menus missing after install on Rstudio-server

[urielcarrasquilla]

Ubuntu 16.04.6 LTS R 3.6.1 Access to Radiant via browser using Rstudio-server

Messages received:

radiant::radiant()

Starting radiant in the default browser ...

Use radiant::radiant_viewer() in Rstudio to open radiant in the Rstudio viewer or radiant::radiant_window() in Rstudio to open radiant in an Rstudio window

Listening on http://127.0.0.1:7682

However, the Menus on the left pane where the datasets can be uploaded are missing. I suspect the "git clone" of the Radiant source is not in the correct location. I put it under /home/rstudio (same place where R directory is located for all of the R packages in use by user=rstudio).

[vnijs]

Please review the "Installing R, Rstudio, and Radiant on Linux" section at the link below. You don't need to clone the sources if you are running from Rstudio. If all ubuntu dependencies are available, running the below should get you the latest version of all relevant packages.

install.packages("radiant.update", repos = "https://radiant-rstats.github.io/minicran/")
radiant.update::radiant.update()

https://radiant-rstats.github.io/docs/install.html

[urielcarrasquilla]

Thank you for your reply. I ran the two commands. When I do the radiant::radiant() I still don't see anything under the top menu: "Radiant Data Design BASICS MODEL Multivariate Report". A picture: [image: image.png] Uri Carrasquilla Senior Data Scientist / Planner "adventure is just bad planning" - Roald Amundsen (561) 900-8296 <555-555-5555> ucarrasquilla@digitalocean.com

On Wed, Apr 15, 2020 at 6:14 AM Vincent Nijs notifications@github.com wrote:

Please review the "Installing R, Rstudio, and Radiant on Linux" section at the link below. You don't need to clone the sources if you are running from Rstudio. If all ubuntu dependencies are available, running the below should get you the latest version of all relevant packages.

install.packages("radiant.update", repos = "https://radiant-rstats.github.io/minicran/") radiant.update::radiant.update()

https://radiant-rstats.github.io/docs/install.html

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/radiant-rstats/radiant/issues/131#issuecomment-613949502, or unsubscribe https://github.com/notifications/unsubscribe-auth/AJPWUIDSGGNZN27ATQX6HODRMWCG5ANCNFSM4MIHQADA .

[vnijs]

Can you post the screenshot again? I can't see it on github. Also, are there any messages shown in Rstudio or in the Developer Console of the web-browser?

[urielcarrasquilla]

Before I do that let me share some findings. When I reinstalled all the packages as per your instructions, I noticed that some of them are being reported with a non-zero exit. I went back to see why and in some cases it is due to a prerequisite being missing such as openssl, igraph and rgdal. When I did an install.packages and re-installed the ones with non-zero exit, they completed without the warning. I may have missed some. As a reference here is the list of all the packages that were selected for updates: install.packages(c("radiant", "radiant.basics", "radiant.data", "radiant.design", "radiant.model", "shinyAce", "shinyFiles", "AlgDesign", "BH", "DBI", "DEoptimR", "DiagrammeR", "DiceDesign", "Formula", "GPArotation", "GPfit", "Gmedian", "Hmisc", "ISOcodes", "KernSmooth", "Matrix", "MatrixModels", "Metrics", "ModelMetrics", "NLP", "NeuralNetTools", "PerformanceAnalytics", "Quandl", "R.cache", "R.methodsS3", "R.oo", "R.utils", "R6", "RColorBrewer", "RPostgreSQL", "RSQLite", "RSelenium", "RSpectra", "Rcpp", "RcppArmadillo", "RcppEigen", "RcppParallel", "RgoogleMaps", "RhpcBLASctl", "Rook", "Rttf2pt1", "SQUAREM", "SnowballC", "SparseM", "StanHeaders", "TH.data", "TTR", "XML", "abind", "acepack", "alphavantager", "anytime", "arm", "arrow", "askpass", "assertthat", "backports", "bayesplot", "binman", "bit", "bit64", "bitops", "blob", "bookdown", "boot", "brew", "caTools", "callr", "car", "carData", "caret", "cellranger", "checkmate", "class", "classInt", "cli", "clipr", "clisymbols", "clustMixType", "cluster", "coda", "codetools", "coin", "collections", "colorspace", "colourpicker", "colourvalues", "commonmark", "config", "covr", "crayon", "crosstalk", "cyclocomp", "data.table", "dbplyr", "desc", "devtools", "dials", "dichromat", "digest", "downloader", "dtplyr", "dygraphs", "e1071", "ellipsis", "evaluate", "extrafont", "extrafontdb", "fansi", "farver", "fastmap", "fastmatch", "flexdashboard", "forcats", "foreach", "forecast", "foreign", "forge", "formatR", "fracdiff", "fs", "furrr", "future", "future.apply", "gargle", "gbm", "gdalUtils", "gdtools", "generics", "geojsonsf", "gganimate", "ggforce", "ggraph", "ggrepel", "ggridges", "gh", "gifski", "git2r", "gitgadget", "glmnet", "globals", "glue", "googleAuthR", "googlePolylines", "gower", "graphlayouts", "gridExtra", "gtable", "gtools", "gtrendsR", "hardhat", "haven", "here", "hexbin", "highr", "hms", "htmlTable", "htmltools", "htmlwidgets", "httpuv", "httr", "hunspell", "igraph", "iml", "infer", "influenceR", "ini", "inline", "inum", "ipred", "isoband", "iterators", "janeaustenr", "jpeg", "jsonify", "keras", "labeling", "languageserver", "later", "lattice", "latticeExtra", "lava", "lazyeval", "lda", "leafem", "leaflet", "leaflet.providers", "leafpop", "leafsync", "lfe", "lhs", "libcoin", "lifecycle", "lime", "lintr", "listenv", "lme4", "lmtest", "loo", "lwgeom", "magick", "magrittr", "mapdeck", "maptools", "mapview", "matrixStats", "memoise", "mgcv", "mime", "miniUI", "minqa", "mnormt", "modelr", "modeltools", "multcomp", "munsell", "network", "nlme", "nloptr", "numDeriv", "odbc", "openssl", "openxlsx", "pROC", "packrat", "padr", "pageviews", "parsnip", "party", "partykit", "pbkrtest", "pdp", "pillar", "pkgbuild", "pkgconfig", "pkgload", "plogr", "plotly", "plyr", "polyclip", "polycor", "pool", "praise", "prediction", "prettyunits", "processx", "prodlim", "progress", "promises", "proxyC", "ps", "purrr", "pwr", "quadprog", "quanteda", "quantmod", "quantreg", "r2d3", "randomForest", "rapidjsonr", "rappdirs", "rcmdcheck", "recipes", "rematch", "rematch2", "remotes", "renv", "repr", "reprex", "reshape2", "reticulate", "rex", "rgdal", "rgeos", "rgexf", "riingo", "rio", "rjson", "rlang", "robustbase", "roxygen2", "rpart", "rpart.plot", "rprojroot", "rsample", "rsconnect", "rstan", "rstanarm", "rstantools", "rstudioapi", "rtweet", "rversions", "rvest", "sandwich", "satellite", "selectr", "semver", "servr", "sessioninfo", "sfheaders", "shape", "shinydashboard", "shinyjs", "shinystan", "shinythemes", "slam", "sna", "sourcetools", "sp", "spacyr", "sparklyr", "sparkxgb", "spatialwidget", "stargazer", "stars", "statnet.common", "stm", "stopwords", "stringdist", "stringr", "strucchange", "styler", "survival", "svglite", "sys", "systemfonts", "tensorflow", "testthat", "tfestimators", "tfruns", "threejs", "tidygraph", "tidymodels", "tidyposterior", "tidypredict", "tidyquant", "tidyselect", "tidytext", "timeDate", "timetk", "tinytex", "tm", "tmap", "tmaptools", "tokenizers", "topicmodels", "tseries", "tune", "tweenr", "units", "urca", "usethis", "utf8", "uuid", "vctrs", "vip", "viridis", "viridisLite", "visNetwork", "wdman", "webshot", "whisker", "withr", "wordcloud", "workflows", "xaringan", "xfun", "xml2", "xmlparsedata", "xopen", "xptr", "xtable", "xts", "yaImpute", "yaml", "yardstick", "zeallot", "zip", "zoo"), lib = "/home/rstudio/R/x86_64-pc-linux-gnu-library/3.6", repos = " https://rsm-compute-01.ucsd.edu:4242/rsm-msba/__linux__/bionic/latest", type = "source", INSTALL_opts = "")

When I start Rstudio-server and run radiant::rediant() I get the following messages:

Starting radiant in the default browser ...

Use radiant::radiant_viewer() in Rstudio to open radiant in the Rstudio viewer or radiant::radiant_window() in Rstudio to open radiant in an Rstudio window Listening on http://127.0.0.1:6580

At this point I go to the window opened by radiant and I find the following in the display:

Radiant Data Design Basics Model Multivariate Report

This is followed by the icons for saving power ? (for help)

All of them are grey so I can't select anything.

Uri Carrasquilla Senior Data Scientist / Planner "adventure is just bad planning" - Roald Amundsen (561) 900-8296 <555-555-5555> ucarrasquilla@digitalocean.com

On Wed, Apr 15, 2020 at 4:56 PM Vincent Nijs notifications@github.com wrote:

Can you post the screenshot again? I can't see it on github. Also, are there any messages shown in Rstudio or in the Developer Console of the web-browser?

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/radiant-rstats/radiant/issues/131#issuecomment-614275802, or unsubscribe https://github.com/notifications/unsubscribe-auth/AJPWUIBHP6NXX3XA7IY6D5LRMYNQXANCNFSM4MIHQADA .

[urielcarrasquilla]

[image: image.png] Uri Carrasquilla Senior Data Scientist / Planner "adventure is just bad planning" - Roald Amundsen (561) 900-8296 <555-555-5555> ucarrasquilla@digitalocean.com

On Wed, Apr 15, 2020 at 4:56 PM Vincent Nijs notifications@github.com wrote:

Can you post the screenshot again? I can't see it on github. Also, are there any messages shown in Rstudio or in the Developer Console of the web-browser?

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/radiant-rstats/radiant/issues/131#issuecomment-614275802, or unsubscribe https://github.com/notifications/unsubscribe-auth/AJPWUIBHP6NXX3XA7IY6D5LRMYNQXANCNFSM4MIHQADA .

[urielcarrasquilla]

[vnijs]

I'm 99% sure you are still missing some linux dependencies. On Windows and macOS these dependencies are automatically include. This is not possible on Linux however. Did you follow the dependency instructions for linux listed on the page below?

https://radiant-rstats.github.io/docs/install.html

We run radiant in linux servers and through Rstudio on Ubuntu 18.04 without any issues. I'm not sure what shinyapps.io uses but likely 16 or 18. See demo below.

Free-tier instance on shinyapps.io: https://vnijs.shinyapps.io/radiant/

[urielcarrasquilla]

When Running: https://raw.githubusercontent.com/radiant-rstats/minicran/gh-pages/update.R

################################################# Updating previously installed packages #################################################

Error in update.packages(lib.loc = .libPaths()[1], ask = FALSE, repos = repos_run, : object 'repos_run' not found

err <- c("yaml", "Matrix", "radiant", "radiant.model")

err <- c("yaml", "Matrix")

err <- c()

err <- err[!err %in% installed.packages()] Error: object 'err' not found Uri Carrasquilla Senior Data Scientist / Planner "adventure is just bad planning" - Roald Amundsen (561) 900-8296 <555-555-5555> ucarrasquilla@digitalocean.com

On Wed, Apr 15, 2020 at 6:49 PM Vincent Nijs notifications@github.com wrote:

I'm 99% sure you are still missing some linux dependencies. On Windows and macOS these dependencies are automatically include. This is not possible on Linux however. Did you follow the dependency instructions for linux listed on the page below?

https://radiant-rstats.github.io/docs/install.html

We run radiant in linux servers and through Rstudio on Ubuntu 18.04 without any issues. I'm not sure what shinyapps.io uses but likely 16 or

18. See demo below.

Free-tier instance on shinyapps.io: https://vnijs.shinyapps.io/radiant/

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/radiant-rstats/radiant/issues/131#issuecomment-614318144, or unsubscribe https://github.com/notifications/unsubscribe-auth/AJPWUIHIZTGRIKDPCUHZZ5DRMY2YXANCNFSM4MIHQADA .

[vnijs]

Ah. You found a bug in the update script! Thanks for reporting @urielcarrasquilla. Can you try again now?

BTW I have Rstudio Package Manager running at the url below. However, this only provides binaries for Ubuntu 18.04

https://rsm-compute-01.ucsd.edu:4242/client/

[vnijs]

Also, you may be interested in the docker container I have that includes shiny-server, rstudio-server and radiant

Images: https://hub.docker.com/r/vnijs/radiant Docker and launch files: https://github.com/radiant-rstats/docker

[urielcarrasquilla]

I managed to run the refreshed script. Followed the remaining steps in the install.html link you provided. I did an "rstudio-server stop" followed by a start. From the RStudio Server issued:

Stopped Radiant

Attaching package: ‘radiant.data’ The following objects are masked from ‘package:lubridate’:

month, wday

The following object is masked from ‘package:ggplot2’:

diamonds

radiant::radiant()Starting radiant in the default browser ...

Use radiant::radiant_viewer() in Rstudio to open radiant in the Rstudio viewer or radiant::radiant_window() in Rstudio to open radiant in an Rstudio window Listening on http://127.0.0.1:6827

Stopped Radiant

No Luck. I am still not getting the left hand side Pane.

Uri Carrasquilla Senior Data Scientist / Planner "adventure is just bad planning" - Roald Amundsen (561) 900-8296 <555-555-5555> ucarrasquilla@digitalocean.com

On Wed, Apr 15, 2020 at 10:11 PM Vincent Nijs notifications@github.com wrote:

Ah. You found a bug in the update script! Thanks for reporting @urielcarrasquilla https://github.com/urielcarrasquilla. Can you try again now?

BTW I have Rstudio Package Manager running at the url below. However, this only provides binaries for Ubuntu 18.04

https://rsm-compute-01.ucsd.edu:4242/client/

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/radiant-rstats/radiant/issues/131#issuecomment-614373520, or unsubscribe https://github.com/notifications/unsubscribe-auth/AJPWUIFQZUUS6QNNIMCDBXDRMZSONANCNFSM4MIHQADA .

[vnijs]

Wow. I can't see any issues in the install process. However, (1) I can't reproduce the issue on any computer I have access to (see e.g., screenshot below for Rstudio server) and (2) there are no error messages in Rstudio or in the developer log for me to work from.

Is the docker container an option for you? Or is there any way for me to temporarily access the server to see if I can spot something? My work email is vnijs@ucsd.edu

[vnijs]

I did also just update radiant on CRAN. Could you just try:

install.packages("radiant.data")
radiant.data::radiant.data()

I just tried this on rstudio cloud and it is running fine

[vnijs]

radiant also installed and ran without a hitch in rstudio cloud. So nice to have binary packages from Rstudio so it doesn't take HOURS to install packages :)

install.packages("radiant")
radiant::radiant()

[urielcarrasquilla]

Hi Vincent.

Installed docker and it is working now. This was done on Ubuntu version 18 04 4 LTS

Got the following error messages after running from bash cli: docker run --rm -p 8080:8080 -p 8787:8787 -v ~:/home/jovyan vnijs/radiant

Status: Downloaded newer image for vnijs/radiant:latest 2020-04-16 10:16:05,862 INFO supervisord started with pid 1 2020-04-16 10:16:06,864 INFO spawned: 'shinyserver' with pid 8 2020-04-16 10:16:06,866 INFO spawned: 'rserver' with pid 9 2020-04-16 10:16:06,868 INFO spawned: 'userconf' with pid 10 2020-04-16 10:16:06,877 INFO success: rserver entered RUNNING state, process has stayed up for > than 0 seconds (startsecs) 2020-04-16 10:16:06,877 INFO success: userconf entered RUNNING state, process has stayed up for > than 0 seconds (startsecs) 2020-04-16 10:16:06,890 INFO exited: rserver (exit status 0; expected) 2020-04-16 10:16:06,891 INFO exited: userconf (exit status 0; expected) 2020-04-16 10:16:08,228 INFO success: shinyserver entered RUNNING state, process has stayed up for > than 1 seconds (startsecs)

Then, went to browser and pointed to the server where docker installed. Added :8080 to the end of the URL. Nothing found. Added: 8787 and got sign on panel for RStudio. How do I find out the user_id and password?

Thank you.

Uri Carrasquilla Senior Data Scientist / Planner "adventure is just bad planning" - Roald Amundsen (561) 900-8296 <555-555-5555> ucarrasquilla@digitalocean.com

On Wed, Apr 15, 2020 at 10:14 PM Vincent Nijs notifications@github.com wrote:

Also, you may be interested in the docker container I have that includes shiny-server, rstudio-server and radiant

Images: https://hub.docker.com/r/vnijs/radiant Docker and launch files: https://github.com/radiant-rstats/docker

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/radiant-rstats/radiant/issues/131#issuecomment-614374211, or unsubscribe https://github.com/notifications/unsubscribe-auth/AJPWUIF4VMOB4RAFWKR5JV3RMZSYRANCNFSM4MIHQADA .

[vnijs]

For radiant, use 8181:8181 instead. Username: jovyan, Password: rstudio

docker run --rm -p 8181:8181 -p 8787:8787 -v ~:/home/jovyan vnijs/radiant

[urielcarrasquilla]

That worked for me. 8181 is the port. I can now load files from my laptop. Thank you. I have a file system that is hosted via Apache. Is there any way I can point radiant to it instead of only being able to look at my laptop file system? Thank you.

Uri Carrasquilla Senior Data Scientist / Planner "adventure is just bad planning" - Roald Amundsen (561) 900-8296 <555-555-5555> ucarrasquilla@digitalocean.com

On Thu, Apr 16, 2020 at 12:21 PM Vincent Nijs notifications@github.com wrote:

For radiant, use 8181:8181 instead. Username: jovyan, Password: rstudio

docker run --rm -p 8181:8181 -p 8787:8787 -v ~:/home/jovyan vnijs/radiant

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/radiant-rstats/radiant/issues/131#issuecomment-614753808, or unsubscribe https://github.com/notifications/unsubscribe-auth/AJPWUIAAQOAK4A7ZIKMWY33RM4WATANCNFSM4MIHQADA .

[vnijs]

If you start Radiant from RStudio on a server you should have access to the filesystem on the server as well. You can also load any data you have access to through R > Rmarkdown if you can (1) store it in a data.frame (e.g., my_data) and then (2) use register("my_data") so the data shows up from the dataset dropdowns.

If you prefer using Radiant through shiny-server (i.e., port 8181) then adding the options below to your .Rprofile file should allow you to look at files in your home-directory on the server. This last part is not that well tested because I have most students use Radiant through Rstudio.

If you want to have a quick zoom call about what you are trying to achieve, reach out to me through vnijs@ucsd.edu

options(radiant.maxRequestSize = -1)
options(radiant.report = TRUE)
options(radiant.shinyFiles = TRUE