Hi guys,

Following the instructions in the README.md file from the successful
installation of the tool, I copied deseq.R to tool-data/

I've been trying to get the deseq_and_sam2counts tool on our local
galaxy-dist here:
http://toolshed.g2.bx.psu.edu/repos/nikhil-joshi/deseq_and_sam2counts
I note a prior message from Greg on certain <requirements>  tags that
should be added to get some things working in:
http://dev.list.galaxyproject.org/environment-variables-and-paths-for-toolshed-tools-td4656231.html
It's probably not relevant to the error that I am getting at the moment
since we've managed to install all those packages manually through R -

source("http://bioconductor.org/biocLite.R";)

biocLite("DESeq")
biocLite("aroma.light")

The following dataset was used:

dataset:

12345aba1345355777888aba24567888689


This is the error we get when running the tool. Note, it has executed the
actual tool and made use of tool-data/deseq.R

29: Diagnostic Plots for DE Seq on data
27<https://galaxy-qld-dev.genome.edu.au/history>
0 bytes
An error occurred running this job:*Error: Loading required package: Biobase
Loading required package: BiocGenerics
Loading required package: methods

Attaching package: ‘BiocGenerics’

The following object(s) are masked from ‘package:stats’:

xtabs

The following object(s) are*
*
*
*
*







Error: Loading required package: Biobase Loading required package:
BiocGenerics Loading required package: methods Attaching package:
‘BiocGenerics’ The following object(s) are masked from ‘package:stats’:
xtabs The following object(s) are masked from ‘package:base’:
anyDuplicated, cbind, colnames, duplicated, eval, Filter, Find, get,
intersect, lapply, Map, mapply, mget, order, paste, pmax, pmax.int, pmin,
pmin.int, Position, rbind, Reduce, rep.int, rownames, sapply, setdiff,
table, tapply, union, unique Welcome to Bioconductor Vignettes contain
introductory material; view with 'browseVignettes()'. To cite Bioconductor,
see 'citation("Biobase")', and for packages 'citation("pkgname")'. Loading
required package: locfit locfit 1.5-8 2012-04-25 Loading required package:
lattice Warning messages: 1: found methods to import for function ‘as.list’
but not the generic itself 2: found methods to import for function ‘eapply’
but not the generic itself Error in glm.fit(x = numeric(0), y = numeric(0),
weights = NULL, start = c(0.1, : object 'fit' not found Calls:
estimateDispersions ... parametricDispersionFit -> glm -> eval -> eval ->
glm.fit In addition: Warning messages: 1: In is.na(rows) : is.na() applied
to non-(list or vector) of type 'NULL' 2: In glm.fit(x = numeric(0), y =
numeric(0), weights = NULL, start = c(0.1, : no observations informative at
iteration 1


Any ideas?
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