Error in downloadEncode

Question

[atsalaki]

When i run this in R downloadEncode(resultSet = query_results[5,], resultOrigin = "searchEncode") I get the following error

Error in if (md5sum_file != md5sums[i]) { : 
  missing value where TRUE/FALSE needed
In addition: Warning messages:
1: running command 'curl -L -s -S "https://www.encodeproject.org/files/ENCFF002DAD/@@download/ENCFF002DAD.bed.gz"  -o "./ENCFF002DAD.bed.gz"' had status 127 
2: In download.file(url = paste0(encode_root, hrefs[i]), quiet = TRUE,  :
  download had nonzero exit status

I can't understand why??

[russhh]

Given your error code, are you sure you have curl installed?

[atsalaki]

I have already installed it through the ENCODE exlporer package

[russhh]

OK, so if you run

curl -L -s -S "https://www.encodeproject.org/files/ENCFF002DAD/@@download/ENCFF002DAD.bed.gz"  -o "./ENCFF002DAD.bed.gz"

at the command line do you get any additional warnings / messages printed out

[atsalaki]

In R it says unexpected string constant in curl bla bla :(. I have installed also curl in windows folder i putted there the curl.exe file. In command prompt it says curl: <23> failed writing body (0!=4096)

But what is the first error above the curl error Error in if (md5sum_file != md5sums[i]) { : missing value where TRUE/FALSE needed?