Good day,
I stepped through the code until execution reached the end of postForm in RCurl
which is called by getBM and obtains the textual result from the server. If I
check the contents of write$value(), the example missing transcript is not
there.
Browse[3]> grep("ENST00000485971", write$value())
integer(0)
write$value is a weird function. It's prototype is function (collapse = "",
...) but its body contains code such as
if (is.null(collapse))
return(txt)
I wonder where txt is created. It's not passed as an extra variable.
Browse[7]> print(list(...))
list()
Searching the R code reveals that txt is created as a global variable in
another function named dynCurlReader by the code statement txt <<- character().
RCurl also uses functions that don't begin with a dot but are undocumented.
ans = encode(ans)
Browse[7]> ?encode
No documentation for ‘encode’ in specified packages and libraries
Anyway, the transcript ID is also missing from txt.
Browse[7]> grep("ENST00000485971", txt)
integer(0)
It's hard to know what the obfuscated code of RCurl is doing.
--------------------------------------
Dario Strbenac
University of Sydney
Camperdown NSW 2050
Australia
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