BioC 3.5: CHECK report for genomation on malbec2

Package: genomation

Version: 1.8.0

Command: /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings genomation_1.8.0.tar.gz

StartedAt: 2017-10-17 23:28:54 -0400 (Tue, 17 Oct 2017)

EndedAt: 2017-10-17 23:33:04 -0400 (Tue, 17 Oct 2017)

EllapsedTime: 249.5 seconds

RetCode: 0

Status:  OK

CheckDir: genomation.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings genomation_1.8.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.5-bioc/meat/genomation.Rcheck’
* using R version 3.4.2 (2017-09-28)
* using platform: x86_64-pc-linux-gnu (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  5.7Mb
  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
  ‘/home/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	1.368	0.060	1.433
ScoreMatrix-methods	3.78	0.20	3.98
ScoreMatrixBin-methods	2.828	0.028	2.857
ScoreMatrixList-methods	0.888	0.000	0.888
annotateWithFeature-methods	0.036	0.000	0.037
annotateWithFeatureFlank-methods	0.304	0.000	0.306
annotateWithFeatures-methods	0.624	0.000	0.606
annotateWithGeneParts-methods	0.684	0.008	0.691
binMatrix-methods	0.220	0.000	0.219
convertBed2Exons-methods	0.088	0.000	0.088
convertBed2Introns-methods	0.132	0.000	0.134
findFeatureComb-methods	0.336	0.000	0.338
getFeatsWithTargetsStats-methods	0.448	0.004	0.452
getFlanks-methods	0.108	0.000	0.106
getRandomEnrichment-methods	0.004	0.000	0.002
getTargetAnnotationStats-methods	0.324	0.004	0.327
gffToGRanges	0.232	0.000	0.233
heatMatrix	1.504	0.188	1.693
heatMeta	1.124	0.004	1.128
heatTargetAnnotation-methods	0.528	0.004	0.513
intersectScoreMatrixList-methods	0.304	0.000	0.303
multiHeatMatrix	0.396	0.000	0.396
orderBy-methods	0.792	0.004	0.797
patternMatrix-methods	0.192	0.000	0.192
plotMeta	0.956	0.000	0.954
plotTargetAnnotation-methods	0.464	0.004	0.466
readBed	0.376	0.016	0.393
readBroadPeak	0.060	0.004	0.065
readFeatureFlank-methods	0.104	0.004	0.110
readGeneric	0.036	0.004	0.038
readNarrowPeak	0.048	0.000	0.048
readTranscriptFeatures-methods	0.264	0.000	0.264
scaleScoreMatrix-methods	0.276	0.004	0.284
scaleScoreMatrixList	1.300	0.004	1.301