title: How can I interpret my error when deploying Shiny site
body: <p>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 words when I preview it from inside RStudio.</p>
  
  <p>The error says something about Biobase, which doesn't seem to be a dependency for gridExtra ?</p>
  
  <p>Any help appreciated,</p>
  
  <p>thanks</p>
  
  <p>Below is copied from my deployment log.</p>
  
  <pre><code>    ----- 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&amp;x-amz-acl=bucket-owner-full-control&amp;Expires=1566315852&amp;content-md5=BexAlI0tMQtDQFi9S0LZ%2FQ%3D%3D&amp;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... &lt;truncated&gt;
  [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&amp;filter=parent_id:640236284&amp;count=100&amp;offset=0 296ms
  GET /v1/tasks/640236289/logs/ 360ms
  GET /v1/tasks/?filter=account_id:133495&amp;filter=parent_id:640236289&amp;count=100&amp;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
  </code></pre>