BioC 3.0: CHECK report for easyRNASeq on oaxaca

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: 2015-04-09 23:07:34 -0700 (Thu, 09 Apr 2015)

EndedAt: 2015-04-09 23:14:48 -0700 (Thu, 09 Apr 2015)

EllapsedTime: 434.1 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-darwin13.4.0 (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 ... [30s/31s] 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 ... [15s/15s] OK
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘runTests.R’ [99s/107s]
 [99s/108s] 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	0.001	0.001
GenomicRanges-methods	0.455	0.030	0.493
IRanges-methods	0.001	0.000	0.002
Rsamtools-methods	0.092	0.006	0.180
ShortRead-methods	0.002	0.000	0.002
easyRNASeq-AnnotParam-accessors	0.005	0.001	0.006
easyRNASeq-AnnotParam-class	0.001	0.000	0.002
easyRNASeq-AnnotParam	0.002	0.001	0.003
easyRNASeq-BamFileList	0.234	0.012	0.247
easyRNASeq-BamParam-accessors	0.003	0.000	0.003
easyRNASeq-BamParam-class	0.001	0.000	0.001
easyRNASeq-BamParam	0.004	0.000	0.004
easyRNASeq-RnaSeqParam-accessors	0.009	0.000	0.010
easyRNASeq-RnaSeqParam-class	0.001	0.000	0.001
easyRNASeq-RnaSeqParam	0.011	0.001	0.011
easyRNASeq-accessors	0.004	0.001	0.004
easyRNASeq-annotation-methods	0.000	0.000	0.001
easyRNASeq-class	0.001	0.000	0.002
easyRNASeq-correction-methods	0.001	0.000	0.002
easyRNASeq-count	0.001	0.000	0.002
easyRNASeq-coverage-methods	0.001	0.000	0.001
easyRNASeq-deprecated-annotation-methods	0.003	0.000	0.003
easyRNASeq-easyRNASeq	0.002	0.001	0.002
easyRNASeq-island-methods	0.001	0.000	0.001
easyRNASeq-package	0.001	0.000	0.002
easyRNASeq-simpleRNASeq	0.001	0.000	0.002
easyRNASeq-summarization-methods	0.001	0.000	0.002
edgeR-methods	0.000	0.000	0.001
genomeIntervals-methods	0.001	0.001	0.001
parallel-methods	0.001	0.000	0.001