[External] Re: read.csv fails in R console in Ubuntu terminal but works in RStudio after R 3.6.3 upgrade to R 4.0.2?
On my Ubuntu system the download with read.csv succeeds in an R console if I set the HTTPUserAgent and download.file.method options to match the ones used by RStudio. Given how picky the server is being I would worry about whether this use is in line with the site's terms of service. Best, luke
On Thu, 16 Jul 2020, Ista Zahn wrote:
On Thu, Jul 16, 2020 at 5:15 PM Ista Zahn <istazahn at gmail.com> wrote:
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?
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 ?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
. Since there was no answer on stackoverflow I sent this question
also to
this list.
Best regards,
Sam
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Luke Tierney
Ralph E. Wareham Professor of Mathematical Sciences
University of Iowa Phone: 319-335-3386
Department of Statistics and Fax: 319-335-3017
Actuarial Science
241 Schaeffer Hall email: luke-tierney at uiowa.edu
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