[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 23:19:49 CEST 2020
On Thu, Jul 16, 2020 at 5:15 PM Ista Zahn <istazahn using gmail.com> wrote:
>
> 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?
Oh, sorry I misread your message. Nevertheless:
$ curl "https://old.nasdaq.com/screening/companies-by-name.aspx?letter=0&exchange=1&render=download"
<HTML><HEAD>
<TITLE>Access Denied</TITLE>
</HEAD><BODY>
<H1>Access Denied</H1>
You don't have permission to access
"http://old.nasdaq.com/screening/companies-by-name.aspx?"
on this server.<P>
Reference #18.5506d217.1594934303.938edcb
</BODY>
</HTML>
$ wget "https://old.nasdaq.com/screening/companies-by-name.aspx?letter=0&exchange=1&render=download"
--2020-07-16 17:19:12--
https://old.nasdaq.com/screening/companies-by-name.aspx?letter=0&exchange=1&render=download
Loaded CA certificate '/etc/ssl/certs/ca-certificates.crt'
Resolving old.nasdaq.com (old.nasdaq.com)... 2600:1400:9000:28f::1b46,
2600:1400:9000:29b::1b46, 23.78.161.120
Connecting to old.nasdaq.com
(old.nasdaq.com)|2600:1400:9000:28f::1b46|:443... connected.
HTTP request sent, awaiting response... 403 Forbidden
2020-07-16 17:19:12 ERROR 403: Forbidden.
I don't think this is an R problem.
Best,
Ista
>
> 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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