Question: BugReport: genomicFeatures - makeTxDbFromGFF does not work
gravatar for aldobiasova
2.3 years ago by
Czech Republic
aldobiasova0 wrote:


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

ADD COMMENTlink written 2.3 years ago by aldobiasova0

Please you add to your question the complete output, in a new R session, of


and, after loading GenomicFeatures, the output of

ADD REPLYlink written 2.3 years ago by Martin Morgan ♦♦ 21k
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