BioC 3.3: CHECK report for genomation on morelia

Package: genomation

Version: 1.3.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings genomation_1.3.0.tar.gz

StartedAt: 2015-10-20 06:21:04 -0400 (Tue, 20 Oct 2015)

EndedAt: 2015-10-20 06:24:09 -0400 (Tue, 20 Oct 2015)

EllapsedTime: 185.2 seconds

RetCode: 0

Status:  OK

CheckDir: genomation.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 genomation_1.3.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.3-bioc/meat/genomation.Rcheck’
* using R Under development (unstable) (2015-10-08 r69496)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘genomation/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘genomation’ version ‘1.3.0’
* package encoding: latin1
* 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 ‘genomation’ can be installed ... [13s/13s] 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
Unexported objects imported by ':::' calls:
  ‘BiocGenerics:::testPackage’ ‘GenomicAlignments:::invertRleStrand’
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
heatMeta: no visible binding for global variable ‘a’
ScoreMatrixBin,GRanges-GRanges: no visible global function definition
  for ‘runValue’
plotGeneAnnotation,list: no visible binding for global variable
  ‘SampleName’
plotGeneAnnotation,list: no visible binding for global variable ‘value’
randomizeFeature,GRanges : <anonymous>: no visible global function
  definition for ‘Rle’
randomizeFeature,GRanges: no visible global function definition for
  ‘runValue’
Undefined global functions or variables:
  Rle SampleName a runValue value
* 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 line endings in Makefiles ... OK
* checking for GNU extensions in Makefiles ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... NOTE
The following directory looks like a leftover from 'knitr':
  ‘cache’
Please remove from your package.
* checking examples ... [20s/20s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘genomation_unit_tests.R’ [22s/22s]
 [23s/23s] 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

Status: 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.3-bioc/meat/genomation.Rcheck/00check.log’
for details.

* installing *source* package ‘genomation’ ...
** 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 (genomation)

name	user	system	elapsed
AnnotationByGeneParts-methods	0.659	0.022	0.708
ScoreMatrix-methods	2.625	0.118	2.751
ScoreMatrixBin-methods	0.535	0.019	0.554
ScoreMatrixList-methods	0.683	0.006	0.689
annotateWithFeature-methods	0.053	0.001	0.053
annotateWithFeatureFlank-methods	0.271	0.001	0.272
annotateWithGeneParts-methods	0.456	0.004	0.461
binMatrix-methods	0.194	0.004	0.198
convertBed2Exons-methods	0.075	0.000	0.076
convertBed2Introns-methods	0.091	0.001	0.092
findFeatureComb-methods	0.321	0.005	0.325
getFeatsWithTargetsStats-methods	0.386	0.001	0.388
getFlanks-methods	0.140	0.001	0.141
getRandomEnrichment-methods	0.002	0.001	0.002
getTargetAnnotationStats-methods	0.330	0.001	0.332
gffToGRanges	0.069	0.001	0.070
heatMatrix	0.747	0.055	0.802
heatMeta	0.798	0.049	0.847
intersectScoreMatrixList-methods	0.386	0.005	0.390
multiHeatMatrix	0.606	0.048	0.655
orderBy-methods	0.844	0.030	0.873
patternMatrix-methods	0.094	0.002	0.097
plotGeneAnnotation-methods	0.908	0.009	0.921
plotMeta	0.486	0.030	0.516
plotTargetAnnotation-methods	0.406	0.002	0.415
readBed	0.036	0.001	0.037
readBroadPeak	0.032	0.001	0.034
readFeatureFlank-methods	0.136	0.001	0.137
readGeneric	0.028	0.001	0.029
readNarrowPeak	0.025	0.001	0.025
readTranscriptFeatures-methods	0.388	0.014	0.402
scaleScoreMatrix-methods	0.262	0.004	0.265
scaleScoreMatrixList	0.712	0.004	0.717