deployApp failure with private/organization GitHub repo as dependency

[ja...@prismfp.com]

Hi there,

I am trying to deploy our Shiny app to ShinyApps.io._ One of the dependencies of the app is a GitHub project which is a private repo belonging to our organization. Since the repo belongs to the organization and not a user it seems we might have to do things slightly differently than what is recommended in the guide: https://support.rstudio.com/hc/en-us/articles/204536558-Enabling-use-of-private-packages-on-github-com

When I try to install the package locally, as expected it doesn't work without authenticating:

> install_github("mycompany/my-package", subdir="packagex")
Downloading github repo prismfp/prismfp-package@master
Error in download(dest, src, auth) : client error: (404) Not Found

If I try to authenticate using a password (using my personal GH account), it still fails:
> install_github("mycompany/my-package", auth_user="myname", password="trustno1", subdir="packagex")
Downloading github repo prismfp/prismfp-package@master
Error in download(dest, src, auth) : client error: (404) Not Found

I generated an authentication token for my personal account on GitHub, and used this to install instead of the password:

> install_github("mycompany/my-package", subdir="packagex", auth_token="15efaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa414a")
Downloading github repo mycompany/prismfp-package@master
Installing packagex 
...

This seemed to work fine. I had the line library("packagex") in my code, and I hoped for the package to be automatically installed on deploy. However I got the error message:

> shinyapps::deployApp('.')
Preparing to deploy application...DONE
Uploading application bundle...DONE
Deploying application: 41756...
Waiting for task: 32072061
  building: Parsing manifest
  building: Building image: 179292
  building: Building package: packagex
################################## Begin Log ################################## 
################################### End Log ################################### 
Error: Unhandled Exception: Child Task 32072062 failed: Error building image: Error fetching packagex (0.23.0) source. Error accessing GitHub repository mycompany/my-package. HTTP 404: Not Found
I added my personal GitHub account 'myname' to 'GitHub authentication' in the ShinyApps.io dashboard, and ticked 'Private Repository Access'. However I still saw the same message as above when trying to deploy.

I think that possibly shinyapps::deployApp() makes some assumption when installing packages that the first part of the repo identifier (here the organization name 'mycompany') is the same as the user name (here 'myname') and that the installation fails if this is not the case. Am I doing something else wrong or can this problem be fixed or worked around? 

Thanks in advance for your help,
Jack Grahl

[Andy Kipp]

Jack,

Can you send over:

packageDescription('yourpackage')

Also, can you validate that shinyapps.io has access to your GitHub organization? You can check this by going to GitHub settings and going to the 'Applications' page. You should see shinyapps.io, click that, and send over a screenshot of the page (see attached for what it should look like).

Thanks

-Andy

--
You received this message because you are subscribed to the Google Groups "ShinyApps Users" group.
To unsubscribe from this group and stop receiving emails from it, send an email to shinyapps-use...@googlegroups.com.
To post to this group, send email to shinyap...@googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/shinyapps-users/58219b7b-1c5c-43fb-be2a-c00909e82f64%40googlegroups.com.
For more options, visit https://groups.google.com/d/optout.

[Juan]

Hi

I am actually loading the packages from a private organization.

First, make sure you install the packages with the auth token.  

install_github("mycompany/my-package", subdir="packagex", auth_token="15efaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa414a")

Second,

Make sure to tick the organization access when you authorize github on shinyapps.io. Make sure the Check mark is GREEN for the desired organization. I was having the same issue until I realized that the organization chek mark was not green.

That should do it, cheers

[Andy Kipp]

Juan is correct. Within an GitHub organization's settings page, there is a setting for "3rd party access". 3rd party access needs to be enabled with no restrictions to allow the organization's member's authorized GiHub applications (e.g shinyapps.io) to access not only the users's repositories, but the organization's content as well.

-Andy

--
You received this message because you are subscribed to the Google Groups "ShinyApps Users" group.
To unsubscribe from this group and stop receiving emails from it, send an email to shinyapps-use...@googlegroups.com.
To post to this group, send email to shinyap...@googlegroups.com.

To view this discussion on the web visit https://groups.google.com/d/msgid/shinyapps-users/3ef5d8c5-8dd7-4c7e-b538-21507072c5af%40googlegroups.com.

[ja...@prismfp.com]

Thanks very much for this Juan,

I went through enabling the app again using your instructions, and it seems to be working this time, although I'm not sure what I did wrong the first time.

[Alex Whitworth]

I'm having the same problem:

R> rsconnect::deployApp(".")

Preparing to deploy application...

Uploading bundle for application: 99578...

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

- "callProjection"

"callProjection" is a private package internal to my organization. I have linked/enabled my github account. I'm checking with my IT staff to ensure that 3rd party access is allowed to the organization's repos. 

While waiting on that confirmation, is there anything that I need in my server.R file?

For instance, is this fine?

library(callProjection)

........

or do I also need to install the package in the server.R file?

devtools::install_github("<my org folder>", ref= "call_projection",

                          subdir= "callProjection",

                         auth_token= "<my auth token>")

[Joshua Spiewak]

Hi Alex,

You need to use devtools::install_github in order to use a package from GitHub

--
You received this message because you are subscribed to the Google Groups "ShinyApps Users" group.
To unsubscribe from this group and stop receiving emails from it, send an email to shinyapps-use...@googlegroups.com.
To post to this group, send email to shinyap...@googlegroups.com.

To view this discussion on the web visit https://groups.google.com/d/msgid/shinyapps-users/c5b931e0-07b1-4210-b95b-5ab173492886%40googlegroups.com.

For more options, visit https://groups.google.com/d/optout.

--

    -- Josh

[Tareef Kawaf]

After you install_github() you should try deploying again.  the rsconnect package will detect the dependencies at deploy time and push them up to the server.  Please do not put an explicit install call in either the server.R or ui.R files, that will definitely not work.

To view this discussion on the web visit https://groups.google.com/d/msgid/shinyapps-users/CA%2Bk%3DytksLWXZfhTYf3%2B0kuDPhT-YqQZxH7JyeC_q_aop%3DKc1tQ%40mail.gmail.com.

[Alex Whitworth]

Forgive my confusion Tareef / Joshua, but I'm unclear on your suggestions. 

The package is installed on the machine and R instance from which I'm running [rsconnect::deployApp(".")]. If not in my server.R or ui.R files, where do I put the "install_github" command? 

Alex Whitworth
whitwor...@gmail.com
(c) 828.429.7478

[Tareef Kawaf]

Hi Alex,

All Josh and I were saying was that if you have a private package that is in github, you should install it locally using devtools::install_github().  If you could do me a favor and checkout the output of rsconnect::appDependencies() within the directory that you are in, it would be good to see if your package shows up in the list or not.

-Tareef

[Alex Whitworth]

Thanks--the package is installed locally. Here is the requested output:

> rsconnect::appDependencies(".")

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

- "callProjection"

> rsconnect::deployApp(".")

Preparing to deploy application...DONE

Uploading bundle for application: 99676...

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

- "callProjection"

Alex Whitworth
whitwor...@gmail.com
(c) 828.429.7478

[Alex Whitworth]

That appears to have been what the problem was... It needed a fresh install from github to recognize correctly. (Note: I would guess that the most recent install of 'callProjection' was from local, not direct from Github. Not sure if that caused the problem. Are you?)

> devtools::install_github(... redacted...)

Downloading GitHub repo dandb/data-analysis@call_projection

from URL https://api.github.com/repos/dandb/data-analysis/zipball/call_projection

Installing callProjection

"C:/PROGRA~1/R/R-32~1.5/bin/x64/R" --no-site-file --no-environ --no-save --no-restore --quiet CMD INSTALL  \

  "C:/Users/awhitworth/AppData/Local/Temp/RtmpgBJFfa/devtoolsa07462474299/dandb-data-analysis-a60907d11b086d74ca72d67815448d4343c635ab/callProjection"  \

  --library="C:/Users/awhitworth/Documents/R/win-library/3.2" --install-tests 

* installing *source* package 'callProjection' ...

** R

** preparing package for lazy loading

** help

*** installing help indices

** building package indices

** testing if installed package can be loaded

*** arch - i386

*** arch - x64

* DONE (callProjection)

Warning message:

GitHub repo contains submodules, may not function as expected! 

> rsconnect::appDependencies(".")

          package     version source

1            MASS      7.3-45   CRAN

2              R6       2.1.2   CRAN

3    RColorBrewer       1.1-2   CRAN

4           RODBC      1.3-13   CRAN

5            Rcpp      0.12.4   CRAN

6   RcppArmadillo 0.6.700.3.0   CRAN

7  callProjection       0.4.7 github

8           chron      2.3-47   CRAN

9      colorspace       1.2-6   CRAN

10     data.table       1.9.6   CRAN

11      dichromat       2.0-0   CRAN

12         digest       0.6.9   CRAN

13       forecast         7.1   CRAN

14       fracdiff       1.4-2   CRAN

15        ggplot2       2.1.0   CRAN

16         gtable       0.2.0   CRAN

17      htmltools       0.3.5   CRAN

18         httpuv       1.3.3   CRAN

19       jsonlite      0.9.19   CRAN

20       labeling         0.3   CRAN

21        lattice     0.20-33   CRAN

22      lubridate       1.5.6   CRAN

23       magrittr         1.5   CRAN

24           mime         0.4   CRAN

25        munsell       0.4.3   CRAN

26           nnet      7.3-12   CRAN

27        packrat     0.4.7-1   CRAN

28           plyr       1.8.3   CRAN

29       quadprog       1.5-5   CRAN

30       reshape2       1.4.1   CRAN

31         scales       0.4.0   CRAN

32          shiny      0.13.2   CRAN

33        stringi       1.0-1   CRAN

34        stringr       1.0.0   CRAN

35       timeDate    3012.100   CRAN

36        tseries     0.10-34   CRAN

37         xtable       1.8-2   CRAN

38            zoo      1.7-12   CRAN

> rsconnect::deployApp(".")

Preparing to deploy application...

Update application currently deployed at

https://dunbradstreetmalibu.shinyapps.io/forecasts_shiny/? [Y/n] Y

DONE

Uploading bundle for application: 99676...

Detecting system locale ... en_US

DONE

Deploying bundle: 440713 for application: 99676 ...

Waiting for task: 181195350

  building: Parsing manifest

  building: Building image: 433024

  building: Installing system dependencies

  building: Fetching packages

  building: Building package: callProjection

  building: Installing packages

  building: Pushing image: 433024

  deploying: Starting instances

  rollforward: Activating new instances

  success: Stopping old instances

Application successfully deployed to https://....

On Tue, May 3, 2016 at 10:40 AM, Tareef Kawaf <tar...@rstudio.com> wrote:

Could you run the devtools::install_github() call again and capture the output, along with the output of appDependencies()?

Also, can you please send me the output of devtools::session_info()?

-Tareef

[Tareef Kawaf]

Yep, my guess was that the package was installed earlier, or perhaps with an old version of devtools.  I am glad everything is working right now.