[BioC] ChIPpeakAnno

[Brian Gadd]

I am relatively new to R and am trying to use ChIPpeakAnno.  I am
having some difficulty getting the ChIPpeakAnno library to load
correctly. The annotatePeakInBatch function still runs but fails to
properly annotate genes on the minus strand.

Specifically, upon loading the ChIPpeakAnno library a variety of
objects are masked from several attached packages as detailed in the
printout below.  The sessionInfo() print out is below as well.

Any advice on how to ensure everything loads correctly would be
greatly appreciated; I haven't been able to find anything after
scouring bioconductor, CRAN, or Google and I'm at a loss.  Thanks!

> library(ChIPpeakAnno)
Loading required package: biomaRt
Loading required package: multtest
Loading required package: Biobase

Welcome to Bioconductor

  Vignettes contain introductory material. To view, type
  'browseVignettes()'. To cite Bioconductor, see
  'citation("Biobase")' and for packages 'citation("pkgname")'.

Loading required package: IRanges

Attaching package: ‘IRanges’

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

    updateObject

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

    cbind, eval, intersect, Map, mapply, order, paste, pmax, pmax.int,
pmin, pmin.int, rbind, rep.int, setdiff, table, union

Loading required package: Biostrings
Loading required package: BSgenome
Loading required package: GenomicRanges
Loading required package: BSgenome.Ecoli.NCBI.20080805
Loading required package: GO.db
Loading required package: AnnotationDbi
Loading required package: DBI

Loading required package: org.Hs.eg.db

Loading required package: limma
Loading required package: gplots
Loading required package: gtools
Loading required package: gdata
gdata: Unable to locate valid perl interpreter
gdata:
gdata: read.xls() will be unable to read Excel XLS and XLSX files
unless the 'perl=' argument is used to specify the location of a valid
perl
gdata: intrpreter.
gdata:
gdata: (To avoid display of this message in the future, please ensure
perl is installed and available on the executable search path.)
gdata: Unable to load perl libaries needed by read.xls()
gdata: to support 'XLX' (Excel 97-2004) files.

gdata: Unable to load perl libaries needed by read.xls()
gdata: to support 'XLSX' (Excel 2007+) files.

gdata: Run the function 'installXLSXsupport()'
gdata: to automatically download and install the perl
gdata: libaries needed to support Excel XLS and XLSX formats.

Attaching package: ‘gdata’

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

    trim

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

    combine

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

    nobs

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

    object.size

Loading required package: caTools
Loading required package: bitops

Attaching package: ‘caTools’

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

    runmean

Loading required package: grid
Loading required package: KernSmooth
KernSmooth 2.23 loaded
Copyright M. P. Wand 1997-2009

Attaching package: ‘gplots’

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

    space

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

    wapply

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

    lowess

Warning message:
replacing previous import ‘space’ when loading ‘IRanges’
>

> sessionInfo()
R version 2.14.1 (2011-12-22)
Platform: i386-pc-mingw32/i386 (32-bit)

locale:
[1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United
States.1252    LC_MONETARY=English_United States.1252 LC_NUMERIC=C
[5] LC_TIME=English_United States.1252

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

other attached packages:
 [1] ChIPpeakAnno_2.2.0                  gplots_2.10.1
      KernSmooth_2.23-7                   caTools_1.12
 [5] bitops_1.0-4.1                      gdata_2.8.2
      gtools_2.6.2                        limma_3.10.2
 [9] org.Hs.eg.db_2.6.4                  GO.db_2.6.1
      RSQLite_0.11.1                      DBI_0.2-5
[13] AnnotationDbi_1.16.16
BSgenome.Ecoli.NCBI.20080805_1.3.17 BSgenome_1.22.0
 GenomicRanges_1.6.7
[17] Biostrings_2.22.0                   IRanges_1.12.6
      multtest_2.10.0                     Biobase_2.14.0
[21] biomaRt_2.10.0                      BiocInstaller_1.2.1

loaded via a namespace (and not attached):
[1] MASS_7.3-17      RCurl_1.91-1.1   splines_2.14.1
survival_2.36-12 tools_2.14.1     XML_3.9-4.1



I attempted this after getting R and bioconductor up and running first:
Fresh Install of R 2.14.1 in Windows 7.
Assigned write permission to the library folder to allow package installation.
source("http://bioconductor.org/biocLite.R")
biocLite()
biocLite(c("ChIPpeakAnno"))
update.packages(repos=biocinstallRepos(), ask=FALSE)


----
Brian Gadd
PhD Candidate
Cell, Molecular and Developmental Biology
University of California Riverside

Tel: 19513130505
Email: bgadd001 at ucr.edu