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: 2017-08-16 03:17:10 -0400 (Wed, 16 Aug 2017)

EndedAt: 2017-08-16 03:21:53 -0400 (Wed, 16 Aug 2017)

EllapsedTime: 282.0 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 3.4.1 (2017-06-30)
* 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	1.188	0.039	1.286
ScoreMatrix-methods	3.182	0.108	3.398
ScoreMatrixBin-methods	3.630	0.061	3.825
ScoreMatrixList-methods	0.916	0.014	0.973
annotateWithFeature-methods	0.041	0.002	0.045
annotateWithFeatureFlank-methods	0.385	0.002	0.400
annotateWithFeatures-methods	0.744	0.024	0.784
annotateWithGeneParts-methods	0.909	0.019	0.935
binMatrix-methods	0.269	0.005	0.290
convertBed2Exons-methods	0.099	0.001	0.104
convertBed2Introns-methods	0.184	0.003	0.193
findFeatureComb-methods	0.439	0.006	0.455
getFeatsWithTargetsStats-methods	0.476	0.008	0.508
getFlanks-methods	0.146	0.001	0.152
getRandomEnrichment-methods	0.004	0.001	0.005
getTargetAnnotationStats-methods	0.455	0.009	0.496
gffToGRanges	0.328	0.002	0.349
heatMatrix	0.945	0.091	1.092
heatMeta	1.093	0.082	1.258
heatTargetAnnotation-methods	0.694	0.014	0.750
intersectScoreMatrixList-methods	0.445	0.021	0.489
multiHeatMatrix	0.615	0.045	0.689
orderBy-methods	1.372	0.030	1.468
patternMatrix-methods	0.233	0.004	0.247
plotMeta	0.600	0.043	0.658
plotTargetAnnotation-methods	0.419	0.012	0.436
readBed	0.410	0.019	0.434
readBroadPeak	0.071	0.006	0.078
readFeatureFlank-methods	0.135	0.007	0.143
readGeneric	0.032	0.005	0.037
readNarrowPeak	0.037	0.005	0.044
readTranscriptFeatures-methods	0.213	0.006	0.227
scaleScoreMatrix-methods	0.277	0.005	0.287
scaleScoreMatrixList	1.041	0.009	1.103