BioC 3.5: CHECK report for genomation on veracruz2

Package: genomation

Version: 1.8.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings genomation_1.8.0.tar.gz

StartedAt: 2017-10-18 04:03:22 -0400 (Wed, 18 Oct 2017)

EndedAt: 2017-10-18 04:08:02 -0400 (Wed, 18 Oct 2017)

EllapsedTime: 279.3 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_1.8.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/genomation.Rcheck’
* using R version 3.4.2 (2017-09-28)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘1.8.0’
* 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 ... OK
* checking installed package size ... NOTE
  installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc       3.6Mb
    extdata   1.2Mb
* 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
Namespace in Imports field not imported from: ‘RUnit’
  All declared Imports should be used.
Unexported object imported by a ':::' call: ‘BiocGenerics:::testPackage’
  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 ... 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... 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 ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘genomation_unit_tests.R’
 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-3.5-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	1.377	0.055	1.477
ScoreMatrix-methods	3.753	0.150	4.013
ScoreMatrixBin-methods	3.811	0.094	4.015
ScoreMatrixList-methods	1.051	0.015	1.093
annotateWithFeature-methods	0.049	0.002	0.052
annotateWithFeatureFlank-methods	0.405	0.003	0.424
annotateWithFeatures-methods	0.852	0.047	0.804
annotateWithGeneParts-methods	0.961	0.036	0.903
binMatrix-methods	0.231	0.004	0.239
convertBed2Exons-methods	0.098	0.001	0.102
convertBed2Introns-methods	0.148	0.002	0.163
findFeatureComb-methods	0.351	0.005	0.368
getFeatsWithTargetsStats-methods	0.372	0.008	0.397
getFlanks-methods	0.135	0.001	0.139
getRandomEnrichment-methods	0.002	0.001	0.003
getTargetAnnotationStats-methods	0.361	0.006	0.382
gffToGRanges	0.273	0.002	0.282
heatMatrix	0.840	0.079	0.949
heatMeta	0.984	0.053	1.062
heatTargetAnnotation-methods	0.814	0.054	0.582
intersectScoreMatrixList-methods	0.553	0.038	0.301
multiHeatMatrix	0.936	0.064	1.026
orderBy-methods	0.939	0.029	0.997
patternMatrix-methods	0.179	0.006	0.187
plotMeta	0.548	0.042	0.603
plotTargetAnnotation-methods	0.331	0.009	0.352
readBed	0.347	0.015	0.381
readBroadPeak	0.053	0.004	0.058
readFeatureFlank-methods	0.103	0.004	0.110
readGeneric	0.029	0.004	0.032
readNarrowPeak	0.021	0.003	0.027
readTranscriptFeatures-methods	0.175	0.006	0.186
scaleScoreMatrix-methods	0.198	0.005	0.209
scaleScoreMatrixList	0.978	0.011	1.005