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Question: makeTxdbFromUCSC fails to download
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gravatar for lalchungnungabt17
3 months ago by
lalchungnungabt170 wrote:
Hi, 
The following error occur when trying to download hg19 known gene. I am using rtracklayer 1.38.3

>hg19db <- makeTxDbFromUCSC(genome = "hg19",tablename ="knownGene")
Error in names(trackIds) <- sub("^ ", "", nms[nms != "new"]) : 
  'names' attribute [212] must be the same length as the vector [211]

 

Does anybody have the same problems or knows how to solve this?

Thanks in advance!

ADD COMMENTlink modified 3 months ago by James W. MacDonald48k • written 3 months ago by lalchungnungabt170
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gravatar for James W. MacDonald
3 months ago by
United States
James W. MacDonald48k wrote:

That's an old bug that has been fixed. You seem to be using an old version of R/Bioconductor, and should update.

That said, you don't need to build that TxDb package, as one already exists:

library(BiocInstaller)

biocLite("TxDb.Hsapiens.UCSC.hg19.knownGene")

To get the already-built version of the TxDb that you are trying to build.

ADD COMMENTlink written 3 months ago by James W. MacDonald48k
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