BioC 3.1: CHECK report for genomation on zin2

Package: genomation

Version: 1.0.0

Command: /home/biocbuild/bbs-3.1-bioc/R/bin/R CMD check --no-vignettes --timings genomation_1.0.0.tar.gz

StartedAt: 2015-10-09 01:38:57 -0700 (Fri, 09 Oct 2015)

EndedAt: 2015-10-09 01:42:39 -0700 (Fri, 09 Oct 2015)

EllapsedTime: 221.3 seconds

RetCode: 0

Status:  OK

CheckDir: genomation.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.1-bioc/R/bin/R CMD check --no-vignettes --timings genomation_1.0.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.1-bioc/meat/genomation.Rcheck’
* using R version 3.2.2 (2015-08-14)
* 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 ‘1.0.0’
* 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 ... [12s/18s] 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 loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
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
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’
* 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 ... [9s/13s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘genomation_unit_tests.R’ [18s/27s]
 [18s/27s] 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-3.1-bioc/meat/genomation.Rcheck/00check.log’
for details.

* installing *source* package ‘genomation’ ...
** R
** data
** inst
** preparing package for lazy loading
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
* DONE (genomation)

name	user	system	elapsed
AnnotationByGeneParts-methods	0.763	0.008	1.216
ScoreMatrix-methods	0.001	0.000	0.000
ScoreMatrixBin-methods	0.000	0.000	0.001
ScoreMatrixList-methods	0.001	0.000	0.000
annotateWithFeature-methods	0.036	0.000	0.065
annotateWithFeatureFlank-methods	0.218	0.000	0.234
annotateWithGeneParts-methods	0.001	0.000	0.001
binMatrix-methods	0.000	0.000	0.001
convertBed2Exons-methods	0.084	0.000	0.135
convertBed2Introns-methods	0.085	0.000	0.118
findFeatureComb-methods	0.335	0.008	0.378
getFeatsWithTargetsStats-methods	0.420	0.004	0.495
getFlanks-methods	0.131	0.000	0.292
getRandomEnrichment-methods	0	0	0
getTargetAnnotationStats-methods	0.428	0.000	0.735
gffToGRanges	0	0	0
heatMatrix	0.001	0.000	0.001
heatMeta	0.001	0.000	0.000
intersectScoreMatrixList-methods	0.001	0.000	0.001
multiHeatMatrix	0.001	0.000	0.000
orderBy-methods	0.000	0.000	0.001
plotGeneAnnotation-methods	0	0	0
plotMeta	0.000	0.000	0.001
plotTargetAnnotation-methods	0.411	0.000	0.489
readBed	0	0	0
readBroadPeak	0.000	0.000	0.001
readFeatureFlank-methods	0.000	0.000	0.001
readGeneric	0.001	0.000	0.000
readNarrowPeak	0.001	0.000	0.000
readTranscriptFeatures-methods	0.000	0.000	0.001
scaleScoreMatrix-methods	0.001	0.000	0.001
scaleScoreMatrixList	0.001	0.000	0.013