The Rstudio logs can be set to debug level. This is how we do it on our production application. I’d also check out the output.log just to be sure.
If it’s not trying to do something - then there must be an error somewhere. You can see by the link I’ve given you above, there’s potentially another log file the rserver.log.
Ahh, that debug file wasn’t there before, but it’s there now. Debug output below. It says R can’t find libblas.so.3. I’ve added the path to that library before when the rsession.log was complaining about it.
export LD_LIBRARY_PATH="$LD_LIBRARY_PATH:/usr/lib/x86_64-linux-gnu:/usr/local/lib/R/lib:/usr/lib/x86_64-linux-gnu/openblas-pthread"
rserver.log
2024-03-29T21:48:05.384339Z [rserver] INFO No rserver configuration found at /etc/rstudio/rserver.conf
2024-03-29T21:48:05.390329Z [rserver] DEBUG Adding user to cache for user: redmonp:116770 by name
2024-03-29T21:48:05.390946Z [rserver] INFO Running as server user 'redmonp' (without privilege)
2024-03-29T21:48:05.391981Z [rserver] DEBUG (PID 764302): Initialized file locks (lock-type=linkbased, use-symlinks=false, timeout-interval=30s, refresh-rate=20s, log-file=)
2024-03-29T21:48:05.393292Z [rserver] INFO Running without privilege; generating secure key at /home/redmonp/.cache/rstudio/secure-cookie-key
2024-03-29T21:48:05.393853Z [rserver] DEBUG Creating secure key file: "/home/redmonp/.cache/rstudio/secure-cookie-key" key hash: (3B95CD42)
2024-03-29T21:48:05.394607Z [rserver] INFO Reading database configuration from '/etc/rstudio/database.conf'
2024-03-29T21:48:05.395459Z [rserver] INFO Connecting to sqlite3 database at /tmp/lib/rstudio-server/rstudio-os.sqlite
2024-03-29T21:48:05.395986Z [rserver] INFO Creating database connection pool of size 6 (source: default maximum with 6 CPUs)
2024-03-29T21:48:05.404657Z [rserver] DEBUG Current Database Schema Version: 20220610180402900844286 : Spotted Wakerobin
2024-03-29T21:48:05.405253Z [rserver] DEBUG Highest Available Database Schema Version: 20220610180402900844286 : Spotted Wakerobin
2024-03-29T21:48:05.405736Z [rserver] INFO Database schema version is up to date.
2024-03-29T21:48:05.406459Z [rserver] INFO No environment variables found at /etc/rstudio/env-vars
2024-03-29T21:48:05.406980Z [rserver] INFO Running without privilege; generating secure key at /home/redmonp/.cache/rstudio/session-rpc-key
2024-03-29T21:48:05.407465Z [rserver] DEBUG Creating secure key file: "/home/redmonp/.cache/rstudio/session-rpc-key" key hash: (28DA1762)
2024-03-29T21:48:05.409109Z [rserver] INFO Running without privilege; using secure key at /home/redmonp/.cache/rstudio/session-rpc-key
2024-03-29T21:48:05.409632Z [rserver] DEBUG Using secure key file: /home/redmonp/.cache/rstudio/session-rpc-key
2024-03-29T21:48:05.410168Z [rserver] DEBUG Secure key hash: (28DA1762)
2024-03-29T21:48:05.462791Z [rserver] ERROR R did not return any output when queried for directory location information; LOGGED FROM: bool rstudio::core::r_util::{anonymous}::detectRLocationsUsingR(const string&, rstudio::core::FilePath*, rstudio::core::FilePath*, rstudio::core::config_utils::Variables*, std::string*, const string&, const string&, const rstudio::core::FilePath&) src/cpp/core/r_util/REnvironmentPosix.cpp:539
2024-03-29T21:48:05.489795Z [rserver] ERROR system error 71 (Protocol error) [description: Unable to parse version from R, version-info: , r-error: /usr/local/lib/R/bin/exec/R: error while loading shared libraries: libblas.so.3: cannot open shared object file: No such file or directory
]; OCCURRED AT rstudio::core::Error rstudio::core::r_util::rVersion(const rstudio::core::FilePath&, const rstudio::core::FilePath&, const string&, const string&, const string&, const rstudio::core::FilePath&, std::string*) src/cpp/core/r_util/REnvironmentPosix.cpp:947; LOGGED FROM: bool rstudio::core::r_util::detectREnvironment(const rstudio::core::FilePath&, const rstudio::core::FilePath&, const string&, std::string*, std::string*, rstudio::core::r_util::EnvironmentVars*, std::string*, const string&, const string&, const rstudio::core::FilePath&) src/cpp/core/r_util/REnvironmentPosix.cpp:790
2024-03-29T21:48:12.742956Z [rserver] DEBUG Caching auth userIdentifier: redmonp for system username: redmonp
2024-03-29T21:48:12.744560Z [rserver] DEBUG PAM login start - running: /home/redmonp/ondemand/data/sys/dashboard/batch_connect/dev/bc_osc_rstudio_server/output/ecac101f-7884-4fe7-a5c0-4ffef2cc4d5d/bin/auth redmonp rstudio 1 <pw>
2024-03-29T21:48:12.749510Z [rserver] DEBUG PAM login result: for username: redmonp returns: authenticated
2024-03-29T21:48:12.750060Z [rserver] DEBUG User db query start: redmonp
2024-03-29T21:48:12.750867Z [rserver] DEBUG Found user in db: redmonp
2024-03-29T21:48:12.751368Z [rserver] DEBUG Begin update last signIn time
2024-03-29T21:48:12.751908Z [rserver] DEBUG End update last signIn time
2024-03-29T21:48:12.753108Z [rserver] DEBUG Created new UserSession for: redmonp (total: 1)
2024-03-29T21:48:12.753617Z [rserver] DEBUG User db query start: redmonp
2024-03-29T21:48:12.754231Z [rserver] DEBUG Found user in db: redmonp
2024-03-29T21:48:12.754736Z [rserver] DEBUG Adding session cookie: redmonp|Fri%2C%2029%20Mar%202024%2022%3A48%3A12%20GMT|lntMDt8plMEzKlC%2BI4Y51QCbNaAsH6Xc8awuEYqXqQY%3D for user: redmonp
2024-03-29T21:48:12.755251Z [rserver] DEBUG Sign in for user: redmonp redirecting to: /
2024-03-29T21:48:14.619089Z [rserver] DEBUG - Start server proxy request POST /rpc/client_init (redmonp:18) for local stream: /tmp/run/rstudio-rsession/redmonp-d
2024-03-29T21:48:14.620177Z [rserver] DEBUG Launching session for user: redmonp id:
2024-03-29T21:48:14.620735Z [rserver] DEBUG Launching RStudio session for: redmonp id:
2024-03-29T21:48:14.621700Z [rserver] DEBUG Launched session process for user: : /home/redmonp/ondemand/data/sys/dashboard/batch_connect/dev/bc_osc_rstudio_server/output/ecac101f-7884-4fe7-a5c0-4ffef2cc4d5d/rsession.sh pid: 764406
2024-03-29T21:48:15.358982Z [rserver] DEBUG -- rpc error: other error for: /rpc/client_init (redmonp:18) in 0.740s error: asio.misc error 2 (End of file)
2024-03-29T21:48:17.396582Z [rserver] DEBUG - Start server proxy request POST /rpc/client_init (redmonp:19) for local stream: /tmp/run/rstudio-rsession/redmonp-d
2024-03-29T21:48:17.397630Z [rserver] DEBUG Launching session for user: redmonp id:
2024-03-29T21:48:17.398172Z [rserver] DEBUG Launching RStudio session for: redmonp id:
2024-03-29T21:48:17.399121Z [rserver] DEBUG Launched session process for user: : /home/redmonp/ondemand/data/sys/dashboard/batch_connect/dev/bc_osc_rstudio_server/output/ecac101f-7884-4fe7-a5c0-4ffef2cc4d5d/rsession.sh pid: 764436
2024-03-29T21:48:18.992068Z [rserver] DEBUG -- rpc error: other error for: /rpc/client_init (redmonp:19) in 1.595s error: asio.misc error 2 (End of file)
I tried some of the other old versions of rstudio I had downloaded from Rocker. Success! I was able to load rstudio 4.1.0 and 4.2.0. Rstudio 4.3.0, 4.3.2, 4.3.3, latest, and devel all didn’t load.
I have defined TMPDIR=${HOME}/.cache/<%= all_modules %> so the different versions don’t use the same runtime, and so that they persist across different nodes.
I’d still like to get the latest versions working, but this is good enough for me for now. Thanks for your help! I don’t think I would have gotten this far this fast without it.
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