BioC 3.2: CHECK report for genomation on perceval

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: 2015-10-27 08:10:57 -0400 (Tue, 27 Oct 2015)

EndedAt: 2015-10-27 08:15:48 -0400 (Tue, 27 Oct 2015)

EllapsedTime: 290.8 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 Patched (2015-10-08 r69496)
* using platform: x86_64-apple-darwin10.8.0 (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 ... [23s/23s] 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’
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’
ScoreMatrixBin,GRanges-GRanges : .local: 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 ... [35s/35s] OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
ScoreMatrix-methods 4.885  0.178   5.062
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘genomation_unit_tests.R’ [33s/33s]
 [34s/34s] 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	1.083	0.041	1.124
ScoreMatrix-methods	4.885	0.178	5.062
ScoreMatrixBin-methods	0.858	0.011	0.868
ScoreMatrixList-methods	1.344	0.021	1.365
annotateWithFeature-methods	0.049	0.001	0.050
annotateWithFeatureFlank-methods	0.272	0.001	0.274
annotateWithGeneParts-methods	0.590	0.007	0.597
binMatrix-methods	0.453	0.008	0.461
convertBed2Exons-methods	0.113	0.001	0.114
convertBed2Introns-methods	0.117	0.001	0.118
findFeatureComb-methods	0.602	0.004	0.607
getFeatsWithTargetsStats-methods	0.559	0.002	0.561
getFlanks-methods	0.149	0.001	0.150
getRandomEnrichment-methods	0.003	0.001	0.004
getTargetAnnotationStats-methods	0.597	0.002	0.599
gffToGRanges	0.178	0.003	0.181
heatMatrix	1.263	0.091	1.355
heatMeta	1.182	0.077	1.260
intersectScoreMatrixList-methods	0.565	0.004	0.569
multiHeatMatrix	1.208	0.047	1.255
orderBy-methods	1.350	0.012	1.361
patternMatrix-methods	0.336	0.003	0.340
plotGeneAnnotation-methods	1.311	0.006	1.316
plotMeta	1.593	0.064	1.657
plotTargetAnnotation-methods	0.567	0.002	0.569
readBed	0.052	0.002	0.054
readBroadPeak	0.041	0.001	0.043
readFeatureFlank-methods	0.163	0.006	0.169
readGeneric	0.048	0.001	0.050
readNarrowPeak	0.041	0.001	0.042
readTranscriptFeatures-methods	0.293	0.003	0.296
scaleScoreMatrix-methods	0.454	0.004	0.459
scaleScoreMatrixList	1.396	0.006	1.402