I am using Eclipse 2018-09 and StatET 3.6.1. I have two R environments: one for R 3.3.2, another for R 3.5.1. When I execute a command like ?lm to call up a help page in v3.3.2, the page appears in the StatET "R Help" pane, as I want it to. But when I execute the same command to call up a help page in v3.5.1, the console tells me "starting httpd help server," and the help page loads in my browser. How can I get help to load in the "R Help" pane when using v3.5.1?
The problem arises whether or not I run Eclipse as an administrator, and whether or not I "Auto Run" R 3.5.1 upon booting. And as far as I can tell, the configurations for the two versions of R are nearly identical:
Both are running Windows 10 and JRE 1.8.0_121.
Both with version 2.1 of the rj package.
For both, I've checked every box in "Run Configurations > R Console > R Console > Eclipse Integration," including "Enable R Help for StatET."
For both, options("help_type") == 'html'.
Inspection of the different log files that I get when using Auto Run with the two versions of R suggests that there is some sort of StatET config problem that has to do with Derby. These messages appear only when I boot R 3.5.1:
!ENTRY de.walware.statet.r.core 4 -1 2018-11-16 02:50:29.092
!MESSAGE An error occurred when initializing DB for model.
!STACK 1
org.eclipse.core.runtime.CoreException: An error occurred when loading embedded DB (Derby + DBCP)
DB ConnectionURL=[path redacted]\eclipse-workspace\.metadata\.plugins\de.walware.statet.r.core\db
[...]
Caused by: java.sql.SQLException: Another instance of Derby may have already booted the database C:\[path redacted]\eclipse-workspace\.metadata\.plugins\de.walware.statet.r.core\db.
[...]
Caused by: ERROR XSDB6: Another instance of Derby may have already booted the database C:\[path redacted]\eclipse-workspace\.metadata\.plugins\de.walware.statet.r.core\db.
But I don't know what to make of this problem or how to fix it.
Stephan Wahlbrink, the creator of StatET, recommended running this command at startup:
registerS3method("print", "help_files_with_topic", rj::print.help_files_with_topic)
I ran the command, and it solved the problem.
(Stephan added that the Derby errors that I saw in the logs were unrelated to the problem of displaying help in the "R Help" pane.)
Related
From the linux console I run a windows console tool using:
wine console_tool.exe ....
The console tool does not involve any windows. It's output is just textual.
Some output is added repeatedly after a given delay time.
However, besides the output of the console_tool.exe I get repeatedly the following error message also interleaved with the other output:
ERROR: ld.so: object 'libgtk3-nocsd.so.0' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored.
I already tried to export LD_PRELOAD=/usr/lib/x86_64-linux-gnu/libgtk3-nocsd.so.0 but then the only change is that the error message changes:
ERROR: ld.so: object '/usr/lib/x86_64-linux-gnu/libgtk3-nocsd.so.0' from LD_PRELOAD cannot be preloaded (wrong ELF class: ELFCLASS64): ignored.
I also attempted to apt install the :i386 version of the libgtk3-nocsd.so.0 but it doesn't seem to exists.
I don't know why a console application may trigger a gtk error message. This is beyond my knowledge.
My preferred goal would be to tell wine that the .exe does not use windows and it does not need to not use gtk for windows emulation at all. However, as this may not be possible, my second preferred goal would be to solve the gtk issue.
Can you help me achieve at least one of those goals?
I do not know what the error messages mean. However, the wineconsole command runs console executable using wine. Example:
wineconsole console_tool.exe
The Jim Hester YouTube video video looks like a potentially really helpful way to put breakpoints in Rcpp code that passes some variables in unexpected ways. However, when I follow the start up directions (Rstudio console copied below) it fails with a message that is not helpful to a new user of lldb.
gcn#GCN-MacBook-Pro-7 ISIMIPData % R -d lldb
(lldb) target create "/Library/Frameworks/R.framework/Resources/bin/exec/R"
Current executable set to '/Library/Frameworks/R.framework/Resources/bin/exec/R' (x86_64).
(lldb) run
error: process exited with status -1 (attach failed (Not allowed to attach to process. Look in the console messages (Console.app), near the debugserver entries when the attached failed. The subsystem that denied the attach permission will likely have logged an informative message about why it was denied.))
(lldb)
The Console.app output that I could find is not very useful.
A later post post describes an updated process but it too fails in a similar way. I'm using Rstudio version 1.4.1717 with R version 4.1.
I am using JupyterLab as my IDE and I have a couple of packages installed. Namely, the 'jupyterlab-dash' and 'juptyerlab-plotly' packages. My issue is when I go to launch 'juptyer lab' from terminal, I notice the following error:
Failed to fetch package metadata for 'jupyterlab-dash': URLError(gaierror(8, 'nodename nor servname provided, or not known'))
I'm not sure why this error is popping up but I've noticed this error only pops up when I have no internet connection (working on a train etc.). Could it be because these packages are trying to call something as I launch and because I don't have an internet connection it raises the error?
In the end I am able to use JupyterLab and the packages as intended (at-least it seems), but I'm curious why this error to 'fetch metadata' appears?
Thanks,
Some context on my environment:
I am running R Studio in a docker container called rocker/verse.
I downloaded this dataset from Kaggle, which has about 470 MB.
When working with it, at some point RStudio restart. It does't happen after a specific call, and I've seen the same problem when working with other projects. Though it is not related to my code, I am posting it bellow.
library(data.table)
fraud<- fread("path.csv")
fraud1<- sort(sample(nrow(fraud), nrow(fraud)*.7))
train<- fraud[fraud1, ]
test<-fraud[-fraud1, ]
Usually on the console this message is printed:
Error: Error occurred during transmission
And, this pop up is also showed:
I have no idea what is causing it. I would appreciate any help.
Delete the .Rhistory files associated with the installation and any open project.
You have a problem with your user data files for Rstudio. Follow the hints given here: https://community.rstudio.com/t/rstudio-server-error-occurred-during-transmission/84258 and here: https://support.rstudio.com/hc/en-us/articles/218730228-Resetting-a-user-s-state-on-RStudio-Server.
Whenever I run RStudio and want to install packages, it gives me that: "Would you like to use your personal library instead?". If I pick "yes", it suggests me to create a personal library in my working directory. And then it fails to install:
Warning in install.packages : cannot create dir 'C:\Users\Name.Name-Name\OneDrive - ??? ?????? ????? ?????????', reason 'Invalid argument'
Error in install.packages : unable to create ‘C:/Users/Name.Name-name/OneDrive - ??? ?????? ????? ?????????/?????????/R/win-library/3.6’
When I run my R as administrator, packages install.
I have a Windows 10 OS, the source directory of my R and RStudio is "C\ProgrammFiles"
This problem has begun when I started using OneDrive service (as our uni provides us with 1 TB of cloud in OneDrive). Then I got really annoyed by OneDrive and deleted it. But the problem remained.
P. S.: I do not want always running RStudio as administrator — it takes a long time.
P. P. S.: "?????" in the error message is Cyrillic letters. I don't think that they are the cause of this particular problem because as administrator permission it works...