[BioC] ChIPpeakAnno

[Sean Davis]

On Sat, Feb 18, 2012 at 11:11 PM, Brian Gadd <bgadd001 at ucr.edu> wrote:
> 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.

Hi, Brian.

These messages are informational and will likely not affect everyday
use.  I suggest you ignore them for now.

You mention something about chipPeakAnno working but not annotating on
the minus strand.  If you still have questions on that front, perhaps
another email relating those issues is warranted.

Sean


> 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
>
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