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

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

Bogaso
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@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.

______________________________________________
[hidden email] 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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Re: load() failed to load .Rdata file in AWS-Ububtu

Eric Berger
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 <
[hidden email]> 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@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.
>
> ______________________________________________
> [hidden email] 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.
>

        [[alternative HTML version deleted]]

______________________________________________
[hidden email] 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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Re: load() failed to load .Rdata file in AWS-Ububtu

Bogaso
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@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 <[hidden email]> 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
> <[hidden email]> 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@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.
>>
>> ______________________________________________
>> [hidden email] 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.
>
>

______________________________________________
[hidden email] 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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Re: load() failed to load .Rdata file in AWS-Ububtu

Eric Berger
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 <
[hidden email]> 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@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$table = renderTable(head(data.frame(1:20, 1:20), 20))
> })
>
> with above setup when I deploy my shiny app I get below error :
>
> 18.221.184.94:3838 says
> The application unexpectedly exited
> Diagnostic information has been dumped to the JavaScript error console.
>
> appreciate any help to get rid of this error.
>
> Thanks for your time.
>
> On Sun, Oct 8, 2017 at 12:39 AM, Eric Berger <[hidden email]>
> wrote:
> > Hi Christofer,
> > The directory /srv/shiny-server would normally be owned by the root user.
> > Your options would seem to be to either (1) bring up the R session as
> root
> > (dangerous)
> > or (2) try copying the file to your local directory and read it from
> there
> > (if allowed).
> > e.g. from the Unix shell:
> >> cd ~   (i.e. cd to your home directory)
> >> cp /srv/shiny-server/Dat.Rdata .   (Note the '.' at the end. This may
> not
> >> work - if not then you can try the following
> >> sudo cp /srv/shiny-server/Dat.Rdata . (if you have sudo privileges -
> only
> >> do this if the former command did not work)
> >> chmod 777 Dat.Rdata  (a bit of overkill - again preface by sudo if it
> does
> >> not work without it)
> >
> > Then in your R session you can do the load from the file in this
> location.
> > R>  load("~/Dat.Rdata")
> >
> > HTH,
> > Eric
> >
> >
> > On Sat, Oct 7, 2017 at 8:54 PM, Christofer Bogaso
> > <[hidden email]> wrote:
> >>
> >> Hi again,
> >>
> >> I hope this is the right place to post my question on running R within
> >> Ubuntu, however if not, any pointer on right distribution list will be
> >> helpful.
> >>
> >> I am currently using R in Ubuntu which is hosted in Amazon - AWS.
> >>
> >> I have a .Rdata file in AWS which I am trying to load in R. Used
> >> following code, however, fails to load showing some permission issue.
> >> However that same .Rdata file is getting loaded perfectly when I try
> >> in my regular iOS.
> >>
> >> Below is my code and corresponding result :
> >>
> >> ubuntu@ip-172-31-23-148:~$ 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.
> >>
> >> ______________________________________________
> >> [hidden email] 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.
> >
> >
>

        [[alternative HTML version deleted]]

______________________________________________
[hidden email] 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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Open this post in threaded view
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Re: load() failed to load .Rdata file in AWS-Ububtu

Bogaso
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 <[hidden email]> 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
> <[hidden email]> 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@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 <[hidden email]>
>> 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
>> > <[hidden email]> 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@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.
>> >>
>> >> ______________________________________________
>> >> [hidden email] 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.
>> >
>> >
>
>

______________________________________________
[hidden email] mailing list -- To UNSUBSCRIBE and more, see
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Re: load() failed to load .Rdata file in AWS-Ububtu

Eric Berger
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 <
[hidden email]> 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 <[hidden email]>
> 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
> > <[hidden email]> 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@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 <[hidden email]>
> >> 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
> >> > <[hidden email]> 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@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.
> >> >>
> >> >> ______________________________________________
> >> >> [hidden email] 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.
> >> >
> >> >
> >
> >
>

        [[alternative HTML version deleted]]

______________________________________________
[hidden email] 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.