I'm trying to open a bz2 compressed netcdf file from ftp, but can't get it to work. Any help is much appreciated.
I've tried opening it directly using:
url <- 'ftp://podaac-ftp.jpl.nasa.gov/allData/ghrsst/data/L4/GLOB/NCDC/AVHRR_OI/1982/001/19820101-NCDC-L4LRblend-GLOB-v01-fv02_0-AVHRR_OI.nc.bz2'
nc_open(url)
but that doesn't work (I get: Error in R_nc4_open: No such file or directory). I guess because of the compression, so I tried downloading the file first and decompress it.
temp <- tempfile()
download.file(url,temp)
nc_open(bzfile(temp, '19820101-NCDC-L4LRblend-GLOB-v01-fv02_0-AVHRR_OI.nc', 'rb'))
but that doesn't work either and I get both an error and a warning:
Error in bzfile(temp, "19820101-NCDC-L4LRblend-GLOB-v01-fv02_0-AVHRR_OI.nc", :
cannot open the connection
In addition: Warning message:
In bzfile(temp, "19820101-NCDC-L4LRblend-GLOB-v01-fv02_0-AVHRR_OI.nc", :
cannot open bzip2-ed file '/var/folders/hs/k9t_8wxs2hn48qq4vp_7xmgm0000gn/T//Rtmpv9UIBr/filef5659606aee', probable reason 'Invalid argument'
any ideas?
Thanks
This seems to work the way you want it to:
library(ncdf4)
library(R.utils)
URL <- "ftp://podaac-ftp.jpl.nasa.gov/allData/ghrsst/data/L4/GLOB/NCDC/AVHRR_OI/1982/001/19820101-NCDC-L4LRblend-GLOB-v01-fv02_0-AVHRR_OI.nc.bz2"
bzfil <- basename(URL)
if (!file.exists(bzfil)) download.file(URL, bzfil)
fil <- bunzip2(bzfil, overwrite=TRUE, remove=FALSE)
nc <- nc_open(fil)
summary(nc)
## Length Class Mode
## filename 1 -none- character
## writable 1 -none- logical
## id 1 -none- numeric
## safemode 1 -none- logical
## format 1 -none- character
## is_GMT 1 -none- logical
## groups 1 -none- list
## fqgn2Rindex 1 -none- list
## ndims 1 -none- numeric
## natts 1 -none- numeric
## dim 3 -none- list
## unlimdimid 1 -none- numeric
## nvars 1 -none- numeric
## var 4 -none- list