[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
|@t@z@hn @end|ng |rom gm@||@com
Thu Jul 16 23:15:12 CEST 2020
On Thu, Jul 16, 2020 at 8:18 AM Rui Barradas <ruipbarradas using 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
>
> Às 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 using 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 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]]
> >>>
> >>> ______________________________________________
> >>> R-help using 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 using 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 using 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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