BioC 3.2: CHECK report for genomation on oaxaca

Package: genomation

Version: 1.2.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings genomation_1.2.0.tar.gz

StartedAt: 2015-10-20 03:51:57 -0400 (Tue, 20 Oct 2015)

EndedAt: 2015-10-20 03:56:34 -0400 (Tue, 20 Oct 2015)

EllapsedTime: 277.7 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_1.2.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/genomation.Rcheck’
* using R version 3.2.2 (2015-08-14)
* 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 ‘1.2.0’
* 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 ... [20s/36s] 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 : .local: 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’
* 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 ... [30s/30s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘genomation_unit_tests.R’ [31s/31s]
 [31s/31s] 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-3.2-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	0.983	0.028	1.104
ScoreMatrix-methods	3.664	0.135	3.802
ScoreMatrixBin-methods	0.623	0.006	0.630
ScoreMatrixList-methods	1.167	0.013	1.184
annotateWithFeature-methods	0.047	0.001	0.048
annotateWithFeatureFlank-methods	0.285	0.001	0.286
annotateWithGeneParts-methods	0.613	0.006	0.620
binMatrix-methods	0.325	0.004	0.330
convertBed2Exons-methods	0.109	0.000	0.110
convertBed2Introns-methods	0.108	0.002	0.109
findFeatureComb-methods	0.457	0.006	0.462
getFeatsWithTargetsStats-methods	0.663	0.004	0.678
getFlanks-methods	0.160	0.001	0.160
getRandomEnrichment-methods	0.003	0.001	0.004
getTargetAnnotationStats-methods	0.603	0.005	0.609
gffToGRanges	0.102	0.002	0.103
heatMatrix	1.040	0.060	1.099
heatMeta	1.115	0.062	1.177
intersectScoreMatrixList-methods	0.458	0.005	0.463
multiHeatMatrix	1.150	0.062	1.213
orderBy-methods	1.173	0.007	1.182
patternMatrix-methods	0.231	0.005	0.237
plotGeneAnnotation-methods	1.307	0.010	1.318
plotMeta	0.849	0.047	0.896
plotTargetAnnotation-methods	0.877	0.021	0.900
readBed	0.053	0.002	0.055
readBroadPeak	0.043	0.001	0.044
readFeatureFlank-methods	0.164	0.001	0.164
readGeneric	0.045	0.001	0.046
readNarrowPeak	0.040	0.000	0.041
readTranscriptFeatures-methods	0.297	0.003	0.300
scaleScoreMatrix-methods	0.342	0.004	0.347
scaleScoreMatrixList	1.294	0.009	1.305