Hi,

When using chipseq package to try to analyze some CTCF ChIP, I found an (apparent) error in the islandDepthPlot function.

When running the code attached below, the pdf generated is empty, saying "Error using packet 1 could not find function "panel.lines".  This function worked with the same code as recently as 2 months ago, so I suspect something has broken in an update since then.

Links to rdas of the CTCF.cov variable (https://www.dropbox.com/s/uhcg2h92knoyv3h/test.rda?dl=0) and the failed plot (https://www.dropbox.com/s/3mekk3d6uu6h4jd/test.pdf?dl=0).

Traceback shows nothing, because it doesn't throw an explicit error.  Any suggestions?

Thanks,

Winston Timp

Code:

##Load datap                                                                                                                                                                       
CTCF.raw=readGAlignmentPairs("/mithril/Data/NGS/Aligned/081514_chip/CTCF.sorted.bam", use.names=T)

##Get full insert location(that's what we want - from reads)                                                                                                   CTCF.map=granges(CTCF.raw)

##get coverage                                                                                                                                                                     
CTCF.cov=coverage(CTCF.map)

##Plot depth of coverage histogram                                                                                                                                       

library(chipseq)
pdf(file.path(plotdir, "test.pdf"))
islandDepthPlot(CTCF.cov)
dev.off()

sessionInfo():

> sessionInfo()
 R version 3.1.1 (2014-07-10)
 Platform: x86_64-pc-linux-gnu (64-bit)

 locale:
  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
  [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
  [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
  [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
  [9] LC_ADDRESS=C               LC_TELEPHONE=C
 [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

 attached base packages:
 [1] parallel  stats     graphics  grDevices utils     datasets  methods
 [8] base

 other attached packages:
  [1] chipseq_1.14.0          ShortRead_1.22.0        BiocParallel_0.6.1
  [4] ggplot2_1.0.0           GenomicAlignments_1.0.6 BSgenome_1.32.0
  [7] Rsamtools_1.16.1        Biostrings_2.32.1       XVector_0.4.0
 [10] GenomicRanges_1.16.4    GenomeInfoDb_1.0.2      IRanges_1.22.10
 [13] BiocGenerics_0.10.0

 loaded via a namespace (and not attached):
  [1] base64enc_0.1-2     BatchJobs_1.4       BBmisc_1.7
  [4] Biobase_2.24.0      bitops_1.0-6        brew_1.0-6
  [7] checkmate_1.5.0     codetools_0.2-9     colorspace_1.2-4
 [10] compiler_3.1.1      DBI_0.3.1           digest_0.6.4
 [13] fail_1.2            foreach_1.4.2       grid_3.1.1
 [16] gtable_0.1.2        hwriter_1.3.2       iterators_1.0.7
 [19] lattice_0.20-29     latticeExtra_0.6-26 MASS_7.3-35
 [22] munsell_0.4.2       plyr_1.8.1          proto_0.3-10
 [25] RColorBrewer_1.0-5  Rcpp_0.11.3         reshape2_1.4
 [28] RSQLite_0.11.4      scales_0.2.4        sendmailR_1.2-1
 [31] stats4_3.1.1        stringr_0.6.2       tools_3.1.1
 [34] zlibbioc_1.10.0
 >