Running list of errors for each data set up to .friedman.2014 about madtraits HOT 4 CLOSED

On Wed, 11 Apr 2018 at 13:10 Matthew Helmus ***@***.***> wrote: Here is a running list of problems with NATDB downloading on a PC. I give a description of what I think is going on, and then below that the code and the error. First, there are lots that work. Basically anything that is a csv or a txt works. I stopped adding the ones that work. # work fine ------------------------------------------- # .albouy.2015 data <- read.csv(unzip(suppdata("E096-203","Functional_data.zip", "esa_archives"), "Functional_data.csv"), sep=";") # .anderson.2015 data<-read.csv(suppdata("10.1371/journal.pone.0166714",2)) # .artacho.2015 data <- read.csv2(suppdata("10.5061/dryad.qg062", "phenotypictraits.csv"), sep=';') # .augspurger.2016a data <- read.csv(suppdata("10.5061/dryad.56cn4","Data File 1. Diaspore traits.csv"), as.is=TRUE) # .bengtsson.2016 data <- read.csv(suppdata('10.5061/dryad.62054', 'bengtsson_etal_2016_traits.csv'), as.is=TRUE) # .comeault.2013 data <- read.table(suppdata("10.5061/dryad.ck2cm","Tcris_FHA_phenotypes.txt"),header=TRUE) # .edwards.2015a data <- read.csv(suppdata("E096-202", "Table1.csv", "esa_archives")) # stopped adding ones that worked ERROR 1 This is probabally the hardest error. It is with read_excel and suppdata with dryad download. I tried to just use suppdata to download xls from dryad and could not open the downloaded files... so there is some interaction going on here. # does not work ----------------------------------------------------------------- # .ameztegui.2016 data <- as.data.frame(read_excel(suppdata("10.5061/dryad.12b0h/2","FunctionalTraits_Dryad.xlsx"))) # .arnold.2016 data <- as.data.frame(read_excel(suppdata("10.5061/dryad.t3d52", "Arnold_etal_2016_functecol_dataset.xlsx"), as.is = TRUE, skip = 3)) # .aubret.2012a data <- as.data.frame(read_excel(suppdata("10.5061/dryad.14cr5345", "Aubret%2053172.xlsx"), sheet=1)) #all of the above give this error Error in read_fun(path = path, sheet = sheet, limits = limits, shim = shim, : Evaluation error: error -103 with zipfile in unzGetCurrentFileInfo . ERROR 2 This one just runs and runs. It is like the above one but it deals with figshare. So I think the problem is the suppdata and read_excel interaction (it does not matter where you are downloading from). If you can fix this interaction then ERRORS 1 and 2 might go away... # .bello_bedoy.2015b data <- as.data.frame(read_excel( suppdata("10.6084/m9.figshare.1190766.v2","mating occurrencePzoe_2010.xls") )) ERROR 3 Problem with the suppdata function not the unzip I think. It is having a problem with wiley... is it because these are not open access? # .benesh.2017 data <- read.csv(unzip(suppdata("10.1002/ecy.1680", 1), "CLC_database_lifehistory.csv")) Error in download.file(url, destination, quiet = TRUE) : cannot open URL 'https://onlinelibrary.wiley.com/action/' In addition: Warning message: In download.file(url, destination, quiet = TRUE) : cannot open URL 'https://onlinelibrary.wiley.com/action/': HTTP status was '404 Not Found' # .engemann.2016 data <- read.delim(unzip(suppdata("10.1002/ecy.1569", 1), "DataS1/GrowthForm_Final.txt")) Error in download.file(url, destination, quiet = TRUE) : cannot open URL 'https://onlinelibrary.wiley.com/action/' In addition: Warning message: In download.file(url, destination, quiet = TRUE) : cannot open URL 'https://onlinelibrary.wiley.com/action/': HTTP status was '404 Not Found' ERROR 4 this one needs a file extension # .cariveau.2016 data <- as.data.frame(read_excel(suppdata("10.1371/journal.pone.0151482", 3), sheet="TableS1_v2")) Error: Missing file extension. ERROR 5 This one crashes R and gives me a bomb in R studio! .friedman.2014 <- function(...){ data <- as.data.frame(read_excel(suppdata("10.5061/dryad.489c7","NILs_rawdata.xls"))) fread: wanted 1 got 0 loc=570826752 seek: wanted to seek to sector... THEN R ABORTS OK I got through to .friedman.2014 ... — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#73>, or mute the thread <https://github.com/notifications/unsubscribe-auth/ABLcUu9bRjGYqa1C14-psyYSX2gwEvKlks5tnlUWgaJpZM4TQlfJ> .

On Wed, 11 Apr 2018 at 18:06 Matthew Helmus ***@***.***> wrote: Yes, it is no problem at all if you do not get to this anytime soon. I am going to have the class code for csv/txt files, not xls or zips to make things easier. I had them all fork your package... so now NATDB is probably one of your most forked! — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#73 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/ABLcUskddfLW9Xi_p48QxPdggqcKA6ENks5tnpp_gaJpZM4TQlfJ> .