[Bioc-devel] Fwd: [bioc] DEXSeqHTML getListElement GRanges error

Lance Parsons lp@r@on@ @ending from princeton@edu
Wed Nov 14 20:43:41 CET 2018

I submitted a question to the support site, but thought it might be useful
to post here as well. My apologies for the cross-posting.

---------- Forwarded message ---------
From: Lance Parsons [bioc] <noreply using bioconductor.org>
Date: Wed, Nov 14, 2018 at 2:39 PM
Subject: [bioc] DEXSeqHTML getListElement GRanges error
To: <lance using lanceparsons.net>

Activity on a post you are following on support.bioconductor.org

User Lance Parsons <https://support.bioconductor.org/u/7336/> wrote Question:
DEXSeqHTML getListElement GRanges error

When running DEXSeqHTML, I got the following error:

Fatal error: An undefined error occured, please check your input
carefully and contact your administrator.
converting counts to integer mode
Warning message:
In DESeqDataSet(rse, design, ignoreRank = TRUE) :
  some variables in design formula are characters, converting to factors
using supplied model matrix
using supplied model matrix
using supplied model matrix
Error in getListElement(x, i, ...) :
  GRanges objects don't support [[, as.list(), lapply(), or unlist() at
  the moment
Calls: DEXSeqHTML ... tryCatch -> tryCatchList -> tryCatchOne ->

This was run using the Galaxy wrapper
<https://toolshed.g2.bx.psu.edu/view/iuc/dexseq/f89c9b25feb4>. However, the
error appears to be coming from the DEXSeqHTML function and I can't quite
tell where in that function it's failing. Another user on Biostars ran into
the same error <https://www.biostars.org/p/347443/>. Any help tracking down
the source of the problme would be much appreciated.


Post tags: dexseq, software error, bug

You may reply via email or visit https://support.bioconductor.org/p/115115/

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