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Old 01-21-2016, 12:34 PM   #1
TPH
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Location: USA

Join Date: Jan 2016
Posts: 19
Question cummeRbund error

Hello,

After completing all the analysis steps from Tophat to Cudiff, I am trying to plot the data using CummeRbund. But I get this error message saying "semi-transparency is not supported on this device: reported only once per page".
I work in a cluster using Linux and use R/3.2.2 compiled with Cairo. Could you please help me to fugure out the issue here.

These are the commands and their outputs I received.

$ module load R/3.2.2
$ R

>library(cummeRbund)
>cuff_data <‐ readCufflinks('/Path to cuffdiff output folder/cuffdiff_out')
>csDensity(genes(cuff_data))

Removed 8804 rows containing non-finite values (stat_density).
2: In grid.Call.graphics(L_polygon, x$x, x$y, index) :
semi-transparency is not supported on this device: reported only once per page




---------------------------------------------------------------

I feel like there is an issue with the cummeRbund loading. But I can't figure out what is it. This is the output I get when cummeRbund Loads.



Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: ‘BiocGenerics’

The following objects are masked from ‘packagearallel’:

clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from ‘package:stats’:

IQR, mad, xtabs

The following objects are masked from ‘package:base’:

anyDuplicated, append, as.data.frame, as.vector, cbind, colnames,
do.call, duplicated, eval, evalq, Filter, Find, get, grep, grepl,
intersect, is.unsorted, lapply, lengths, Map, mapply, match, mget,
order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank,
rbind, Reduce, rownames, sapply, setdiff, sort, table, tapply,
union, unique, unlist, unsplit

Loading required package: RSQLite
Loading required package: DBI
Loading required package: ggplot2
Loading required package: reshape2
Loading required package: fastcluster

Attaching package: ‘fastcluster’

The following object is masked from ‘package:stats’:

hclust

Loading required package: rtracklayer
Loading required package: GenomicRanges
Loading required package: S4Vectors
Loading required package: stats4
Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: Gviz
Loading required package: grid

Attaching package: ‘cummeRbund’

The following object is masked from ‘package:GenomicRanges’:

promoters

The following object is masked from ‘package:IRanges’:

promoters

The following object is masked from ‘package:BiocGenerics’:

Conditions



Could you please help.

Thank you very much.

TPH

Last edited by TPH; 01-21-2016 at 12:37 PM.
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cummerbund plots, r/3.2.2

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