[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?

Ista Zahn
Thu, 16 Jul 2020 21:15:12 -0000

On Thu, Jul 16, 2020 at 8:18 AM Rui Barradas <ruipbarradas at sapo.pt>
wrote:
>
> Hello,
>
> Thanks, but no, download.file still gives 403 Forbidden with both method
> = "libcurl" and method = "wget".

I think that makes it "not an R question". Ask on
https://unix.stackexchange.com/ maybe?

Best,
Ista

>
> Rui Barradas
>
> ?s 05:31 de 16/07/20, Jeff Newmiller escreveu:
> > Perhaps read FAQ 7.43? [1]
> >
> > [1]
https://cran.r-project.org/doc/FAQ/R-FAQ.html#How-can-I-enable-secure-https-downloads-in-R_003f
> >
> > On July 15, 2020 4:02:27 PM PDT, Rui Barradas <ruipbarradas at
sapo.pt> wrote:
> >> 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 at 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 at 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 at 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
> >>
> >>
> >>
> >> ?s 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]]
> >>>
> >>> ______________________________________________
> >>> 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.
> >>>
> >>
> >> ______________________________________________
> >> 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.
> >
>
> ______________________________________________
> 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.