[R] read.csv fails in R console in Ubuntu terminal but works in RStudio after R 3.6.3 upgrade to R 4.0.2?

[Rui Barradas]

Hello,

R 4.0.2 on Ubuntu 20.04 LTS, sessionInfo below.

I'm also unable to read the file with Rscript from the Ubuntu terminal 
but the error is not the same as the OP's.


The first try was a file test1.R with the following commands.

x<-"https://old.nasdaq.com/screening/companies-by-name.aspx?letter=0&exchange=1&render=download"
read.csv(x, as.is=TRUE, na="n/a")


And run with Rscript

rui using rui:~$ Rscript --vanilla test1.R
Error in file(file, "rt") :
   cannot open the connection to 
'https://old.nasdaq.com/screening/companies-by-name.aspx?letter=0&exchange=1&render=download'
Calls: read.csv -> read.table -> file
In addition: Warning message:
In file(file, "rt") :
   cannot open URL 
'https://old.nasdaq.com/screening/companies-by-name.aspx?letter=0&exchange=1&render=download': 
HTTP status was '403 Forbidden'
Execution halted



The second try was download.file() and then read it.
File test2.R is:

x<-"https://old.nasdaq.com/screening/companies-by-name.aspx?letter=0&exchange=1&render=download"
download.file(x, "companylist.csv")
read.csv("companylist.csv", as.is=TRUE, na="n/a")


But this too failed with error 403 Forbiden.

rui using rui:~$ Rscript --vanilla test2.R
trying URL 
'https://old.nasdaq.com/screening/companies-by-name.aspx?letter=0&exchange=1&render=download'
Error in download.file(x, "companylist.csv") :
   cannot open URL 
'https://old.nasdaq.com/screening/companies-by-name.aspx?letter=0&exchange=1&render=download'
In addition: Warning message:
In download.file(x, "companylist.csv") :
   cannot open URL 
'https://old.nasdaq.com/screening/companies-by-name.aspx?letter=0&exchange=1&render=download': 
HTTP status was '403 Forbidden'
Execution halted


This is my session info.

rui using rui:~$ Rscript --vanilla -e 'sessionInfo()'
R version 4.0.2 (2020-06-22)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 20.04 LTS

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.9.0
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.9.0

locale:
  [1] LC_CTYPE=pt_PT.UTF-8       LC_NUMERIC=C
  [3] LC_TIME=pt_PT.UTF-8        LC_COLLATE=pt_PT.UTF-8
  [5] LC_MONETARY=pt_PT.UTF-8    LC_MESSAGES=pt_PT.UTF-8
  [7] LC_PAPER=pt_PT.UTF-8       LC_NAME=C
  [9] LC_ADDRESS=C               LC_TELEPHONE=C
[11] LC_MEASUREMENT=pt_PT.UTF-8 LC_IDENTIFICATION=C

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

loaded via a namespace (and not attached):
[1] compiler_4.0.2



Às 08:45 de 15/07/20, Sam H escreveu:
> Hi,
> 
> I am trying to download some data using read.csv and it works perfectly in
> RStudio and fails in the R console in the terminal in Ubuntu 18.04 after
> upgrading from R 3.6.3 to 4.0.2. Before upgrading this worked in the R
> console in the terminal also without any issues.
> 
> Why would that be? How to fix this?
> 
> Below please find R code output and sessionInfo().
> 
> *Works in RStudio*
> 
>> read.csv("https://old.nasdaq.com/screening/companies-by-name.aspx?letter=0&exchange=1&render=download", header=TRUE, as.is=TRUE, na="n/a")
>      Symbol                                                Name
> LastSale MarketCap IPOyear1      TXG
> 10x Genomics, Inc.  87.4400     $8.6B    20192       YI
>                             111, Inc.   6.4800  $533.69M    20183
> PIH              1347 Property Insurance Holdings, Inc.   4.5350
> $27.52M    2014
>   sessionInfo()
> R version 4.0.2 (2020-06-22)
> Platform: x86_64-pc-linux-gnu (64-bit)
> Running under: Ubuntu 18.04.4 LTS
> 
> Matrix products: default
> BLAS:   /usr/lib/x86_64-linux-gnu/openblas/libblas.so.3
> LAPACK: /usr/lib/x86_64-linux-gnu/libopenblasp-r0.2.20.so
> 
> locale:
>   [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
> LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
>   [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
> LC_PAPER=en_US.UTF-8       LC_NAME=C
>   [9] LC_ADDRESS=C               LC_TELEPHONE=C
> LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
> 
> attached base packages:[1] stats     graphics  grDevices utils
> datasets  methods   base
> 
> loaded via a namespace (and not attached):[1] compiler_4.0.2 tools_4.0.2
> 
> *Fails in R console in terminal*
> 
>      > read.csv("https://old.nasdaq.com/screening/companies-by-name.aspx?letter=0&exchange=1&render=download",
> header=TRUE, as.is=TRUE, na="n/a")
> Error in file(file, "rt") :
>    cannot open the connection to
> 'https://old.nasdaq.com/screening/companies-by-name.aspx?letter=0&exchange=1&render=download'
> In addition: Warning message:
> In file(file, "rt") :
>    URL 'https://old.nasdaq.com/screening/companies-by-name.aspx?letter=0&exchange=1&render=download':
> status was 'Failure when receiving data from the peer'> traceback()3:
> file(file, "rt")2: read.table(file = file, header = header, sep = sep,
> quote = quote,
>         dec = dec, fill = fill, comment.char = comment.char, ...)1:
> read.csv("https://old.nasdaq.com/screening/companies-by-name.aspx?letter=0&exchange=1&render=download",
>         header = TRUE, as.is = TRUE, na = "n/a")>  sessionInfo()
> R version 4.0.2 (2020-06-22)
> Platform: x86_64-pc-linux-gnu (64-bit)
> Running under: Ubuntu 18.04.4 LTS
> 
> Matrix products: default
> BLAS:   /usr/lib/x86_64-linux-gnu/openblas/libblas.so.3
> LAPACK: /usr/lib/x86_64-linux-gnu/libopenblasp-r0.2.20.so
> 
> locale:
>   [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
>   [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
>   [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
>   [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
>   [9] LC_ADDRESS=C               LC_TELEPHONE=C            [11]
> LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
> 
> attached base packages:[1] stats     graphics  grDevices utils
> datasets  methods   base
> 
> loaded via a namespace (and not attached):[1] compiler_4.0.2>
> 
> I also asked this question here
> https://stackoverflow.com/questions/62898008/why-read-csv-fails-in-r-console-in-ubuntu-terminal-but-works-in-rstudio-after-r
> . Since there was no answer on stackoverflow I sent this question also to
> this list.
> 
> Best regards,
> Sam
> 
> 	[[alternative HTML version deleted]]
> 
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