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rJava loads in Terminal, not in Console (RServer/Ubuntu) #3491

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MichaelChirico opened this issue Sep 17, 2018 · 3 comments
Closed

rJava loads in Terminal, not in Console (RServer/Ubuntu) #3491

MichaelChirico opened this issue Sep 17, 2018 · 3 comments
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@MichaelChirico
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@MichaelChirico MichaelChirico commented Sep 17, 2018

I'm on RStudio server.

library(rJava) fails on the Console tab:

screen shot 2018-09-17 at 12 33 15 pm

but succeeds in the Terminal tab:

screen shot 2018-09-17 at 12 33 32 pm

sessionInfo() & JAVA_HOME in both are identical:

R version 3.5.1 (2018-07-02)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 16.04.3 LTS

Matrix products: default
BLAS: /usr/lib/libblas/libblas.so.3.6.0
LAPACK: /usr/lib/lapack/liblapack.so.3.6.0

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C               LC_TIME=en_US.UTF-8       
 [4] LC_COLLATE=en_US.UTF-8     LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                  LC_ADDRESS=C              
[10] LC_TELEPHONE=C             LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

loaded via a namespace (and not attached):
[1] compiler_3.5.1 tools_3.5.1 

I've tried running sudo R CMD javareconf in both tabs to no apparent effect.

@MichaelChirico
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@MichaelChirico MichaelChirico commented Sep 17, 2018

I think this is related to some staleness....

This is created as part of a Docker image that is run with some mounted persistent memory. This memory is re-persisted on shutdown of the image.

I have a feeling there may be some leftover files being copied back and forth that are interfering with the session in Console being able to load correctly.... not sure how to confirm this suspicion though...

which of these files/directories is likely to be the source of consternation here?

would like to avoid destroying my editor settings if possible 😅

ls -hl .rstudio/
total 36K
-rw-r--r--  1 michael.chirico michael.chirico    3 Sep 17 07:01 addin_registry
drwxrwxr-x  2 michael.chirico michael.chirico  130 Sep 17 07:01 client-state
drwxr-xr-x  2 michael.chirico michael.chirico   58 Sep 17 06:37 console06
drwxr-xr-x  2 michael.chirico michael.chirico    6 Sep 17 07:01 ctx
drwxr-xr-x  4 michael.chirico michael.chirico   42 Sep  7 07:54 dictionaries
-rw-r--r--  1 michael.chirico michael.chirico  15K Sep 17 06:29 history_database
drwxr-xr-x  6 michael.chirico michael.chirico   82 Sep  7 07:51 monitored
drwxr-xr-x  2 michael.chirico michael.chirico   31 Sep  7 07:51 notebooks
drwxrwxr-x  2 michael.chirico michael.chirico  140 Sep 17 07:01 pcs
-rw-r--r--  1 michael.chirico michael.chirico  442 Sep 17 06:27 persistent-state
drwxr-xr-x  2 michael.chirico michael.chirico    6 Sep  7 07:51 presentation
drwxr-xr-x  2 michael.chirico michael.chirico    6 Sep  7 07:51 profiles-cache
drwxr-xr-x  2 michael.chirico michael.chirico   59 Sep 17 03:51 projects_settings
drwxr-xr-x  2 michael.chirico michael.chirico   86 Sep  7 07:56 rversion-settings
-rw-r--r--  1 michael.chirico michael.chirico   27 Sep 17 07:01 saved_source_markers
drwxr-xr-x  3 michael.chirico michael.chirico   20 Sep  7 07:51 sessions
drwxr-xr-x  4 michael.chirico michael.chirico   35 Sep 17 04:03 sources

@jmcphers
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@jmcphers jmcphers commented Sep 17, 2018

This is probably an issue with LD_LIBRARY_PATH or similar, but we can't generally offer support for rJava and friends here (this issue tracker is for bugs in RStudio itself). I'd suggest asking on our community site:

https://community.rstudio.com/c/rstudio-ide

@MichaelChirico
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@MichaelChirico MichaelChirico commented Sep 18, 2018

@jmcphers I don't think so, as simply rstudio-server stop and then rstudio-server start solves the problem.

I don't think this is a problem with rJava per se, and I do think it's entirely an RStudio issue... however I agree at this point it's not much of a bug 🐛 on RStudio's part as much as it's my own fault.

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