Can't deploy my app, Error in install.packages() 'lib = "/usr/lib/R/library"' is not writable

[Nikolay Braykov]

> shinyapps::deployApp('/Users/nbraykov/Google Drive/SYNC w HOME/Grad Skool/Pronaca rotation/pronaca/data/R files/Shiny EDA to load/',appName="ShinyPronacaEDA")

The following potential problems were identified in the project files:

---------------

my.ggparallel.R

---------------

The following lines contain absolute paths:

173:   label.stats$labels <- gsub(sprintf("(%s):(.*)", varnames), "\\2", as.character(label.stats$Nodeset))

--------

server.R

--------

The following lines contain absolute paths:

6: install.packages(c('lme4','car','MASS', 'scales', 'mixtools','arm','plyr', 'ggparallel','RColorBrewer', 'vegan','grid','gridExtra', 'sjPlot', 'MuMIn'),repos="http://cran.rstudio.com" ,lib="/usr/lib/R/library")

Paths should be to files within the project directory.

Do you want to proceed with deployment? [Y/n]: Y

Preparing to deploy application...

Update application currently deployed at

http://nbrayko.shinyapps.io/ShinyPronacaEDA? [Y/n] Y

DONE

Uploading application bundle...DONE

Deploying application: 33692...

Waiting for task: 14522919

  building: Parsing manifest

  building: Installing packages

  building: Installing files

  building: Pushing image: 138181

  deploying: Starting instances

  rollforward: Activating new instances

  terminating: Stopping old instances

Application successfully deployed to http://nbrayko.shinyapps.io/ShinyPronacaEDA

> shinyapps::showLogs()

2015-03-03T19:47:10.241624+00:00 shinyapps[33692]: R version: 3.1.0

2015-03-03T19:47:10.242933+00:00 shinyapps[33692]: rmarkdown version: 0.0.0

2015-03-03T19:47:10.241692+00:00 shinyapps[33692]: Shiny version: 0.10.2.1

2015-03-03T19:47:10.243431+00:00 shinyapps[33692]: knitr version: 0.0.0

2015-03-03T19:47:10.540198+00:00 shinyapps[33692]: 

2015-03-03T19:47:10.540203+00:00 shinyapps[33692]: Starting Shiny with process ID: '12'

2015-03-03T19:47:10.547275+00:00 shinyapps[33692]: 

2015-03-03T19:47:10.547277+00:00 shinyapps[33692]: Listening on http://0.0.0.0:55076

2015-03-03T19:47:18.418733+00:00 shinyapps[33692]: R version: 3.1.0

2015-03-03T19:47:18.419937+00:00 shinyapps[33692]: rmarkdown version: 0.0.0

2015-03-03T19:47:18.418781+00:00 shinyapps[33692]: Shiny version: 0.10.2.1

2015-03-03T19:47:18.420357+00:00 shinyapps[33692]: knitr version: 0.0.0

2015-03-03T19:47:18.706515+00:00 shinyapps[33692]: 

2015-03-03T19:47:18.706517+00:00 shinyapps[33692]: Starting Shiny with process ID: '25'

2015-03-03T19:47:18.712620+00:00 shinyapps[33692]: 

2015-03-03T19:47:18.712622+00:00 shinyapps[33692]: Listening on http://0.0.0.0:36125

2015-03-03T19:47:21.262792+00:00 shinyapps[33692]: [1] "/usr/local/lib/R/site-library" "/usr/lib/R/site-library"      

2015-03-03T19:47:21.262796+00:00 shinyapps[33692]: [3] "/usr/lib/R/library"           

2015-03-03T19:47:21.264819+00:00 shinyapps[33692]: Warning in install.packages(c("lme4", "car", "MASS", "scales", "mixtools",  :

2015-03-03T19:47:21.264821+00:00 shinyapps[33692]:   'lib = "/usr/lib/R/library"' is not writable

2015-03-03T19:47:21.265246+00:00 shinyapps[33692]: Error in install.packages(c("lme4", "car", "MASS", "scales", "mixtools",  : 

2015-03-03T19:47:21.265248+00:00 shinyapps[33692]:   unable to install packages

Why is the shiny server not installing my packages? 

[Andy Kipp]

Hi,

Shinyapps.io detects and installs packages for you automatically when you call deployApp(). You do not need, nor should have any calls to install.packages() anywhere in your source code.

-Andy

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[Nikolay Braykov]

thank you Andy, I think i figured out what's wrong. 

I put the install.packages only after using the code below failed, so I thought I needed to tell the server to install. Turns out the lapply + required trick is what was failing me. I need to call each package one by one with "library" in order for shinyapps to fetch them. 

 libs <- c('lme4','car','MASS', 'scales', 'mixtools','arm','plyr', 'ggparallel','RColorBrewer', 'vegan','grid','gridExtra', 'sjPlot', 'MuMIn')
 lapply(libs, require, character.only = T)

[Andy Kipp]

You are correct. The shinyapps.io dependency detector works by looking for library() and require() as well as double/triple colon function calls. Unfortunately it is not sophisticated enough to understand lapply.

Cheers

-Andy

To view this discussion on the web visit https://groups.google.com/d/msgid/shinyapps-users/a999105c-2ef5-40cd-a36d-7a947d7538bf%40googlegroups.com.

[Felipe Andres Concha Sepúlveda]

Thanks good i fix it!!

[Felipe Andres Concha Sepúlveda]

Thanks Andy!!!