[R] load() failed to load .Rdata file in AWS-Ububtu

Eric Berger ericjberger at gmail.com
Mon Oct 9 21:29:21 CEST 2017 

Hi Christofer,
A few comments.
1. Your experiment seems to show (I hope) that the issue may not be a shiny
issue.
     If that is the case you can try to do things in a simpler setting,
such as a (non-shiny) R session,
     say from the shell. i.e. start an interactive R session and enter the
load command within that session.
2. Perhaps your RData file contains objects that need some libraries to be
loaded? (Not sure why that would cause a problem but on your local system
you can look at the variables resulting from the load command and see if
any of them require some libraries to be loaded.)
3. I found this reference which gives some useful information about RData
files that might also be helpful:
https://www.r-bloggers.com/safe-loading-of-rdata-files-2/

Good luck,
Eric


On Mon, Oct 9, 2017 at 8:24 PM, Christofer Bogaso <
bogaso.christofer at gmail.com> wrote:

> Hi Eric, thanks for your further pointer.
>
> I have put a line with load() function just as an illustration of a
> bigger project of mine, which appears failing due to load() function
> issue.
>
> If I comment out that line my shiny app is working correctly locally
> and globally.
>
> otherwise, locally my shiny app is working but not with AWS.
>
> On Mon, Oct 9, 2017 at 12:37 PM, Eric Berger <ericjberger at gmail.com>
> wrote:
> > Hi Christofer,
> > The shiny code you have written does not depend on loading the Dat.RData
> > file.
> > I commented out that line and ran your shiny app on my machine and it
> works
> > fine.
> > What happens if you comment out  (or remove) the line
> >      load("/home/ubuntu/Dat.RData)
> > Does your shiny app still fail? If so, then your problem is quite basic
> with
> > your  AWS setup.
> > Try to work through a simple tutorial/documentation example that shows
> how
> > to get shiny running on AWS and see if following the steps helps you
> > discover the problem.
> >
> > Good luck,
> > Eric
> >
> >
> >
> >
> > On Sun, Oct 8, 2017 at 8:05 PM, Christofer Bogaso
> > <bogaso.christofer at gmail.com> wrote:
> >>
> >> Thanks Eric for your pointer. However I just altered the argument of
> >> load() function a little bit to get that loaded. Below is the line
> >> what I tried.
> >>
> >> ubuntu at ip-172-31-23-148:~$ R
> >>
> >>
> >> R version 3.4.2 (2017-09-28) -- "Short Summer"
> >>
> >> Copyright (C) 2017 The R Foundation for Statistical Computing
> >>
> >> Platform: x86_64-pc-linux-gnu (64-bit)
> >>
> >>
> >> R is free software and comes with ABSOLUTELY NO WARRANTY.
> >>
> >> You are welcome to redistribute it under certain conditions.
> >>
> >> Type 'license()' or 'licence()' for distribution details.
> >>
> >>
> >>   Natural language support but running in an English locale
> >>
> >>
> >> R is a collaborative project with many contributors.
> >>
> >> Type 'contributors()' for more information and
> >>
> >> 'citation()' on how to cite R or R packages in publications.
> >>
> >>
> >> Type 'demo()' for some demos, 'help()' for on-line help, or
> >>
> >> 'help.start()' for an HTML browser interface to help.
> >>
> >> Type 'q()' to quit R.
> >>
> >>
> >> During startup - Warning message:
> >>
> >> Setting LC_CTYPE failed, using "C"
> >>
> >> > load("/home/ubuntu/Dat.RData")
> >>
> >> >
> >>
> >> However it still failing when I try that within my shiny app in AWS.
> >>
> >> Below are my ui.R and server.R files respectively.
> >>
> >> library(shiny)
> >>
> >> # Define UI for miles per gallon application
> >> fluidPage(
> >>       fluidRow(
> >>         column(12,
> >>           tableOutput('table')
> >>         )
> >>       )
> >>     )
> >>
> >> server.R :
> >>
> >> library(shiny)
> >>
> >> load("/home/ubuntu/Dat.RData")
> >>
> >> shinyServer(function(input, output) {
> >> output$table = renderTable(head(data.frame(1:20, 1:20), 20))
> >> })
> >>
> >> with above setup when I deploy my shiny app I get below error :
> >>
> >> 18.221.184.94:3838 says
> >> The application unexpectedly exited
> >> Diagnostic information has been dumped to the JavaScript error console.
> >>
> >> appreciate any help to get rid of this error.
> >>
> >> Thanks for your time.
> >>
> >> On Sun, Oct 8, 2017 at 12:39 AM, Eric Berger <ericjberger at gmail.com>
> >> wrote:
> >> > Hi Christofer,
> >> > The directory /srv/shiny-server would normally be owned by the root
> >> > user.
> >> > Your options would seem to be to either (1) bring up the R session as
> >> > root
> >> > (dangerous)
> >> > or (2) try copying the file to your local directory and read it from
> >> > there
> >> > (if allowed).
> >> > e.g. from the Unix shell:
> >> >> cd ~   (i.e. cd to your home directory)
> >> >> cp /srv/shiny-server/Dat.Rdata .   (Note the '.' at the end. This may
> >> >> not
> >> >> work - if not then you can try the following
> >> >> sudo cp /srv/shiny-server/Dat.Rdata . (if you have sudo privileges -
> >> >> only
> >> >> do this if the former command did not work)
> >> >> chmod 777 Dat.Rdata  (a bit of overkill - again preface by sudo if it
> >> >> does
> >> >> not work without it)
> >> >
> >> > Then in your R session you can do the load from the file in this
> >> > location.
> >> > R>  load("~/Dat.Rdata")
> >> >
> >> > HTH,
> >> > Eric
> >> >
> >> >
> >> > On Sat, Oct 7, 2017 at 8:54 PM, Christofer Bogaso
> >> > <bogaso.christofer at gmail.com> wrote:
> >> >>
> >> >> Hi again,
> >> >>
> >> >> I hope this is the right place to post my question on running R
> within
> >> >> Ubuntu, however if not, any pointer on right distribution list will
> be
> >> >> helpful.
> >> >>
> >> >> I am currently using R in Ubuntu which is hosted in Amazon - AWS.
> >> >>
> >> >> I have a .Rdata file in AWS which I am trying to load in R. Used
> >> >> following code, however, fails to load showing some permission issue.
> >> >> However that same .Rdata file is getting loaded perfectly when I try
> >> >> in my regular iOS.
> >> >>
> >> >> Below is my code and corresponding result :
> >> >>
> >> >> ubuntu at ip-172-31-23-148:~$ R
> >> >>
> >> >>
> >> >> R version 3.4.2 (2017-09-28) -- "Short Summer"
> >> >>
> >> >> Copyright (C) 2017 The R Foundation for Statistical Computing
> >> >>
> >> >> Platform: x86_64-pc-linux-gnu (64-bit)
> >> >>
> >> >>
> >> >> R is free software and comes with ABSOLUTELY NO WARRANTY.
> >> >>
> >> >> You are welcome to redistribute it under certain conditions.
> >> >>
> >> >> Type 'license()' or 'licence()' for distribution details.
> >> >>
> >> >>
> >> >>   Natural language support but running in an English locale
> >> >>
> >> >>
> >> >> R is a collaborative project with many contributors.
> >> >>
> >> >> Type 'contributors()' for more information and
> >> >>
> >> >> 'citation()' on how to cite R or R packages in publications.
> >> >>
> >> >>
> >> >> Type 'demo()' for some demos, 'help()' for on-line help, or
> >> >>
> >> >> 'help.start()' for an HTML browser interface to help.
> >> >>
> >> >> Type 'q()' to quit R.
> >> >>
> >> >>
> >> >> During startup - Warning message:
> >> >>
> >> >> Setting LC_CTYPE failed, using "C"
> >> >>
> >> >> > file.exists('/srv/shiny-server/Dat.Rdata')
> >> >>
> >> >> [1] TRUE
> >> >>
> >> >> > load('/srv/shiny-server/Dat.Rdata')
> >> >>
> >> >> Error in readChar(con, 5L, useBytes = TRUE) : cannot open the
> >> >> connection
> >> >>
> >> >> In addition: Warning message:
> >> >>
> >> >> In readChar(con, 5L, useBytes = TRUE) :
> >> >>
> >> >>   cannot open compressed file '/srv/shiny-server/Dat.Rdata', probable
> >> >> reason 'Permission denied'
> >> >>
> >> >> > readRDS('/srv/shiny-server/Dat.Rdata')
> >> >>
> >> >> Error in gzfile(file, "rb") : cannot open the connection
> >> >>
> >> >> In addition: Warning message:
> >> >>
> >> >> In gzfile(file, "rb") :
> >> >>
> >> >>   cannot open compressed file '/srv/shiny-server/Dat.Rdata', probable
> >> >> reason 'Permission denied'
> >> >>
> >> >>
> >> >> Can someone help me to understand where it went wrong with Ubuntu? I
> >> >> also tried with changing the extension from .Rdata to .RData, however
> >> >> observing the same error.
> >> >>
> >> >> Any pointer will be highly appreciated.
> >> >>
> >> >> Thanks for your time.
> >> >>
> >> >> ______________________________________________
> >> >> R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see
> >> >> https://stat.ethz.ch/mailman/listinfo/r-help
> >> >> PLEASE do read the posting guide
> >> >> http://www.R-project.org/posting-guide.html
> >> >> and provide commented, minimal, self-contained, reproducible code.
> >> >
> >> >
> >
> >
>

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