[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?

Jeff Newmiller
Thu, 16 Jul 2020 04:31:22 -0000

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.

--
Sent from my phone. Please excuse my brevity.