Problem deploying app

I am having problems re-deploying an app (that is it was published, I made a few changes and am trying to re-publish a slightly different version). I'm pretty sure that the only thing that I've changed is that I am now using the package "gridExtra". And I've added a few files to download. Everything works when I preview it from inside RStudio.

The error says something about Biobase, which doesn't seem to be a dependency for gridExtra ? A second attempt had an error about a different bioconductor package. I"m not even sure why bioconductor is being used.

Here are the libraries I"m using.
library('shiny')
library('ggplot2')
library('ggpubr')
library('gridExtra')
library('reshape2')
library('rsconnect')
library("vegan")

I've read a similar post and it talked about repos.

getOption("repos")
CRAN
"@CRAN@"
BioCsoft
"https://bioconductor.org/packages/3.8/bioc"
BioC
"https://bioconductor.org/packages/3.8/bioc"

Any help appreciated,

thanks

Below is copied from my deployment log.

>  Deployment log started at  2019-08-20 10:43:54  -----
> Deploy command: 
>  rsconnect::deployApp(appDir = "~/Documents/Professional/Brock/Bidochka_Microbiome/shiny3",      appFileManifest = "/var/folders/x8/c40rtd594gvgp_bzrjt0ljmh0000gq/T/6d26-734e-ec61-1402",      account = "metarhiz-microbiome", server = "shinyapps.io",      appName = "shiny3", launch.browser = function(url) {         message("Deployment completed: ", url)     }, lint = FALSE, metadata = list(asMultiple = FALSE, asStatic = FALSE,          ignoredFiles = "app_test.R"), logLevel = "verbose") 
> 
> Session information: 
> R version 3.5.2 (2018-12-20)
> Platform: x86_64-apple-darwin15.6.0 (64-bit)
> Running under: macOS Mojave 10.14
> 
> Matrix products: default
> BLAS: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRblas.0.dylib
> LAPACK: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRlapack.dylib
> 
> locale:
> [1] en_CA.UTF-8/en_CA.UTF-8/en_CA.UTF-8/C/en_CA.UTF-8/en_CA.UTF-8
> 
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base     
> 
> loaded via a namespace (and not attached):
> [1] compiler_3.5.2   rsconnect_0.8.13
> Cookies: 
> [1] "None"
> GET /v1/applications/810708 361ms
> ----- Bundle upload started at  2019-08-20 10:43:55  -----
> [2019-08-20 10:43:55] Inferring App mode and parameters 
> [2019-08-20 10:43:55] Bundling app dir 
> [2019-08-20 10:43:55] Generate manifest.json 
> [2019-08-20 10:44:09] Writing Rmd index if necessary 
> [2019-08-20 10:44:09] Compressing the bundle 
> POST /v1/bundles 341ms
> [2019-08-20 10:44:12] Starting upload now 
> PUT /bundles/application-810708/13f71d8c7013483da51cf7e1d9963c1f.tar.gz?AWSAccessKeyId=ASIA54P7SCTK2OR32UYU&x-amz-acl=bucket-owner-full-control&Expires=1566315852&content-md5=BexAlI0tMQtDQFi9S0LZ%2FQ%3D%3D&x-amz-security-token=AgoJb3JpZ2luX2VjEAoaCXVzLWVhc3QtMSJGMEQCIDzzcqq%2F8vQTzGOTxuTOfVrAZS8skjMfZlu7Gz%2BsDDlAAiBd44JKB69Ctesd4rOut%2FkB0PTJpYsedmHxD5UjKw5fVSrjAwij%2F%2F%2F%2F%2F%2F%2F%2F%2F%2F8BEAAaDDk1NDU1NTU2OTM2NSIMWonJBJmW40ejTRvyKrcDP2hOYnNIPjm5wqfPlfgWZJafWrvWWmrQY2IlSU6DVHITCXMXNf7GsNH7wttsVWh5Hmpkj5Hq2%2Fg%2B8hYEGg147BkzSL8hiwD9XSK7hPguHliPzrZnTjHXyPMB6xk5nfkubIS1xQPNYY4r5BgVTgrsg9x37zxA61qBySptfKtSoj9NFBQtySiWr5yG3MwgZBXvysOuc8RTAJ%2BbHybgK%2B3BcNQeVzdPzDmLGttjrFpBFo%2FiwpOL88ZZPDPMsEsicgpGT8meVJKs1aIKptj1GXp%2FMosK0iw70%2F03DYNFyz8znUzb8jc%2FK3HDTiV%2B5KwA1tkcl7QP%2BXxCDDRDiokJAejGVR0UTOlZM2qnMWXB6GbnXDChNjDJ4GgUv7%2BBhBnoqmCJyQLTOe7sq8Rh1qJEJTUmeZI6QhhG9NMW5xB%2FWaN5QjY2DsCIdMVRXkyaPSNGoyF%2ByqE5gAi7GeedM1HkmkfkF5WutfhukgIezhT1oZbLenp9B1er2JixXtft1w3HVuIA%2F%2Fsw0wT1aaCTp... <truncated>
> [2019-08-20 10:57:19] Upload complete 
> POST /v1/bundles/2337837/status 403ms
> GET /v1/bundles/2337837 277ms
> [2019-08-20 10:57:20] Saving deployment record for shiny3 -  
> ----- Server deployment started at  2019-08-20 10:57:20  -----
> POST /v1/applications/810708/deploy 422ms
> Waiting for task: 640236284
> GET /v1/tasks/640236284 271ms
> GET /v1/tasks/640236284 273ms
>   building: Parsing manifest
> GET /v1/tasks/640236284 322ms
> GET /v1/tasks/640236284 291ms
> GET /v1/tasks/640236284 372ms
> ################################ Begin Task Log ################################ 
> GET /v1/tasks/640236284/logs/ 459ms
> GET /v1/tasks/?filter=account_id:133495&filter=parent_id:640236284&count=100&offset=0 296ms
> GET /v1/tasks/640236289/logs/ 360ms
> GET /v1/tasks/?filter=account_id:133495&filter=parent_id:640236289&count=100&offset=0 269ms
> ################################# End Task Log ################################# 
> ----- Deployment error -----
> Error: Unhandled Exception: Child Task 640236289 failed: Error parsing manifest: Unable to determine package source for Bioconductor package Biobase: Repository must be specified
> 
> ----- Error stack trace -----
> 3: stop(status$error, call. = FALSE)
> 2: client$waitForTask(taskId, quiet)
> 1: rsconnect::deployApp(appDir = "~/Documents/Professional/Brock/Bidochka_Microbiome/shiny3", 
>        appFileManifest = "/var/folders/x8/c40rtd594gvgp_bzrjt0ljmh0000gq/T/6d26-734e-ec61-1402", 
>        account = "metarhiz-microbiome", server = "shinyapps.io", 
>        appName = "shiny3", launch.browser = function(url) {
>            message("Deployment completed: ", url)
>        }, lint = FALSE, metadata = list(asMultiple = FALSE, asStatic = FALSE, 
>            ignoredFiles = "app_test.R"), logLevel = "verbose")
> Error: Unhandled Exception: Child Task 640236289 failed: Error parsing manifest: Unable to determine package source for Bioconductor package Biobase: Repository must be specified
> Execution halted
> ```

I am replying to myself.
I figured out the problem was because I had added two R scripts to be downloaded from the site.
I saved them at .txt files (although through the Shiny filename I changed it back to .R) and then the app deploys fine.