BioC 3.0: CHECK report for easyRNASeq on perceval

Package: easyRNASeq

Version: 2.2.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch easyRNASeq_2.2.1.tar.gz

StartedAt: 2015-04-10 01:01:32 -0700 (Fri, 10 Apr 2015)

EndedAt: 2015-04-10 01:10:46 -0700 (Fri, 10 Apr 2015)

EllapsedTime: 553.7 seconds

RetCode: 0

Status:  OK

CheckDir: easyRNASeq.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch easyRNASeq_2.2.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.0-bioc/meat/easyRNASeq.Rcheck’
* using R version 3.1.3 (2015-03-09)
* 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 ‘2.2.1’
* 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 ... [41s/47s] 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’
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.getGffRange: no visible binding for global variable ‘ANNOTATION.TYPE’
.getGtfRange: no visible binding for global variable ‘ANNOTATION.TYPE’
.getGtfRange: no visible binding for global variable ‘GTF.FIELDS’
.readGffGtf: no visible binding for global variable ‘ANNOTATION.TYPE’
.validate: no visible binding for global variable ‘GTF.FIELDS’
coerce,Genome_intervals-RangedData: no visible global function
  definition for ‘isSingleString’
plotDispLSD,CountDataSet: no visible binding for global variable ‘cds’
* 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/23s] OK
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘runTests.R’ [117s/125s]
 [118s/125s] 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
* DONE

NOTE: There were 2 notes.
See
  ‘/Users/biocbuild/bbs-3.0-bioc/meat/easyRNASeq.Rcheck/00check.log’
for details.

* installing *source* package ‘easyRNASeq’ ...
** R
** inst
** preparing package for lazy loading
Creating a generic function for ‘basename’ from package ‘base’ in package ‘easyRNASeq’
Creating a generic function for ‘file.exists’ from package ‘base’ in package ‘easyRNASeq’
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
* DONE (easyRNASeq)

name	user	system	elapsed
DESeq-methods	0.001	0.000	0.001
GenomicRanges-methods	0.762	0.040	0.812
IRanges-methods	0.001	0.001	0.002
Rsamtools-methods	0.087	0.011	0.815
ShortRead-methods	0.003	0.000	0.003
easyRNASeq-AnnotParam-accessors	0.005	0.002	0.006
easyRNASeq-AnnotParam-class	0.002	0.000	0.002
easyRNASeq-AnnotParam	0.003	0.001	0.003
easyRNASeq-BamFileList	0.223	0.017	0.307
easyRNASeq-BamParam-accessors	0.003	0.000	0.009
easyRNASeq-BamParam-class	0.001	0.000	0.001
easyRNASeq-BamParam	0.004	0.000	0.004
easyRNASeq-RnaSeqParam-accessors	0.009	0.001	0.010
easyRNASeq-RnaSeqParam-class	0.001	0.001	0.001
easyRNASeq-RnaSeqParam	0.011	0.001	0.012
easyRNASeq-accessors	0.004	0.000	0.020
easyRNASeq-annotation-methods	0.000	0.000	0.001
easyRNASeq-class	0.002	0.001	0.002
easyRNASeq-correction-methods	0.002	0.001	0.016
easyRNASeq-count	0.001	0.000	0.002
easyRNASeq-coverage-methods	0.001	0.000	0.001
easyRNASeq-deprecated-annotation-methods	0.002	0.001	0.003
easyRNASeq-easyRNASeq	0.002	0.000	0.002
easyRNASeq-island-methods	0.001	0.000	0.017
easyRNASeq-package	0.002	0.000	0.002
easyRNASeq-simpleRNASeq	0.002	0.000	0.002
easyRNASeq-summarization-methods	0.001	0.000	0.002
edgeR-methods	0.001	0.001	0.001
genomeIntervals-methods	0.001	0.000	0.002
parallel-methods	0.001	0.001	0.001