On 7/15/20 1:35 PM, Dirk Eddelbuettel wrote:
On 15 July 2020 at 16:16, Sam H wrote:
| 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")
Ok, let's stop right here. First off, for good debugging it helps to separate
- downloading a file via R from
- reading a file
- maybe varying the arguments you give there
In my case this got easier. I clicked on the link (in Ubuntu 20.04) and it
downloaded it. From there few problems. `read.csv()` just reads it:
In fact one can use the fread approach directly, rather than first using
your system or your browser to download the copy:
z <-
data.table::fread("https://old.nasdaq.com/screening/companies-by-name.aspx?letter=0&exchange=1&render=download";,
header=TRUE)
Downloaded 486840 bytes...>
> str(z)
Classes ‘data.table’ and 'data.frame': 3631 obs. of 9 variables:
$ Symbol : chr "TXG" "YI" "PIH" "PIHPP" ...
$ Name : chr "10x Genomics, Inc." "111, Inc." "1347 Property
Insurance Holdings, Inc." "1347 Property Insurance Holdings, Inc." ...
$ LastSale : chr "90.93" "6.31" "4.528" "24.35" ...
$ MarketCap : chr "$8.94B" "$519.69M" "$27.48M" "n/a" ...
$ IPOyear : chr "2019" "2018" "2014" "n/a" ...
$ Sector : chr "Capital Goods" "Health Care" "Finance"
"Finance" ...
$ industry : chr "Biotechnology: Laboratory Analytical
Instruments" "Medical/Nursing Services" "Property-Casualty Insurers"
"Property-Casualty Insurers" ...
$ Summary Quote: chr "https://old.nasdaq.com/symbol/txg";
"https://old.nasdaq.com/symbol/yi"; "https://old.nasdaq.com/symbol/pih";
"https://old.nasdaq.com/symbol/pihpp"; ...
$ V9 : logi NA NA NA NA NA NA ...
- attr(*, ".internal.selfref")=<externalptr>
I had earlier experienced the hanging of the original example in Ubuntu
18.04 using R 3.6.1. I get teh same result in either a Terminal hosted R
session or an Rstudio R session.
(It does leave hanging the question of why `read.csv` is failing.)
--
David.
edd@rob:~/Downloads$ Rscript -e 'data.table::fread("companylist.csv",
header=TRUE)'
Symbol Name LastSale MarketCap IPOyear
Sector industry
Summary Quote V9
1: TXG 10x Genomics, Inc. 88.91 $8.75B 2019
Capital Goods Biotechnology: Laboratory Analytical Instruments
https://old.nasdaq.com/symbol/txg NA
2: YI 111, Inc. 6.64 $546.87M 2018
Health Care Medical/Nursing Services
https://old.nasdaq.com/symbol/yi NA
3: PIH 1347 Property Insurance Holdings, Inc. 4.528 $27.48M 2014
Finance Property-Casualty Insurers
https://old.nasdaq.com/symbol/pih NA
4: PIHPP 1347 Property Insurance Holdings, Inc. 24.8631 n/a n/a
Finance Property-Casualty Insurers
https://old.nasdaq.com/symbol/pihpp NA
5: TURN 180 Degree Capital Corp. 1.67 $51.97M n/a
Finance Finance/Investors Services
https://old.nasdaq.com/symbol/turn NA
---
3622: ZS Zscaler, Inc. 122.43 $15.98B 2018
Technology EDP Services
https://old.nasdaq.com/symbol/zs NA
3623: ZUMZ Zumiez Inc. 25.55 $649.76M 2005
Consumer Services Clothing/Shoe/Accessory Stores
https://old.nasdaq.com/symbol/zumz NA
3624: ZYNE Zynerba Pharmaceuticals, Inc. 3.41 $85.08M 2015
Health Care Major Pharmaceuticals
https://old.nasdaq.com/symbol/zyne NA
3625: ZYXI Zynex, Inc. 26.22 $870.31M n/a
Health Care Biotechnology: Electromedical & Electrotherapeutic Apparatus
https://old.nasdaq.com/symbol/zyxi NA
3626: ZNGA Zynga Inc. 9.82 $10.54B 2011
Technology EDP Services
https://old.nasdaq.com/symbol/znga NA
edd@rob:~/Downloads$
For kicks, same with data.table:
edd@rob:~/Downloads$ Rscript -e 'str(read.csv("companylist.csv"))'
'data.frame': 3626 obs. of 9 variables:
$ Symbol : chr "TXG" "YI" "PIH" "PIHPP" ...
$ Name : chr "10x Genomics, Inc." "111, Inc." "1347 Property Insurance Holdings,
Inc." "1347 Property Insurance Holdings, Inc." ...
$ LastSale : chr "88.91" "6.64" "4.528" "24.8631" ...
$ MarketCap : chr "$8.75B" "$546.87M" "$27.48M" "n/a" ...
$ IPOyear : chr "2019" "2018" "2014" "n/a" ...
$ Sector : chr "Capital Goods" "Health Care" "Finance" "Finance" ...
$ industry : chr "Biotechnology: Laboratory Analytical Instruments" "Medical/Nursing
Services" "Property-Casualty Insurers" "Property-Casualty Insurers" ...
$ Summary.Quote: chr "https://old.nasdaq.com/symbol/txg"; "https://old.nasdaq.com/symbol/yi";
"https://old.nasdaq.com/symbol/pih"; "https://old.nasdaq.com/symbol/pihpp"; ...
$ X : logi NA NA NA NA NA NA ...
edd@rob:~/Downloads$
So in short, if you have a problem, it is not likely coming from the Ubuntu
binary for R 4.0.2 which I am running here.
Maybe start by downloading the file? You could have firewall or other
issues. We can't tell. And we can't reproduce the issue.
Good luck, Dirk
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