BioC 3.4: CHECK report for ChromHeatMap on zin1

Package: ChromHeatMap

Version: 1.27.0

Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings ChromHeatMap_1.27.0.tar.gz

StartedAt: 2016-09-20 04:29:32 -0700 (Tue, 20 Sep 2016)

EndedAt: 2016-09-20 04:31:59 -0700 (Tue, 20 Sep 2016)

EllapsedTime: 147.4 seconds

RetCode: 1

Status:  ERROR

CheckDir: ChromHeatMap.Rcheck

Warnings: NA

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### Running command:
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###   /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings ChromHeatMap_1.27.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/ChromHeatMap.Rcheck’
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ChromHeatMap/DESCRIPTION’ ... OK
* this is package ‘ChromHeatMap’ version ‘1.27.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘ChromHeatMap’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
calculateCytoband: no visible global function definition for ‘data’
createChrMatrix: no visible global function definition for ‘new’
makeRangedDataList : makeRangedData: no visible global function
  definition for ‘as’
paintCytobands: no visible global function definition for ‘data’
plotChrMap: no visible global function definition for ‘new’
makeChrStrandData,matrix: no visible global function definition for
  ‘new’
Undefined global functions or variables:
  as data new
Consider adding
  importFrom("methods", "as", "new")
  importFrom("utils", "data")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘ChromHeatMap-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: makeRangedDataList
> ### Title: Plot expression data as tracks in the UCSC genome browser
> ### Aliases: makeRangedDataList
> 
> ### ** Examples
> 
> data('demo')
> r <- makeRangedDataList( data=chrdata, chr=22, cytoband='q11.23', genome='hg18' )
Loading required package: hgu95av2.db
Loading required package: org.Hs.eg.db
Error: RangedDataList objects are defunct in favor of GRangesList objects (the
  GRangesList class is defined in the GenomicRanges package).
Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.4-bioc/meat/ChromHeatMap.Rcheck/00check.log’
for details.

* installing *source* package ‘ChromHeatMap’ ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (ChromHeatMap)

name	user	system	elapsed
ChrMapPlot-class	0.388	0.012	0.411
ChrStrandData-class	0.076	0.000	0.096
ChrStrandMatrix-class	0.060	0.000	0.063
chrHeatMap	0.048	0.000	0.050
createChrMatrix	0.024	0.004	0.028
drawMapDendro	0.048	0.000	0.049
grabChrMapProbes	0.476	0.000	0.475
makeChrStrandData	0.068	0.000	0.066