I have two problems with bioconductor package GenomicFeatures. Firstly, I am unable to install package by bioclite() function. Installing from source downloaded tar.gz worked fine.
Secondly, the function makeTxDbFromGFF does not work for locally saved gtf file.
txdb <- makeTxDbFromGFF("/media/Data/Homo_sapiens.GRCh37.75.gtf", format="gtf")
Import genomic features from the file as a GRanges object ... Error in .local(con, format, text, ...) :
object 'GFF_FEATURE_TYPES' not found
when I changed GFF_FEATURE_TYPES in makeTxDbFromGFF code to NULL, this error occured:
Import genomic features from the file as a GRanges object ... Error in .tidy_seqinfo(gr, circ_seqs, chrominfo) :
could not find function "make_circ_flags_from_circ_seqs"
Ubuntu 14.04, R 3.2.1