[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?

Rui Barradas
Thu, 16 Jul 2020 12:17:52 -0000

Hello,

Thanks, but no, download.file still gives 403 Forbidden with both method
= "libcurl" and method = "wget".

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.
>