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DS4PS / cpp-526-fall-2019

Course material for CPP 526 Foundations of Data Science I
http://ds4ps.org/cpp-526-fall-2019
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shinyapps.io issues #29

Open lecy opened 4 years ago

lecy commented 4 years ago

I'm migrating the shinyapps.io issue to a new ticket.

When trying to deploy the app, I get the message: ERROR: An error has occurred. Check your logs or contact the app author for clarification. It is showing up in the viewer, in R, but not in Shinyapps.

Originally posted by @RickyDuran in https://github.com/DS4PS/cpp-526-fall-2019/issues/27#issuecomment-540819726

lecy commented 4 years ago

Ricky, is that while running the app, or publishing on shinyapps.io?

lecy commented 4 years ago

There is a discussion about the error message here:

https://stackoverflow.com/questions/47727806/error-an-error-has-occurred-check-your-logs-or-contact-the-app-author-for-clar?rq=1

Did you install any packages from GitHub? If they are still in development phase that version will not yet be on CRAN.

I suspect when you upload an app to shinyapp.io it will create a new server partition for you with R installed, then install all of the packages required for your app from the CRAN. If it can't find the package it will give this error.

castower commented 4 years ago

Hello all, I have tried many times to get my .rmd file uploaded to Shinyapp.io, but it simply won't upload. I was able to get a detailed output of what's wrong and it seems to be something with Knitr, but I have no idea what to do with that....

here is the output:

----- Deployment log started at  2019-10-11 03:17:07  -----
Deploy command: 
 rsconnect::deployApp(appDir = "~/Documents/ASU/Fall 2019/CPP 526",      appFileManifest = "/var/folders/xq/pbc8kv2n6_nbnhwjhy0483zh0000gn/T/f518-db45-b050-48b3",      appPrimaryDoc = "Code-Through-Project-Stowers.Rmd", appSourceDoc = "~/Documents/ASU/Fall 2019/CPP 526/Code-Through-Project-Stowers.Rmd",      account = "castower", server = "shinyapps.io", appName = "Code-Through-Project-Stowers",      appId = 1317344, launch.browser = function(url) {         message("Deployment completed: ", url)     }, lint = FALSE, metadata = list(asMultiple = FALSE, asStatic = FALSE),      logLevel = "verbose") 

Session information: 
R version 3.6.1 (2019-07-05)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: OS X El Capitan 10.11.6

Matrix products: default
BLAS:   /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRblas.0.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

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

loaded via a namespace (and not attached):
[1] compiler_3.6.1   rsconnect_0.8.15
Cookies: 
[1] "None"
GET /v1/applications/1317344 1561ms
----- Bundle upload started at  2019-10-11 03:17:09  -----
[2019-10-11 03:17:09] Inferring App mode and parameters 
[2019-10-11 03:17:09] Bundling app dir 
[2019-10-11 03:17:10] Generate manifest.json 
[2019-10-11 03:18:18] Writing Rmd index if necessary 
[2019-10-11 03:18:18] Compressing the bundle 
POST /v1/bundles 1115ms
[2019-10-11 03:18:19] Starting upload now 
[2019-10-11 03:18:21] Upload complete 
POST /v1/bundles/2490652/status 594ms
GET /v1/bundles/2490652 573ms
[2019-10-11 03:18:22] Saving deployment record for Code-Through-Project-Stowers -  
----- Server deployment started at  2019-10-11 03:18:22  -----
POST /v1/applications/1317344/deploy 763ms
Waiting for task: 657075928
GET /v1/tasks/657075928 554ms
  building: Processing bundle: 2490652
GET /v1/tasks/657075928 618ms
  building: Parsing manifest
GET /v1/tasks/657075928 609ms
  building: Building image: 2680343
GET /v1/tasks/657075928 647ms
  building: Installing system dependencies
GET /v1/tasks/657075928 555ms
GET /v1/tasks/657075928 548ms
GET /v1/tasks/657075928 552ms
GET /v1/tasks/657075928 638ms
  building: Fetching packages
GET /v1/tasks/657075928 980ms
  error: Building package: knitr
################################ Begin Task Log ################################ 
GET /v1/tasks/657075928/logs/ 564ms
GET /v1/tasks/?filter=account_id:323453&filter=parent_id:657075928&count=100&offset=0 566ms
GET /v1/tasks/657075929/logs/ 573ms
[2019-10-11T10:18:28.886256269+0000] Execute script: packages/build/sys.sh
+ set -e
+ apt-get update -qq
+ apt-get install -y libapparmor-dev
Reading package lists...
Building dependency tree...
Reading state information...
The following NEW packages will be installed:
  libapparmor-dev
0 upgraded, 1 newly installed, 0 to remove and 72 not upgraded.
Need to get 67.8 kB of archives.
After this operation, 229 kB of additional disk space will be used.
Get:1 http://us-east-1.ec2.archive.ubuntu.com/ubuntu xenial-updates/main amd64 libapparmor-dev amd64 2.10.95-0ubuntu2.11 [67.8 kB]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 67.8 kB in 0s (0 B/s)
Selecting previously unselected package libapparmor-dev:amd64.
(Reading database ... 119718 files and directories currently installed.)
Preparing to unpack .../libapparmor-dev_2.10.95-0ubuntu2.11_amd64.deb ...
Unpacking libapparmor-dev:amd64 (2.10.95-0ubuntu2.11) ...
Processing triggers for man-db (2.7.5-1) ...
Setting up libapparmor-dev:amd64 (2.10.95-0ubuntu2.11) ...
GET /v1/tasks/?filter=account_id:323453&filter=parent_id:657075929&count=100&offset=0 549ms
################################# End Task Log ################################# 
----- Deployment error -----
Error: Unhandled Exception: Child Task 657075929 failed: Error building image: Error fetching knitr (1.25.1) source. <CRANPackageSource repo='http://cran.rstudio.org'> unable to satisfy package: knitr (1.25.1)

----- Error stack trace -----
3: stop(status$error, call. = FALSE)
2: client$waitForTask(taskId, quiet)
1: rsconnect::deployApp(appDir = "~/Documents/ASU/Fall 2019/CPP 526", 
       appFileManifest = "/var/folders/xq/pbc8kv2n6_nbnhwjhy0483zh0000gn/T/f518-db45-b050-48b3", 
       appPrimaryDoc = "Code-Through-Project-Stowers.Rmd", appSourceDoc = "~/Documents/ASU/Fall 2019/CPP 526/Code-Through-Project-Stowers.Rmd", 
       account = "castower", server = "shinyapps.io", appName = "Code-Through-Project-Stowers", 
       appId = 1317344, launch.browser = function(url) {
           message("Deployment completed: ", url)
       }, lint = FALSE, metadata = list(asMultiple = FALSE, asStatic = FALSE), 
       logLevel = "verbose")
Error: Unhandled Exception: Child Task 657075929 failed: Error building image: Error fetching knitr (1.25.1) source. <CRANPackageSource repo='http://cran.rstudio.org'> unable to satisfy package: knitr (1.25.1)
In addition: There were 12 warnings (use warnings() to see them)
Execution halted

I have tried to type warnings() into my console, but it doesn't produce anything.

lecy commented 4 years ago

It looks like you have a developer's version of knitr. Try installing the older version:

require( devtools )
install_version( "knitr", version = "1.25", repos = "http://cran.us.r-project.org" )
castower commented 4 years ago

It looks like you have a developer's version of knitr. Try installing the older version:

require( devtools )
install_version( "knitr", version = "1.25", repos = "http://cran.us.r-project.org" )

That fixed it! However, I am now getting the same error as Ricky. Likely because my waffle package does come from github: https://github.com/hrbrmstr/waffle. Does that mean that there isn't a way for me to deploy my file?

lecy commented 4 years ago

This R Studio discussion board says you should be able to:

I've run into instances of this as well. When deploying, make sure to have your GitHub package installed from GitHub ( devtools::install_github() ), not installed from a local folder (devtools::install()). When installed from GitHub, devtools will store the GitHub location and hash for shinyapps to download. (If installed from a local folder, there is no location to download from.)

How did you install your GitHub package?

castower commented 4 years ago

This R Studio discussion board says you should be able to:

I've run into instances of this as well. When deploying, make sure to have your GitHub package installed from GitHub ( devtools::install_github() ), not installed from a local folder (devtools::install()). When installed from GitHub, devtools will store the GitHub location and hash for shinyapps to download. (If installed from a local folder, there is no location to download from.)

How did you install your GitHub package?

I removed the package and then re-installed using the devtools::install_github() option and it's now working!

RickyDuran commented 4 years ago

The only thing that may have been installed, was htmltools, but it kept prompting me to install, but would say it couldn't install. I restarted and the and it stopped promting to install. Not sure if it was installed afterall or not. The version I have is 0.4.0.

RickyDuran commented 4 years ago

FINALLY! Thanks @castower ! That helped! Remove Knitr use to install from github: 'devtools::install_github("yihui/knitr", force = TRUE)' removed 'library(knitr)' from code

castower commented 4 years ago

FINALLY! Thanks @castower ! That helped! Remove Knitr use to install from github: 'devtools::install_github("yihui/knitr", force = TRUE)' removed 'library(knitr)' from code

@RickyDuran glad that helped, it was such a frustrating error!

To clarify all of my steps to solve my problem for anyone else that may read this:

First, I uninstalled and reinstalled knitr using:

remove.packages("knitr")
require( devtools )
install_version( "knitr", version = "1.25", repos = "http://cran.us.r-project.org" )

As a note, I did leave

library(knitr)

in my file and it didn't cause any problems.

Next, to stop the error message that was produced by my waffle package:

ERROR: An error has occurred. Check your logs or contact the app author for clarification.

I also uninstalled and re-installed, but this time instead of using the first install option that was listed on the GitHub page:

install.packages("waffle", repos = "https://cinc.rud.is")

I selected the devtools::install_github() option:

remove.packages("waffle")
devtools::install_github("hrbrmstr/waffle")

During the download from install_github() it indicated that it was importing the repos info. As noted in the linked R Studio Discussion Board, this is key so that shinyapps can find the necessary info. By default, it only searches CRAN and not GitHub.

I found some helpful readings on this here: https://github.com/rstudio/rsconnect/issues/88 and in section 2.4.0.1 here: https://docs.rstudio.com/shinyapps.io/getting-started.html#managing-r-versions

lecy commented 4 years ago

Thank you both for sharing your steps!

lecy commented 4 years ago

And just to note that Shiny Apps are fairly cutting edge.

As I mentioned in the lecture notes, R has figured out a way to replace full-stack development of web apps, which requires six or seven different languages and a live server, with these translational shiny widgets and render functions, and integration to a server through shinyapps.io.

You can see the progression to the frontiers and wilderness of open source development.

Core R --> very stable and predictable

Popular packages (dplyr) --> often easier to use and poweful, usually very stable and reliable but syntax is distinct from Core R

Custom niche packages --> usually cool, but sometimes have issues with dependencies

Fully customized platform development (shiny apps) --> usually some work making sure all of the part are playing nicely together