BioC 2.13: CHECK report for easyRNASeq on perceval

* using log directory ‘/Users/biocbuild/bbs-2.13-bioc/meat/easyRNASeq.Rcheck’
* using R version 3.0.3 (2014-03-06)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘easyRNASeq/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘easyRNASeq’ version ‘1.8.8’
* 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 ‘easyRNASeq’ can be installed ... [40s/40s] 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 dependencies in R code ... NOTE
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘.convertToUCSC’
See the information on DESCRIPTION files in the chapter ‘Creating R
packages’ of the ‘Writing R Extensions’ manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [21s/22s] OK
* 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

NOTE: There was 1 note.
See
  ‘/Users/biocbuild/bbs-2.13-bioc/meat/easyRNASeq.Rcheck/00check.log’
for details.

* installing *source* package ‘easyRNASeq’ ...
** R
** inst
** preparing package for lazy loading
Warning: replacing previous import by ‘intervals::coerce’ when loading ‘genomeIntervals’
Warning: replacing previous import by ‘intervals::initialize’ when loading ‘genomeIntervals’
Creating a generic function for ‘print’ from package ‘base’ in package ‘easyRNASeq’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning: replacing previous import by ‘intervals::coerce’ when loading ‘genomeIntervals’
Warning: replacing previous import by ‘intervals::initialize’ when loading ‘genomeIntervals’
* DONE (easyRNASeq)

name	user	system	elapsed
DESeq-edgeR-common-methods	0.592	0.008	0.606
DESeq-methods	0.011	0.003	0.014
GenomicRanges-methods	0.016	0.006	0.022
IRanges-methods	0.011	0.003	0.015
ShortRead-methods	0.033	0.008	0.042
easyRNASeq-accessors	0.014	0.004	0.019
easyRNASeq-annotation-methods	0.023	0.006	0.031
easyRNASeq-class	0.016	0.005	0.021
easyRNASeq-correction-methods	0.028	0.008	0.036
easyRNASeq-count	0.020	0.003	0.024
easyRNASeq-coverage-methods	0.018	0.004	0.022
easyRNASeq-easyRNASeq	0.024	0.008	0.032
easyRNASeq-island-methods	0.015	0.004	0.020
easyRNASeq-package	0.020	0.001	0.023
easyRNASeq-summarization-methods	0.020	0.007	0.028
edgeR-methods	0.014	0.007	0.030
genomeIntervals-methods	0.007	0.003	0.011
parallel-methods	0.013	0.002	0.019

BioC 2.13: CHECK report for easyRNASeq on perceval

Summary

Command output