74299104/rstudio-server-community-cant-find-libr-so-even-though-it-is-in-path

/usr/local/lib64/R/lib/libR.so: cannot open shared object file: No such file or directory - Stack Overflow
https://stackoverflow.com/questions/69013147/usr-local-lib64-r-lib-libr-so-cannot-open-shared-object-file-no-such-file-or

r - Error with shared library with RStudio Server - Stack Overflow
https://stackoverflow.com/questions/33897998/error-with-shared-library-with-rstudio-server

r - error while loading shared libraries: libR.so - Stack Overflow
https://stackoverflow.com/questions/37967497/error-while-loading-shared-libraries-libr-so

error while loading shared libraries: libR.so: cannot open shared object file
https://groups.google.com/g/epacts/c/5JNFkpmyuSU

ubuntu - libR.so not found in R Rstudio - Stack Overflow
https://stackoverflow.com/questions/60893387/libr-so-not-found-in-r-rstudio

R shared library (/usr/local/lib/R/lib/libR.so) not found. If this is a custom build of R, was it built with the --enable-R-shlib option? - RStudio IDE - Posit Community
https://community.rstudio.com/t/r-shared-library-usr-local-lib-r-lib-libr-so-not-found-if-this-is-a-custom-build-of-r-was-it-built-with-the-enable-r-shlib-option/126418

Rstudio error "R shared library (/usr/local/lib/R/lib/libR.so) not found." - RStudio IDE - Posit Community
https://community.rstudio.com/t/rstudio-error-r-shared-library-usr-local-lib-r-lib-libr-so-not-found/62598

[R] R shared library (/usr/lib64/R/lib/libR.so) not found.
https://stat.ethz.ch/pipermail/r-help/2018-August/455984.html

RStudio Server (community) can't find libR.so even though it is in path. · Issue #12281 · rstudio/rstudio
#12281

abalter · 2023-10-10T04:50:07Z

How about just adding a switch to rstudio-server? Then I could run sudo rstudio-server start --r_path=/home/balter/micromamba/bin/R r_libs=/home/balter/micromamba/lib/R/lib

Add check for the LibR.so that rsession believes it's using

c49afd9

cm421 requested review from MariaSemple and valerie-rstudio September 27, 2021 22:46

cm421 and others added 2 commits September 28, 2021 11:33

Update NEWS.md

424d126

Merge branch 'main' into bugfix/check-custom-r-version

9b7fb46

cm421 marked this pull request as ready for review September 28, 2021 17:34

MariaSemple requested changes Sep 28, 2021

View reviewed changes

Remove static warning string

7cd2e0b

Add warning to user's console Update warning text Clean up verifyLibrary() prototype

cm421 requested a review from MariaSemple September 28, 2021 22:38

MariaSemple approved these changes Sep 29, 2021

View reviewed changes

cm421 merged commit ff301e8 into main Sep 30, 2021

valerie-rstudio deleted the bugfix/check-custom-r-version branch January 21, 2022 17:54

abalter mentioned this pull request Jun 8, 2023

RStudio will not run with R installed in location other than /usr/bin #13184

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Add check for the LibR.so that rsession believes it's using #9893

Add check for the LibR.so that rsession believes it's using #9893

cm421 commented Sep 27, 2021 •

edited

MariaSemple left a comment

MariaSemple Sep 28, 2021

MariaSemple Sep 28, 2021

MariaSemple Sep 28, 2021

MariaSemple Sep 28, 2021

MariaSemple left a comment

abalter commented May 31, 2023 •

edited

abalter commented Oct 10, 2023

abalter commented Oct 10, 2023

	error.addProperty("lib-path", libPath);
	error.addProperty("path", libPath);

Add check for the LibR.so that rsession believes it's using #9893

Add check for the LibR.so that rsession believes it's using #9893

Conversation

cm421 commented Sep 27, 2021 • edited

Intent

Approach

Automated Tests

QA Notes

Checklist

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abalter commented May 31, 2023 • edited

abalter commented Oct 10, 2023

abalter commented Oct 10, 2023

cm421 commented Sep 27, 2021 •

edited

abalter commented May 31, 2023 •

edited