[Bioc-devel] exonsBy dropping genes from TxDb

[Dario Strbenac]

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