BioC 3.6: CHECK report for genomation on veracruz1

Package: genomation

Version: 1.9.3

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings genomation_1.9.3.tar.gz

StartedAt: 2017-08-16 03:33:32 -0400 (Wed, 16 Aug 2017)

EndedAt: 2017-08-16 03:38:03 -0400 (Wed, 16 Aug 2017)

EllapsedTime: 270.4 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_1.9.3.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.6-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 ‘1.9.3’
* 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 ... NOTE
ScoreMatrixBin,RleList-GRangesList: no visible binding for global
  variable ‘cvg’
ScoreMatrixBin,RleList-GRangesList: no visible binding for global
  variable ‘id’
ScoreMatrixBin,RleList-GRangesList: no visible global function
  definition for ‘:=’
Undefined global functions or variables:
  := cvg id
* 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: 4 NOTEs
See
  ‘/Users/biocbuild/bbs-3.6-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	1.087	0.036	1.160
ScoreMatrix-methods	2.671	0.118	2.837
ScoreMatrixBin-methods	2.600	0.084	2.761
ScoreMatrixList-methods	0.796	0.018	0.839
annotateWithFeature-methods	0.042	0.002	0.043
annotateWithFeatureFlank-methods	0.459	0.004	0.478
annotateWithFeatures-methods	0.905	0.075	0.739
annotateWithGeneParts-methods	0.963	0.044	0.866
binMatrix-methods	0.203	0.004	0.231
convertBed2Exons-methods	0.083	0.000	0.084
convertBed2Introns-methods	0.142	0.000	0.148
findFeatureComb-methods	0.355	0.005	0.377
getFeatsWithTargetsStats-methods	0.379	0.008	0.401
getFlanks-methods	0.134	0.001	0.142
getRandomEnrichment-methods	0.003	0.001	0.013
getTargetAnnotationStats-methods	0.381	0.006	0.420
gffToGRanges	0.300	0.003	0.313
heatMatrix	1.152	0.055	1.252
heatMeta	0.858	0.050	0.920
heatTargetAnnotation-methods	0.815	0.063	0.587
intersectScoreMatrixList-methods	0.589	0.043	0.332
multiHeatMatrix	0.536	0.036	0.605
orderBy-methods	0.891	0.029	0.944
patternMatrix-methods	0.181	0.003	0.191
plotMeta	0.492	0.030	0.555
plotTargetAnnotation-methods	0.327	0.006	0.340
readBed	0.313	0.024	0.344
readBroadPeak	0.052	0.005	0.063
readFeatureFlank-methods	0.119	0.005	0.133
readGeneric	0.027	0.004	0.032
readNarrowPeak	0.026	0.006	0.032
readTranscriptFeatures-methods	0.168	0.006	0.181
scaleScoreMatrix-methods	0.225	0.004	0.231
scaleScoreMatrixList	0.994	0.008	1.022