Multiple issues with deploying Shiny app

[Dina Jankovic]

I have coded an App in Shiny and I am trying to deploy it to shinyapp.io. It is the the first time I am deploying an app and I am encountering a number of issues. Ultimately the error messages are

    Warning: unable to access index for repository /src/contrib:

        unsupported URL scheme

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

        - "RSVGTipsDevice", "Sxslt", "devtools"

    Warning: In value[[3L]](cond) :

        Failed to parse C:/.../AppData/Local/Temp/Rtmpoj4mKO/file113c6c947958/RCurl/examples/CIS/cis.R ; dependencies in this file will not be discovered.

    Warning: In fileDependencies.R(tempfile) :

        No file at path 'C:\....\AppData\Local\Temp\Rtmpoj4mKO\file113c1ac64dbd'. (for many differentnumbers in the last part of the path).

    Warning: In readLines(file) :

        incomplete final line found on 'C:/Users/dj657/AppData/Local/Temp/Rtmpoj4mKO/file113c6c947958/knitr/examples/child/knitr-main.Rnw'

    Warning: In FUN(X[[i]], ...) : Package 'RCurl' not available in repository or locally (for many different packages, all of which are available).

With regards to the error message, RSVGTipsDevice package is no longer available. Can I use rsvg instead? If so, how can I convince R that this is the case?

Installing package Sxslt requires installing  'libxslt-dev on your linux machine' - I do not know what this means.

Why am I getting the message that the package is not available in repository or locally??

What do the other warning messages mean?

Any help would be really appreciated!

[Joshua Spiewak]

Does your shiny application run properly locally?

libxslt-dev is a package that Sxslt requires be installed, apparently. I cannot find Sxslt on CRAN to read its documentation, from where are you obtaining it? In general, if one finds that dependencies for packages are not present on shinyapps.io, one should create an issue on the shinyapps-package-dependencies GitHub project, and preferably contribute a pull request with the install script and test per contributing instructions.

How have you installed your other packages? What is the output of devtools::session_info() and rsconnect::appDependencies() ?

If the warnings that include paths to files that start with "C:\" appear during your deployment, please know that all paths in code you deploy must be relative paths and that shinyapps.io runs on Ubuntu 14.04, so Windows paths will not work.

[Dina Jankovic]

Thank you for the quick response!

The application runs perfectly when ran locally, yes.

I have since fiddled with a couple of things and reduced the number of warning messages. I now get the following:

Error in eval(expr, envir, enclos) : object 'dothis' not found

I am not sure what this is refering to, there is no 'dothis' anywhere in my code.

I also get the following warning message:

In value[[3L]](cond) :
Failed to parse

C:/Users/.../AppData/Local/Temp/RtmpSkJz4V/file21bc16a75ff/RCurl/examples/CIS/cis.R

; dependencies in this file will not be discovered.

This is the case for 9 different C:/ paths, all for RCurl and RGtk2 packages. I understand from your reply that all paths in code I deploy must be relative paths, but I am not sure how to change it. I have not specified the above ('C/Users/...) anywhere in my code. I am not sure where they come from.

When I try to parse manually (as advised on an R forum) I get the following error message

Error in
parse("C:/Users/dj657/AppData/Local/Temp/RtmpSkJz4V/file21bc16a75ff/RCurl/examples/CIS/cis.R")
:

C:/Users/dj657/AppData/Local/Temp/RtmpSkJz4V/file21bc16a75ff/RCurl/examples/CIS/cis.R:4:10:
unexpected symbol
3:
4: scis <- "http

I am not sure what this means though, the forums I have looked at haven't been much help.

Another warning message I get is

1: In FUN(X[[i]], ...) :

  Package 'Sxslt' not available in repository or locally

for all non-CRAN packages. I am trying to install Sxslt using install_github("omegahat/Sxslt") . The error message I get is 

'Downloading GitHub repo omegahat/Sxslt@master

from URL https://api.github.com/repos/omegahat/Sxslt/zipball/master

Error in utils::download.file("/bin/windows/Rtools/Rtools33.exe", "C:/Users/dj657/AppData/Local/Temp/7a71-fae1-8a9e-dcb7/Rtools33.exe",  : 

  unsupported URL scheme

Error: Could not find build tools necessary to build Sxslt'

When I run devtools::session_info() I get

Error in desc$Priority : $ operator is invalid for atomic vectors

In addition: Warning message:

In packageDescription(pkg) :

  DESCRIPTION file of package 'cluster' is missing or broken

When I run rsconnect::appDependencies() I get

Error in eval(expr, envir, enclos) : object 'dothis' not found

In addition: Warning messages:

1: In value[[3L]](cond) :

  Failed to parse C:/Users/dj657/AppData/Local/Temp/RtmpsBm6mn/file3fdc71d5625a/RCurl/examples/CIS/cis.R ; dependencies in this file will not be discovered.

2: In value[[3L]](cond) :

  Failed to parse C:/Users/dj657/AppData/Local/Temp/RtmpsBm6mn/file3fdc71d5625a/RGtk2/examples/GAsyncResult.R ; dependencies in this file will not be discovered.

3: In value[[3L]](cond) :

  Failed to parse C:/Users/dj657/AppData/Local/Temp/RtmpsBm6mn/file3fdc71d5625a/RGtk2/examples/GSocketConnectable.R ; dependencies in this file will not be discovered.

4: In value[[3L]](cond) :

  Failed to parse C:/Users/dj657/AppData/Local/Temp/RtmpsBm6mn/file3fdc71d5625a/RGtk2/examples/GtkDialog-4.R ; dependencies in this file will not be discovered.

5: In value[[3L]](cond) :

  Failed to parse C:/Users/dj657/AppData/Local/Temp/RtmpsBm6mn/file3fdc71d5625a/RGtk2/examples/GtkDrawingArea.R ; dependencies in this file will not be discovered.

6: In value[[3L]](cond) :

  Failed to parse C:/Users/dj657/AppData/Local/Temp/RtmpsBm6mn/file3fdc71d5625a/RGtk2/examples/GtkExpander.R ; dependencies in this file will not be discovered.

7: In value[[3L]](cond) :

  Failed to parse C:/Users/dj657/AppData/Local/Temp/RtmpsBm6mn/file3fdc71d5625a/RGtk2/examples/GtkRecentManager-2.R ; dependencies in this file will not be discovered.

8: In value[[3L]](cond) :

  Failed to parse C:/Users/dj657/AppData/Local/Temp/RtmpsBm6mn/file3fdc71d5625a/RGtk2/examples/cairo-version-info-3.R ; dependencies in this file will not be discovered.

9: In value[[3L]](cond) :

  Failed to parse C:/Users/dj657/AppData/Local/Temp/RtmpsBm6mn/file3fdc71d5625a/RGtk2/examples/gtk-High-level-Printing-API-3.R ; dependencies in this file will not be discovered.

10: In readLines(file) :

  incomplete final line found on 'C:/Users/dj657/AppData/Local/Temp/RtmpsBm6mn/file3fdc71d5625a/knitr/examples/child/knitr-main.Rnw'

Error in eval(expr, envir, enclos) : object 'dothis' not found

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

- "ALL", "Sxslt", "foreign", "hgu95av2"

In addition: Warning messages:

1: In FUN(X[[i]], ...) :

  Package 'Sxslt' not available in repository or locally

2: In FUN(X[[i]], ...) :

  Package 'multtest' not available in repository or locally

3: In FUN(X[[i]], ...) :

  Package 'ALL' not available in repository or locally

4: In FUN(X[[i]], ...) :

  Package 'hgu95av2' not available in repository or locally

5: In read.dcf(file.path(p, "DESCRIPTION"), c("Package", "Version")) :

  cannot open compressed file '\\userfs/dj657/w2k/R/R-3.2.5/library/cluster/DESCRIPTION', probable reason 'No such file or directory'

> 

This is pretty much the same error I get when I try to deploy.

Apologies if the answer is obvious, I have no computer expertise.... Help would be really appreciated!

[Joshua Spiewak]

Hi Dina,

Sorry you are having such troubles.

Given the number of local errors you are experiencing, I suspect you might have a corrupted or otherwise incorrect installation of either R or RStudio IDE, which I am really not equipped to help sort out. You could try purging all the local packages or completely reinstalling and see if that helps.

If you end up getting past these and are then still having difficulties deploying to shinyapps.io, please post a follow up.