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ge11232002 / TFBSTools

Software Package for Transcription Factor Binding Site (TFBS) Analysis
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runMEME fails #4

Closed ge11232002 closed 8 years ago

ge11232002 commented 8 years ago

motifSet <- runMEME(file.path(system.file("extdata",

  • package="TFBSTools"), "crp0.s"),
  • binary="meme",
  • arguments=list("-nmotifs"=3)
  • ) meme /usr/local/lib/R/site-library/TFBSTools/extdata/crp0.s -text -dna -nmotifs 3 2>/dev/null Error in seq.default(from = indexNames[i] + 4, to = indexNames[i] + 4 + : 'to' cannot be NA, NaN or infinite In addition: Warning messages: 1: In run_MEME(x, binary = binary, seqtype = seqtype, arguments = arguments) : NAs introduced by coercion 2: In run_MEME(x, binary = binary, seqtype = seqtype, arguments = arguments) : NAs introduced by coercion 3: In run_MEME(x, binary = binary, seqtype = seqtype, arguments = arguments) : NAs introduced by coercion motifSet Error: object 'motifSet' not found
ge11232002 commented 8 years ago

closed via f08c1575fcd203acd02d399a5392b1660f0c08e1

PietaSchofield commented 8 years ago

Hullo

I am experiencing this issue which I notice you have fixed. I am running the TFBSTools_1.8.2 devtools_1.10.0 which I installed from Bioconductor. I have attempted to install the code from GitHub but get a message about the wrong version of S4Vectors when I attempt that. Should it be possible to install the GitHub version on the current R3.2.4 release or do I need to be running a development version of R?

Many thanks

Pieta

ge11232002 commented 8 years ago

I updated the release branch. The change will take some time to appear in Bioconductor. But you can see the changes from https://github.com/Bioconductor-mirror/TFBSTools and install with 

devtools::install_github("Bioconductor-mirror/TFBSTools", ref="b12485a308b49db53982a86caca193ed1bf45693")