David Winsemius
2020-Jul-16 02:15 UTC
[R-sig-Debian] 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 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 at 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 $10.54B 2011 Technology EDP Services https://old.nasdaq.com/symbol/znga NA > edd at rob:~/Downloads$ > > For kicks, same with data.table: > > edd at 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 at 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 >
Dirk Eddelbuettel
2020-Jul-16 03:33 UTC
[R-sig-Debian] 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 15 July 2020 at 19:15, David Winsemius wrote: | (It does leave hanging the question of why `read.csv` is failing.) If I had to guess: due to the dark magic behind download.file() and the numerous different ways it could use (see the help page, it is truly impressive!) some of which involve `libcurl` (i.e. the C library from the curl project), some involve `curl` (the package for R), some involve `wget` (the binary), some involve internal code -- plus all that can cross with the SSL libraries use by curl and whatnot. Which is why my post suggested to separate the _download_ from the _file read_ aspect. Dirk -- https://dirk.eddelbuettel.com | @eddelbuettel | edd at debian.org
Sam H
2020-Jul-19 01:43 UTC
[R-sig-Debian] read.csv fails in R console in Ubuntu terminal but works in RStudio after R 3.6.3 upgrade to R 4.0.2
This issue was now solved in TTR::stockSymbols() by package author https://github.com/joshuaulrich/TTR/commit/98dec2b5aa68c3cee750397c7d11b164895e0140 Thanks for all the help and ideas. Best, Sam On Thu, Jul 16, 2020, 05:33 Dirk Eddelbuettel <edd at debian.org> wrote:> > On 15 July 2020 at 19:15, David Winsemius wrote: > | (It does leave hanging the question of why `read.csv` is failing.) > > If I had to guess: due to the dark magic behind download.file() and the > numerous different ways it could use (see the help page, it is truly > impressive!) some of which involve `libcurl` (i.e. the C library from the > curl project), some involve `curl` (the package for R), some involve `wget` > (the binary), some involve internal code -- plus all that can cross with > the > SSL libraries use by curl and whatnot. > > Which is why my post suggested to separate the _download_ from the _file > read_ aspect. > > Dirk > > -- > https://dirk.eddelbuettel.com | @eddelbuettel | edd at debian.org >[[alternative HTML version deleted]]