Publish Shiny App - Requires XML Package

michaelgloven · August 24, 2020, 10:23pm

I'm trying to publish my app to Shiny.io and get the following error:

Preparing to deploy document...DONE
Uploading bundle for document: 2700710...Error: Unable to retrieve package records for the following packages:

"XML"
In addition: Warning message:
In FUN(X[[i]], ...) : Package 'XML' not available in repository or locally
Execution halted

I'm not explicitly using this package and could not find it on the CRAN. Publishing fails at this point. Any suggestions on how to resolve this issue? I've published other applications no problem from my environment.

cderv · August 25, 2020, 9:03am

The package is on CRAN: https://cran.r-project.org/web/packages/XML/index.html
but it is now bound to R > 4.0.0
I guess you are using an older version ?

You need to install a previous version of the package that is available with your R version. remotes::install_version could help for that.

michaelgloven · August 25, 2020, 8:13pm

thanks for your reply. I'm not using the XML package for my application.

I have two issues - I'm not using XML and my app runs fine locally without it, and there's no such package I can find called XML thru my CRAN unless its called something different. I see your link to the package, but am not sure what all of the links, etc. mean. Maybe if I knew how to get the package thru other means I'd just install it and be done. It is odd that the XML package is being called out in the first place when I believe I'm not using it.

josh · August 26, 2020, 12:33pm

What is the output of rsconnect::appDependencies()?

michaelgloven · August 26, 2020, 4:32pm

I usually don't run the console, but here's what I get:

Error: Unable to retrieve package records for the following packages:

"XML"
In addition: Warning messages:
1: In fileDependencies.R(tempfile) :
Failed to parse C:\Users\mikeg\AppData\Local\Temp\RtmpOacE1Q\file2c50793b65f5 ; dependencies in this file will not be discovered.
2: In FUN(X[[i]], ...) :
Package 'XML' not available in repository or locally

michaelgloven · August 29, 2020, 11:29pm

Josh,

Appreciate any ideas you may have as I'm not making any progress on this issue. Here's what I've done:

Updated RStudio to Version 1.3.1073, then updated all my packages
Tried to publish my app and get the following error:
Preparing to deploy document...DONE
Uploading bundle for document: 2700710...Error: Unable to retrieve package records for the following packages:

"XML"
In addition: Warning message:
In FUN(X[[i]], ...) : Package 'XML' not available in repository or locally
Execution halted

ran rsconnect::appDependencies("app_course_v4.R") for my app and get the following error:
Error in if (tolower(source) %in% c("github", "bitbucket", "source")) { :
argument is of length zero
In addition: Warning message:
Unable to package DESCRIPTION files: subscript out of bounds
Ran install.packages("XML") and get the following message:
Installing package into �C:/Users/mikeg/Documents/R/win-library/3.6�
(as �lib� is unspecified)
Warning in install.packages :
package ‘XML’ is not available (for R version 3.6.1)
My app does not use the XML package

josh · August 31, 2020, 1:09pm

If the rsconnect package is unable to determine the dependencies of your application, it will not be able to deploy it to shinyapps.io.

I don't think that you want to run rsconnect::appDependencies() on a singular R file. Instead run on your application directory (the default behavior with no arguments, assuming the current working directly is the top directory of your application).

If you are still unable to determine the cause of the issue, I would suggest opening an issue with the rsconnect package itself.

michaelgloven · August 31, 2020, 5:11pm

thanks, when I run this on my application directory I get:

Error: Unable to retrieve package records for the following packages: - "XML"

Again, I am not installing or need this package. Is my only option to recreate my 2000 line application and bring in one library at a time to determine which package or something else is requiring XML?

josh · August 31, 2020, 6:00pm

I am not a developer of the rsconnect package, and so I can't say why it is failing to scan your application directory successfully. I will bring this topic to their attention and see if they can be of assistance.

kevinushey · August 31, 2020, 6:18pm

What is the output of:

renv::dependencies()

within your project? (be sure to install renv via install.packages("renv") if you don't already have it installed)

michaelgloven · August 31, 2020, 9:48pm

let me remove the archive folder and resend the list of packages...

michaelgloven · August 31, 2020, 9:50pm

Source	Package	Dev
C:/Users/mikeg/OneDrive/R/Course/app_course_v4.R	ada	FALSE
C:/Users/mikeg/OneDrive/R/Course/courseDev.Rmd	ada	FALSE
C:/Users/mikeg/OneDrive/R/Course/app_course_v4.R	AppliedPredictiveModeling	FALSE
C:/Users/mikeg/OneDrive/R/Course/courseDev.Rmd	AppliedPredictiveModeling	FALSE
C:/Users/mikeg/OneDrive/R/Course/app_course_v4.R	C50	FALSE
C:/Users/mikeg/OneDrive/R/Course/courseDev.Rmd	C50	FALSE
C:/Users/mikeg/OneDrive/R/Course/app_course_v4.R	caret	FALSE
C:/Users/mikeg/OneDrive/R/Course/courseDev.Rmd	caret	FALSE
C:/Users/mikeg/OneDrive/R/Course/app_course_v4.R	caretEnsemble	FALSE
C:/Users/mikeg/OneDrive/R/Course/courseDev.Rmd	caretEnsemble	FALSE
C:/Users/mikeg/OneDrive/R/Course/app_course_v4.R	corrplot	FALSE
C:/Users/mikeg/OneDrive/R/Course/courseDev.Rmd	corrplot	FALSE
C:/Users/mikeg/OneDrive/R/Course/app_course_v4.R	DBI	FALSE
C:/Users/mikeg/OneDrive/R/Course/courseDev.Rmd	DBI	FALSE
C:/Users/mikeg/OneDrive/R/Course/app_course_v4.R	dbplyr	FALSE
C:/Users/mikeg/OneDrive/R/Course/courseDev.Rmd	dbplyr	FALSE
C:/Users/mikeg/OneDrive/R/Course/app_course_v4.R	distr	FALSE
C:/Users/mikeg/OneDrive/R/Course/courseDev.Rmd	distr	FALSE
C:/Users/mikeg/OneDrive/R/Course/app_course_v4.R	dplyr	FALSE
C:/Users/mikeg/OneDrive/R/Course/courseDev.Rmd	dplyr	FALSE
C:/Users/mikeg/OneDrive/R/Course/courseDev.Rmd	dplyr	FALSE
C:/Users/mikeg/OneDrive/R/Course/courseDev.Rmd	dplyr	FALSE
C:/Users/mikeg/OneDrive/R/Course/app_course_v4.R	DT	FALSE
C:/Users/mikeg/OneDrive/R/Course/courseDev.Rmd	DT	FALSE
C:/Users/mikeg/OneDrive/R/Course/app_course_v4.R	ellipse	FALSE
C:/Users/mikeg/OneDrive/R/Course/courseDev.Rmd	ellipse	FALSE
C:/Users/mikeg/OneDrive/R/Course/app_course_v4.R	evd	FALSE
C:/Users/mikeg/OneDrive/R/Course/courseDev.Rmd	evd	FALSE
C:/Users/mikeg/OneDrive/R/Course/app_course_v4.R	extRemes	FALSE
C:/Users/mikeg/OneDrive/R/Course/courseDev.Rmd	extRemes	FALSE
C:/Users/mikeg/OneDrive/R/Course/app_course_v4.R	FinCal	FALSE
C:/Users/mikeg/OneDrive/R/Course/courseDev.Rmd	FinCal	FALSE
C:/Users/mikeg/OneDrive/R/Course/app_course_v4.R	funModeling	FALSE
C:/Users/mikeg/OneDrive/R/Course/courseDev.Rmd	funModeling	FALSE
C:/Users/mikeg/OneDrive/R/Course/app_course_v4.R	gbm	FALSE
C:/Users/mikeg/OneDrive/R/Course/courseDev.Rmd	gbm	FALSE
C:/Users/mikeg/OneDrive/R/Course/app_course_v4.R	ggplot2	FALSE
C:/Users/mikeg/OneDrive/R/Course/courseDev.Rmd	ggplot2	FALSE
C:/Users/mikeg/OneDrive/R/Course/courseDev.Rmd	ggplot2	FALSE
C:/Users/mikeg/OneDrive/R/Course/app_course_v4.R	gumbel	FALSE
C:/Users/mikeg/OneDrive/R/Course/courseDev.Rmd	gumbel	FALSE
C:/Users/mikeg/OneDrive/R/Course/app_course_v4.R	h2o	FALSE
C:/Users/mikeg/OneDrive/R/Course/courseDev.Rmd	h2o	FALSE
C:/Users/mikeg/OneDrive/R/Course/app_course_v4.R	Hmisc	FALSE
C:/Users/mikeg/OneDrive/R/Course/courseDev.Rmd	Hmisc	FALSE
C:/Users/mikeg/OneDrive/R/Course/app_course_v4.R	htmltools	FALSE
C:/Users/mikeg/OneDrive/R/Course/courseDev.Rmd	htmltools	FALSE
C:/Users/mikeg/OneDrive/R/Course/courseDev.Rmd	knitr	FALSE
C:/Users/mikeg/OneDrive/R/Course/app_course_v4.R	leaflet	FALSE
C:/Users/mikeg/OneDrive/R/Course/courseDev.Rmd	leaflet	FALSE
C:/Users/mikeg/OneDrive/R/Course/app_course_v4.R	lubridate	FALSE
C:/Users/mikeg/OneDrive/R/Course/courseDev.Rmd	lubridate	FALSE
C:/Users/mikeg/OneDrive/R/Course/app_course_v4.R	miceadds	FALSE
C:/Users/mikeg/OneDrive/R/Course/courseDev.Rmd	miceadds	FALSE
C:/Users/mikeg/OneDrive/R/Course/app_course_v4.R	normalr	FALSE
C:/Users/mikeg/OneDrive/R/Course/courseDev.Rmd	normalr	FALSE
C:/Users/mikeg/OneDrive/R/Course/app_course_v4.R	plotly	FALSE
C:/Users/mikeg/OneDrive/R/Course/courseDev.Rmd	plotly	FALSE
C:/Users/mikeg/OneDrive/R/Course/app_course_v4.R	prc	FALSE
C:/Users/mikeg/OneDrive/R/Course/courseDev.Rmd	prc	FALSE
C:/Users/mikeg/OneDrive/R/Course/app_course_v4.R	pROC	FALSE
C:/Users/mikeg/OneDrive/R/Course/courseDev.Rmd	pROC	FALSE
C:/Users/mikeg/OneDrive/R/Course/app_course_v4.R	R.utils	FALSE
C:/Users/mikeg/OneDrive/R/Course/courseDev.Rmd	R.utils	FALSE
C:/Users/mikeg/OneDrive/R/Course/app_course_v4.R	randomForest	FALSE
C:/Users/mikeg/OneDrive/R/Course/courseDev.Rmd	randomForest	FALSE
C:/Users/mikeg/OneDrive/R/Course/app_course_v4.R	raster	FALSE
C:/Users/mikeg/OneDrive/R/Course/courseDev.Rmd	raster	FALSE
C:/Users/mikeg/OneDrive/R/Course/app_course_v4.R	rattle	FALSE
C:/Users/mikeg/OneDrive/R/Course/courseDev.Rmd	rattle	FALSE
C:/Users/mikeg/OneDrive/R/Course/app_course_v4.R	readxl	FALSE
C:/Users/mikeg/OneDrive/R/Course/courseDev.Rmd	readxl	FALSE
C:/Users/mikeg/OneDrive/R/Course/courseDev.Rmd	readxl	FALSE
C:/Users/mikeg/OneDrive/R/Course/courseDev.Rmd	remotes	FALSE
C:/Users/mikeg/OneDrive/R/Course/courseDev.Rmd	renv	FALSE
C:/Users/mikeg/OneDrive/R/Course/app_course_v4.R	rgdal	FALSE
C:/Users/mikeg/OneDrive/R/Course/courseDev.Rmd	rmarkdown	FALSE
C:/Users/mikeg/OneDrive/R/Course/app_course_v4.R	rpart	FALSE
C:/Users/mikeg/OneDrive/R/Course/courseDev.Rmd	rpart	FALSE
C:/Users/mikeg/OneDrive/R/Course/app_course_v4.R	rpart.plot	FALSE
C:/Users/mikeg/OneDrive/R/Course/courseDev.Rmd	rpart.plot	FALSE
C:/Users/mikeg/OneDrive/R/Course/app_course_v4.R	rpivotTable	FALSE
C:/Users/mikeg/OneDrive/R/Course/courseDev.Rmd	rpivotTable	FALSE
C:/Users/mikeg/OneDrive/R/Course/app_course_v4.R	rsconnect	FALSE
C:/Users/mikeg/OneDrive/R/Course/courseDev.Rmd	rsconnect	FALSE
C:/Users/mikeg/OneDrive/R/Course/courseDev.Rmd	rsconnect	FALSE
C:/Users/mikeg/OneDrive/R/Course/app_course_v4.R	RSQLite	FALSE
C:/Users/mikeg/OneDrive/R/Course/courseDev.Rmd	RSQLite	FALSE
C:/Users/mikeg/OneDrive/R/Course/courseDev.Rmd	RWeka	FALSE
C:/Users/mikeg/OneDrive/R/Course/courseDev.Rmd	RWekajars	FALSE
C:/Users/mikeg/OneDrive/R/Course/app_course_v4.R	scales	FALSE
C:/Users/mikeg/OneDrive/R/Course/courseDev.Rmd	scales	FALSE
C:/Users/mikeg/OneDrive/R/Course/app_course_v4.R	sf	FALSE
C:/Users/mikeg/OneDrive/R/Course/courseDev.Rmd	sf	FALSE
C:/Users/mikeg/OneDrive/R/Course/app_course_v4.R	shiny	FALSE
C:/Users/mikeg/OneDrive/R/Course/courseDev.Rmd	shiny	FALSE
C:/Users/mikeg/OneDrive/R/Course/courseDev.Rmd	shiny	FALSE
C:/Users/mikeg/OneDrive/R/Course/app_course_v4.R	shinydashboard	FALSE
C:/Users/mikeg/OneDrive/R/Course/courseDev.Rmd	shinydashboard	FALSE
C:/Users/mikeg/OneDrive/R/Course/app_course_v4.R	shinydashboardPlus	FALSE
C:/Users/mikeg/OneDrive/R/Course/courseDev.Rmd	shinydashboardPlus	FALSE
C:/Users/mikeg/OneDrive/R/Course/app_course_v4.R	shinyFeedback	FALSE
C:/Users/mikeg/OneDrive/R/Course/courseDev.Rmd	shinyFeedback	FALSE
C:/Users/mikeg/OneDrive/R/Course/app_course_v4.R	shinyFiles	FALSE
C:/Users/mikeg/OneDrive/R/Course/app_course_v4.R	shinythemes	FALSE
C:/Users/mikeg/OneDrive/R/Course/courseDev.Rmd	shinythemes	FALSE
C:/Users/mikeg/OneDrive/R/Course/app_course_v4.R	skimr	FALSE
C:/Users/mikeg/OneDrive/R/Course/courseDev.Rmd	skimr	FALSE
C:/Users/mikeg/OneDrive/R/Course/app_course_v4.R	smotefamily	FALSE
C:/Users/mikeg/OneDrive/R/Course/courseDev.Rmd	smotefamily	FALSE
C:/Users/mikeg/OneDrive/R/Course/app_course_v4.R	sqldf	FALSE
C:/Users/mikeg/OneDrive/R/Course/courseDev.Rmd	sqldf	FALSE
C:/Users/mikeg/OneDrive/R/Course/app_course_v4.R	stringr	FALSE
C:/Users/mikeg/OneDrive/R/Course/courseDev.Rmd	stringr	FALSE
C:/Users/mikeg/OneDrive/R/Course/app_course_v4.R	summarytools	FALSE
C:/Users/mikeg/OneDrive/R/Course/courseDev.Rmd	summarytools	FALSE
C:/Users/mikeg/OneDrive/R/Course/app_course_v4.R	tidyverse	FALSE
C:/Users/mikeg/OneDrive/R/Course/courseDev.Rmd	tidyverse	FALSE
C:/Users/mikeg/OneDrive/R/Course/app_course_v4.R	writexl	FALSE
C:/Users/mikeg/OneDrive/R/Course/courseDev.Rmd	writexl	FALSE
C:/Users/mikeg/OneDrive/R/Course/courseDev.Rmd	writexl	FALSE
C:/Users/mikeg/OneDrive/R/Course/app_course_v4.R	xgboost	FALSE
C:/Users/mikeg/OneDrive/R/Course/courseDev.Rmd	xgboost	FALSE

michaelgloven · August 31, 2020, 10:02pm

Kevin,

Once I moved my "archive" folder with old dev files & versions out of my development environment folder which only includes the list above, I'm not able to "Run App" and get the following error.

Warning in FUN(X[[i]], ...) :
Package 'XML' not available in repository or locally
Error: Unable to retrieve package records for the following packages:

"XML"

It looks like this XML related package was somewhere in my development folder, but now it's not available to even run my app since I moved my archive folder to another back-up location. I still don't see the XML package anywhere in my current dev directory or archived, and don't see the package "XML" available to install?

kevinushey · August 31, 2020, 10:46pm

The rattle package depends on XML:

https://cran.r-project.org/web/packages/rattle/index.html

hence why it's inferred as a dependency for your project.

michaelgloven · August 31, 2020, 10:49pm

I can't seem to figure out how to get the XML package installed from any source (lots of posts on the issue)...maybe I should remove rattle and find something else, unless there's a process to get XML into my app?

michaelgloven · September 1, 2020, 2:17am

thanks, this resolved the issue as I find an alternative to rattle

system · September 22, 2020, 2:17am

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