BioC 3.3: CHECK report for ChIPpeakAnno on oaxaca

Package: ChIPpeakAnno

Version: 3.6.5

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings ChIPpeakAnno_3.6.5.tar.gz

StartedAt: 2016-10-13 00:03:50 -0700 (Thu, 13 Oct 2016)

EndedAt: 2016-10-13 00:11:33 -0700 (Thu, 13 Oct 2016)

EllapsedTime: 463.1 seconds

RetCode: 0

Status:  OK

CheckDir: ChIPpeakAnno.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 ChIPpeakAnno_3.6.5.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.3-bioc/meat/ChIPpeakAnno.Rcheck’
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ChIPpeakAnno/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ChIPpeakAnno’ version ‘3.6.5’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  ‘grid’ ‘IRanges’ ‘Biostrings’ ‘GenomicRanges’ ‘S4Vectors’
  ‘VennDiagram’
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 ‘ChIPpeakAnno’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is 20.0Mb
  sub-directories of 1Mb or more:
    data     12.7Mb
    doc       1.6Mb
    extdata   5.2Mb
* 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
BED2RangedData: no visible global function definition for 'read.delim'
GFF2RangedData: no visible global function definition for 'read.delim'
addGeneIDs : is.installed: no visible global function definition for
  'installed.packages'
binOverFeature: no visible global function definition for 'par'
binOverFeature : plotErrBar: no visible global function definition for
  'segments'
binOverFeature : plotErrBar: no visible global function definition for
  'par'
binOverFeature : <anonymous>: no visible global function definition for
  'plot'
binOverFeature : <anonymous>: no visible global function definition for
  'abline'
binOverFeature : <anonymous>: no visible global function definition for
  'axis'
buildBindingDistribution: no visible global function definition for
  'boxplot.stats'
buildBindingDistribution: no visible global function definition for
  'hist'
df2GRanges : <anonymous>: no visible global function definition for
  'rgb'
egOrgMap: no visible global function definition for 'adist'
featureAlignedDistribution: no visible global function definition for
  'matplot'
featureAlignedDistribution: no visible global function definition for
  'axis'
featureAlignedDistribution: no visible global function definition for
  'legend'
featureAlignedHeatmap: no visible global function definition for
  'colorRampPalette'
featureAlignedHeatmap : areColors : <anonymous>: no visible global
  function definition for 'col2rgb'
findOverlappingPeaks : <anonymous>: no visible binding for global
  variable 'data'
makeVennDiagram : plotVenn: no visible global function definition for
  'par'
makeVennDiagram : plotVenn: no visible global function definition for
  'plot.new'
mergePlusMinusPeaks: no visible global function definition for
  'read.table'
mergePlusMinusPeaks: no visible global function definition for
  'write.table'
newAnnoGR: no visible global function definition for 'setNames'
oligoSummary : subgroupMotif: no visible global function definition for
  'adist'
oligoSummary : subgroupMotif : <anonymous>: no visible global function
  definition for 'combn'
oligoSummary : subgroupMotif : <anonymous> : <anonymous>: no visible
  global function definition for 'combn'
oligoSummary: no visible global function definition for 'adist'
oligoSummary: no visible global function definition for 'hclust'
oligoSummary: no visible global function definition for 'kmeans'
oligoSummary: no visible global function definition for 'as.dendrogram'
oligoSummary: no visible binding for global variable 'nobs'
pie1: no visible global function definition for 'as.graphicsAnnot'
pie1: no visible global function definition for 'plot.new'
pie1: no visible global function definition for 'par'
pie1: no visible global function definition for 'dev.hold'
pie1: no visible global function definition for 'dev.flush'
pie1: no visible global function definition for 'plot.window'
pie1: no visible global function definition for 'polygon'
pie1: no visible global function definition for 'lines'
pie1: no visible global function definition for 'text'
pie1: no visible global function definition for 'title'
randPeaks: no visible global function definition for 'rexp'
summarizePatternInPeaks: no visible global function definition for
  'write.table'
toGRanges,character: no visible global function definition for
  'read.table'
toGRanges,connection: no visible global function definition for
  'read.table'
Undefined global functions or variables:
  abline adist as.dendrogram as.graphicsAnnot axis boxplot.stats
  col2rgb colorRampPalette combn data dev.flush dev.hold hclust hist
  installed.packages kmeans legend lines matplot nobs par plot plot.new
  plot.window polygon read.delim read.table rexp rgb segments setNames
  text title write.table
Consider adding
  importFrom("grDevices", "as.graphicsAnnot", "boxplot.stats", "col2rgb",
             "colorRampPalette", "dev.flush", "dev.hold", "rgb")
  importFrom("graphics", "abline", "axis", "hist", "legend", "lines",
             "matplot", "par", "plot", "plot.new", "plot.window",
             "polygon", "segments", "text", "title")
  importFrom("stats", "as.dendrogram", "hclust", "kmeans", "nobs",
             "rexp", "setNames")
  importFrom("utils", "adist", "combn", "data", "installed.packages",
             "read.delim", "read.table", "write.table")
to your NAMESPACE file.
* 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’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                user system elapsed
findEnhancers 24.896  0.203  25.556
addGeneIDs     1.276  0.237  35.457
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’
 OK
* checking for unstated dependencies in vignettes ... NOTE
'library' or 'require' call not declared from: ‘trackViewer’
* 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-3.3-bioc/meat/ChIPpeakAnno.Rcheck/00check.log’
for details.

* installing *source* package ‘ChIPpeakAnno’ ...
** 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 (ChIPpeakAnno)

name	user	system	elapsed
BED2RangedData	0.060	0.002	0.062
ChIPpeakAnno-package	0.001	0.001	0.002
ExonPlusUtr.human.GRCh37	4.679	0.111	4.810
GFF2RangedData	0.020	0.001	0.021
HOT.spots	0.652	0.034	0.742
IDRfilter	0.002	0.000	0.002
Peaks.Ste12.Replicate1	0.032	0.002	0.035
Peaks.Ste12.Replicate2	0.034	0.002	0.056
Peaks.Ste12.Replicate3	0.034	0.002	0.036
TSS.human.GRCh37	0.176	0.027	0.231
TSS.human.GRCh38	0.659	0.011	0.676
TSS.human.NCBI36	0.160	0.030	0.202
TSS.mouse.GRCm38	0.158	0.032	0.190
TSS.mouse.NCBIM37	0.148	0.028	0.178
TSS.rat.RGSC3.4	0.113	0.028	0.143
TSS.rat.Rnor_5.0	0.107	0.028	0.135
TSS.zebrafish.Zv8	0.112	0.028	0.149
TSS.zebrafish.Zv9	0.151	0.031	0.182
addAncestors	2.513	0.154	2.756
addGeneIDs	1.276	0.237	35.457
addMetadata	0.894	0.074	1.116
annoGR	0.001	0.000	0.043
annoPeaks	1.361	0.111	1.833
annotatePeakInBatch	2.267	0.155	2.465
annotatedPeak	0.138	0.010	0.148
assignChromosomeRegion	0.006	0.001	0.006
bdp	0.001	0.000	0.001
binOverFeature	0.509	0.029	0.549
condenseMatrixByColnames	0.024	0.001	0.025
convert2EntrezID	0.441	0.006	0.447
countPatternInSeqs	0.136	0.001	0.165
egOrgMap	0.001	0.000	0.001
enrichedGO	0.004	0.002	0.015
featureAlignedDistribution	0.580	0.005	0.814
featureAlignedHeatmap	0.779	0.006	0.859
featureAlignedSignal	0.508	0.025	0.534
findEnhancers	24.896	0.203	25.556
findOverlappingPeaks	0.004	0.001	0.004
findOverlapsOfPeaks	0.584	0.004	0.670
getAllPeakSequence	0.654	0.022	0.838
getAnnotation	0.002	0.000	0.001
getEnrichedGO	0.023	0.003	0.026
getEnrichedPATH	0.001	0.000	0.001
getGeneSeq	0.004	0.000	0.004
getUniqueGOidCount	0.002	0.000	0.003
getVennCounts	0.004	0.001	0.004
hyperGtest	0.002	0.000	0.002
makeVennDiagram	0.006	0.001	0.006
mergePlusMinusPeaks	0.003	0.000	0.004
myPeakList	0.050	0.013	0.062
oligoFrequency	0.012	0.002	0.013
oligoSummary	0.002	0.000	0.002
peakPermTest	0.002	0.000	0.003
peaksNearBDP	0.003	0.000	0.003
pie1	0.013	0.000	0.015
preparePool	0.001	0.000	0.002
reCenterPeaks	0.025	0.000	0.025
summarizeOverlapsByBins	0.253	0.132	3.485
summarizePatternInPeaks	0.654	0.062	0.720
toGRanges	0.031	0.001	0.055
translatePattern	0.001	0.000	0.001
wgEncodeTfbsV3	0.257	0.019	0.303
write2FASTA	0.015	0.001	0.015
xget	0.154	0.003	0.158