how to diagnose a shiny deployment log

From

rsconnect::appDependencies()

I can tell that my app will need 60 packages. Then I counted only 21 of them installed with this Log. What else can I do to diagnose which packages are missing and then insure that they get installed? Thank you.

----- Deployment log started at 2019-06-13 18:45:43 -----
Deploy command:
rsconnect::deployApp(appDir = "C:/Users/xxx/Desktop/funShiny/ddance/ddance", appFileManifest = "C:/Users/micks/AppData/Local/Temp/a331-36bc-f5bb-0830", account = "mharbison", server = "shinyapps.io", appName = "ddance", appId = 980577, launch.browser = function(url) { message("Deployment completed: ", url) }, lint = FALSE, metadata = list(asMultiple = FALSE, asStatic = FALSE), logLevel = "verbose")

Session information:
R version 3.6.0 (2019-04-26)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 17134)

Matrix products: default

locale:
[1] LC_COLLATE=English_United States.1252
[2] LC_CTYPE=English_United States.1252
[3] LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C
[5] LC_TIME=English_United States.1252

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

loaded via a namespace (and not attached):
[1] compiler_3.6.0 rsconnect_0.8.13
Cookies:
[1] "None"
GET /v1/applications/980577 1099ms
----- Bundle upload started at 2019-06-13 18:45:45 -----
[2019-06-13 18:45:45] Inferring App mode and parameters
[2019-06-13 18:45:45] Bundling app dir
[2019-06-13 18:45:45] Generate manifest.json
[2019-06-13 18:45:55] Writing Rmd index if necessary
[2019-06-13 18:45:55] Compressing the bundle
POST /v1/bundles 740ms
<< {
"application": 980577,
"content_type": "application/x-tar",
"content_length": 67446,
"checksum": "36df2b39e316aee84cf07809e016b593"
}
[2019-06-13 18:45:56] Starting upload now
PUT /bundles/application-980577/7ba9205705e94c09bb5be5c6c9f8f2ad.tar.gz?AWSAccessKeyId=...&x-amz-acl=bucket-owner-full-control&Expires=1560480355&content-md5=...&x-amz-security-token=...&content-type=application%2Fx-tar 1890ms
[2019-06-13 18:45:58] Upload complete
POST /v1/bundles/2152541/status 640ms
<< {
"status": "ready"
}
GET /v1/bundles/2152541 630ms
[2019-06-13 18:45:59] Saving deployment record for ddance -
----- Server deployment started at 2019-06-13 18:45:59 -----
POST /v1/applications/980577/deploy 580ms
<< {
"bundle": 2152541
}
Waiting for task: 622274503
GET /v1/tasks/622274503 1670ms
building: Parsing manifest
GET /v1/tasks/622274503 800ms
building: Building image: 2269767
GET /v1/tasks/622274503 550ms
building: Installing system dependencies
GET /v1/tasks/622274503 679ms
GET /v1/tasks/622274503 880ms
building: Installing packages
GET /v1/tasks/622274503 989ms
GET /v1/tasks/622274503 869ms
GET /v1/tasks/622274503 690ms
GET /v1/tasks/622274503 550ms
GET /v1/tasks/622274503 870ms
GET /v1/tasks/622274503 660ms
GET /v1/tasks/622274503 570ms
GET /v1/tasks/622274503 519ms
GET /v1/tasks/622274503 670ms
GET /v1/tasks/622274503 660ms
GET /v1/tasks/622274503 609ms
GET /v1/tasks/622274503 580ms
GET /v1/tasks/622274503 509ms
GET /v1/tasks/622274503 699ms
GET /v1/tasks/622274503 750ms
GET /v1/tasks/622274503 629ms
GET /v1/tasks/622274503 550ms
GET /v1/tasks/622274503 710ms
GET /v1/tasks/622274503 629ms
building: Installing files
GET /v1/tasks/622274503 649ms
GET /v1/tasks/622274503 579ms
GET /v1/tasks/622274503 530ms
building: Pushing image: 2269767
GET /v1/tasks/622274503 550ms
GET /v1/tasks/622274503 709ms
GET /v1/tasks/622274503 989ms
GET /v1/tasks/622274503 1149ms
GET /v1/tasks/622274503 1140ms
GET /v1/tasks/622274503 1119ms
GET /v1/tasks/622274503 680ms
GET /v1/tasks/622274503 609ms
GET /v1/tasks/622274503 619ms
GET /v1/tasks/622274503 769ms
GET /v1/tasks/622274503 569ms
GET /v1/tasks/622274503 690ms
GET /v1/tasks/622274503 849ms
deploying: Starting instances
GET /v1/tasks/622274503 579ms
rollforward: Activating new instances
GET /v1/tasks/622274503 820ms
success: Stopping old instances
----- Deployment log finished at 2019-06-13 18:47:13 -----
Deployment completed: https://mharbison.shinyapps.io/ddance/

Also,

rsconnect::showLogs()
2019-06-13T05:18:25.544211+00:00 shinyapps[975039]:
2019-06-13T05:23:26.032176+00:00 shinyapps[975039]: LANG: en_US.UTF-8
2019-06-13T05:23:26.032201+00:00 shinyapps[975039]: R version: 3.6.0
2019-06-13T05:23:26.032173+00:00 shinyapps[975039]: Server version: 1.7.2-7
2019-06-13T05:23:26.032203+00:00 shinyapps[975039]: shiny version: 1.3.2
2019-06-13T05:23:26.183518+00:00 shinyapps[975039]: Starting R with process ID: '19'
2019-06-13T05:23:26.178435+00:00 shinyapps[975039]: Using jsonlite for JSON processing
2019-06-13T05:23:26.183510+00:00 shinyapps[975039]:
2019-06-13T05:23:26.032466+00:00 shinyapps[975039]: Using pandoc at /opt/connect/ext/pandoc2
2019-06-13T05:23:26.032204+00:00 shinyapps[975039]: httpuv version: 1.5.1
2019-06-13T05:23:26.032205+00:00 shinyapps[975039]: rmarkdown version: NA
2019-06-13T05:23:26.032206+00:00 shinyapps[975039]: knitr version: NA
2019-06-13T05:23:26.032280+00:00 shinyapps[975039]: RJSONIO version: NA
2019-06-13T05:23:26.032277+00:00 shinyapps[975039]: jsonlite version: 1.6
2019-06-13T05:23:26.032282+00:00 shinyapps[975039]: htmltools version: 0.3.6
2019-06-13T05:23:26.421251+00:00 shinyapps[975039]: Warning in fun(libname, pkgname) :
2019-06-13T05:23:26.479637+00:00 shinyapps[975039]:
2019-06-13T05:23:26.421254+00:00 shinyapps[975039]: rgeos: versions of GEOS runtime 3.5.0-CAPI-1.9.0
2019-06-13T05:23:26.479630+00:00 shinyapps[975039]: rgeos version: 0.4-3, (SVN revision 595)
2019-06-13T05:23:26.558292+00:00 shinyapps[975039]: Checking rgeos availability: TRUE
2019-06-13T05:23:26.421256+00:00 shinyapps[975039]: and GEOS at installation 3.5.1-CAPI-1.9.1differ
2019-06-13T05:23:26.479636+00:00 shinyapps[975039]: Polygon checking: TRUE
2019-06-13T05:23:26.479634+00:00 shinyapps[975039]: Linking to sp version: 1.3-1
2019-06-13T05:23:26.640286+00:00 shinyapps[975039]: Listening on http://127.0.0.1:43934
2019-06-13T05:23:26.479633+00:00 shinyapps[975039]: GEOS runtime version: 3.5.0-CAPI-1.9.0
2019-06-13T05:23:26.640283+00:00 shinyapps[975039]:
2019-06-13T19:05:17.639198+00:00 shinyapps[975039]: Server version: 1.7.2-7
2019-06-13T19:05:17.639234+00:00 shinyapps[975039]: LANG: en_US.UTF-8
2019-06-13T19:05:17.639239+00:00 shinyapps[975039]: R version: 3.6.0
2019-06-13T19:05:17.639244+00:00 shinyapps[975039]: shiny version: 1.3.2
2019-06-13T19:05:17.780928+00:00 shinyapps[975039]: Using jsonlite for JSON processing
2019-06-13T19:05:17.639244+00:00 shinyapps[975039]: httpuv version: 1.5.1
2019-06-13T19:05:17.639255+00:00 shinyapps[975039]: rmarkdown version: NA
2019-06-13T19:05:17.786156+00:00 shinyapps[975039]:
2019-06-13T19:05:17.639280+00:00 shinyapps[975039]: RJSONIO version: NA
2019-06-13T19:05:17.639471+00:00 shinyapps[975039]: Using pandoc at /opt/connect/ext/pandoc2
2019-06-13T19:05:17.639288+00:00 shinyapps[975039]: htmltools version: 0.3.6
2019-06-13T19:05:17.639277+00:00 shinyapps[975039]: jsonlite version: 1.6
2019-06-13T19:05:17.639265+00:00 shinyapps[975039]: knitr version: NA
2019-06-13T19:05:17.786157+00:00 shinyapps[975039]: Starting R with process ID: '19'
2019-06-13T19:05:18.019185+00:00 shinyapps[975039]: Warning in fun(libname, pkgname) :
2019-06-13T19:05:18.019189+00:00 shinyapps[975039]: rgeos: versions of GEOS runtime 3.5.0-CAPI-1.9.0
2019-06-13T19:05:18.075610+00:00 shinyapps[975039]: rgeos version: 0.4-3, (SVN revision 595)
2019-06-13T19:05:18.075612+00:00 shinyapps[975039]: GEOS runtime version: 3.5.0-CAPI-1.9.0
2019-06-13T19:05:18.019191+00:00 shinyapps[975039]: and GEOS at installation 3.5.1-CAPI-1.9.1differ
2019-06-13T19:05:18.075614+00:00 shinyapps[975039]: Linking to sp version: 1.3-1
2019-06-13T19:05:18.075616+00:00 shinyapps[975039]:
2019-06-13T19:05:18.241333+00:00 shinyapps[975039]: Listening on http://127.0.0.1:33834
2019-06-13T19:05:18.158185+00:00 shinyapps[975039]: Checking rgeos availability: TRUE
2019-06-13T19:05:18.241331+00:00 shinyapps[975039]:
2019-06-13T19:05:18.075615+00:00 shinyapps[975039]: Polygon checking: TRUE

Finally,

devtools::session_info()

  • Session info ------------------------------------------------------------------------------------------
    setting value
    version R version 3.6.0 (2019-04-26)
    os Windows 10 x64
    system i386, mingw32
    ui Rgui
    language (EN)
    collate English_United States.1252
    ctype English_United States.1252
    tz America/Los_Angeles
    date 2019-06-13

  • Packages ----------------------------------------------------------------------------------------------
    package * version date lib source
    askpass 1.1 2019-01-13 [1] CRAN (R 3.6.0)
    assertthat 0.2.1 2019-03-21 [1] CRAN (R 3.6.0)
    backports 1.1.4 2019-04-10 [1] CRAN (R 3.6.0)
    bitops 1.0-6 2013-08-17 [1] CRAN (R 3.6.0)
    callr 3.2.0 2019-03-15 [1] CRAN (R 3.6.0)
    cli 1.1.0 2019-03-19 [1] CRAN (R 3.6.0)
    crayon 1.3.4 2017-09-16 [1] CRAN (R 3.6.0)
    crosstalk 1.0.0 2016-12-21 [1] CRAN (R 3.6.0)
    desc 1.2.0 2018-05-01 [1] CRAN (R 3.6.0)
    devtools * 2.0.2 2019-04-08 [1] CRAN (R 3.6.0)
    digest 0.6.19 2019-05-20 [1] CRAN (R 3.6.0)
    foreign 0.8-71 2018-07-20 [2] CRAN (R 3.6.0)
    fs 1.3.1 2019-05-06 [1] CRAN (R 3.6.0)
    glue 1.3.1 2019-03-12 [1] CRAN (R 3.6.0)
    htmltools 0.3.6 2017-04-28 [1] CRAN (R 3.6.0)
    htmlwidgets * 1.3 2018-09-30 [1] CRAN (R 3.6.0)
    httpuv 1.5.1 2019-04-05 [1] CRAN (R 3.6.0)
    jsonlite 1.6 2018-12-07 [1] CRAN (R 3.6.0)
    later 0.8.0 2019-02-11 [1] CRAN (R 3.6.0)
    lattice 0.20-38 2018-11-04 [2] CRAN (R 3.6.0)
    leaflet * 2.0.2 2018-08-27 [1] CRAN (R 3.6.0)
    magrittr 1.5 2014-11-22 [1] CRAN (R 3.6.0)
    maptools * 0.9-5 2019-02-18 [1] CRAN (R 3.6.0)
    memoise 1.1.0 2017-04-21 [1] CRAN (R 3.6.0)
    mime 0.6 2018-10-05 [1] CRAN (R 3.6.0)
    openssl 1.4 2019-05-31 [1] CRAN (R 3.6.0)
    packrat 0.5.0 2018-11-14 [1] CRAN (R 3.6.0)
    pkgbuild 1.0.3 2019-03-20 [1] CRAN (R 3.6.0)
    pkgload 1.0.2 2018-10-29 [1] CRAN (R 3.6.0)
    prettyunits 1.0.2 2015-07-13 [1] CRAN (R 3.6.0)
    processx 3.3.1 2019-05-08 [1] CRAN (R 3.6.0)
    promises 1.0.1 2018-04-13 [1] CRAN (R 3.6.0)
    ps 1.3.0 2018-12-21 [1] CRAN (R 3.6.0)
    R6 2.4.0 2019-02-14 [1] CRAN (R 3.6.0)
    Rcpp 1.0.1 2019-03-17 [1] CRAN (R 3.6.0)
    RCurl 1.95-4.12 2019-03-04 [1] CRAN (R 3.6.0)
    remotes 2.0.4 2019-04-10 [1] CRAN (R 3.6.0)
    rgeos * 0.4-3 2019-04-24 [1] CRAN (R 3.6.0)
    rlang 0.3.4 2019-04-07 [1] CRAN (R 3.6.0)
    rprojroot 1.3-2 2018-01-03 [1] CRAN (R 3.6.0)
    rsconnect * 0.8.13 2019-01-10 [1] CRAN (R 3.6.0)
    sessioninfo 1.1.1 2018-11-05 [1] CRAN (R 3.6.0)
    shiny * 1.3.2 2019-04-22 [1] CRAN (R 3.6.0)
    sp * 1.3-1 2018-06-05 [1] CRAN (R 3.6.0)
    usethis * 1.5.0 2019-04-07 [1] CRAN (R 3.6.0)
    withr 2.1.2 2018-03-15 [1] CRAN (R 3.6.0)
    xtable 1.8-4 2019-04-21 [1] CRAN (R 3.6.0)
    yaml 2.2.0 2018-07-25 [1] CRAN (R 3.6.0)

[1] C:/Users/xxx/Documents/R/win-library/3.6
[2] C:/Program Files/R/R-3.6.0/library