BioC 3.3: CHECK report for ChIPpeakAnno on morelia

Package: ChIPpeakAnno

Version: 3.5.15

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings ChIPpeakAnno_3.5.15.tar.gz

StartedAt: 2016-04-21 00:14:52 -0700 (Thu, 21 Apr 2016)

EndedAt: 2016-04-21 00:23:22 -0700 (Thu, 21 Apr 2016)

EllapsedTime: 509.6 seconds

RetCode: 0

Status:  OK

CheckDir: ChIPpeakAnno.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings ChIPpeakAnno_3.5.15.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.3-bioc/meat/ChIPpeakAnno.Rcheck’
* using R version 3.3.0 beta (2016-04-06 r70435)
* 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 ‘3.5.15’
* 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 ... [30s/33s] OK
* checking installed package size ... NOTE
  installed size is 20.0Mb
  sub-directories of 1Mb or more:
    data     12.7Mb
    doc       1.5Mb
    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 ... [70s/114s] OK
Examples with CPU or elapsed time > 5s
                user system elapsed
findEnhancers 25.146  0.190  26.532
addGeneIDs     1.564  0.303  45.891
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’ [62s/70s]
 [63s/70s] 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-3.3-bioc/meat/ChIPpeakAnno.Rcheck/00check.log’
for details.

* installing *source* package ‘ChIPpeakAnno’ ...
** R
** data
** inst
** preparing package for lazy loading
Warning: replacing previous import 'GenomicFeatures::transcriptLengths' by 'ensembldb::transcriptLengths' when loading 'ChIPpeakAnno'
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning: replacing previous import 'GenomicFeatures::transcriptLengths' by 'ensembldb::transcriptLengths' when loading 'ChIPpeakAnno'
* DONE (ChIPpeakAnno)

name	user	system	elapsed
BED2RangedData	0.059	0.000	0.060
ChIPpeakAnno-package	0.002	0.000	0.001
ExonPlusUtr.human.GRCh37	4.818	0.128	4.984
GFF2RangedData	0.020	0.001	0.021
HOT.spots	0.165	0.027	0.194
IDRfilter	0.001	0.000	0.001
Peaks.Ste12.Replicate1	0.037	0.002	0.040
Peaks.Ste12.Replicate2	0.038	0.003	0.041
Peaks.Ste12.Replicate3	0.039	0.004	0.041
TSS.human.GRCh37	0.178	0.030	0.210
TSS.human.GRCh38	0.931	0.014	0.955
TSS.human.NCBI36	0.256	0.030	0.290
TSS.mouse.GRCm38	0.686	0.041	0.730
TSS.mouse.NCBIM37	0.159	0.031	0.202
TSS.rat.RGSC3.4	0.116	0.030	0.146
TSS.rat.Rnor_5.0	0.108	0.029	0.137
TSS.zebrafish.Zv8	0.101	0.028	0.130
TSS.zebrafish.Zv9	0.125	0.030	0.156
addAncestors	2.243	0.138	2.394
addGeneIDs	1.564	0.303	45.891
addMetadata	1.199	0.078	1.325
annoGR	0.001	0.001	0.029
annoPeaks	1.581	0.131	1.988
annotatePeakInBatch	2.761	0.153	3.024
annotatedPeak	0.137	0.009	0.146
assignChromosomeRegion	0.003	0.000	0.003
bdp	0.001	0.000	0.000
binOverFeature	0.557	0.035	0.593
condenseMatrixByColnames	0.029	0.000	0.030
convert2EntrezID	0.528	0.007	0.536
countPatternInSeqs	0.183	0.001	0.184
egOrgMap	0.001	0.000	0.002
enrichedGO	0.004	0.002	0.006
featureAlignedDistribution	0.173	0.001	0.175
featureAlignedHeatmap	0.338	0.003	0.342
featureAlignedSignal	0.096	0.019	0.116
findEnhancers	25.146	0.190	26.532
findOverlappingPeaks	0.004	0.001	0.005
findOverlapsOfPeaks	0.567	0.004	0.653
getAllPeakSequence	1.258	0.029	1.442
getAnnotation	0.001	0.000	0.009
getEnrichedGO	0.026	0.003	0.029
getEnrichedPATH	0.002	0.000	0.001
getGeneSeq	0.007	0.000	0.007
getUniqueGOidCount	0.003	0.000	0.004
getVennCounts	0.003	0.000	0.003
hyperGtest	0.003	0.000	0.004
makeVennDiagram	0.008	0.001	0.009
mergePlusMinusPeaks	0.003	0.000	0.003
myPeakList	0.022	0.010	0.032
oligoFrequency	0.011	0.002	0.034
oligoSummary	0.002	0.000	0.002
peakPermTest	0.004	0.000	0.004
peaksNearBDP	0.003	0.000	0.003
pie1	0.016	0.001	0.018
preparePool	0.003	0.000	0.002
reCenterPeaks	0.019	0.000	0.019
summarizeOverlapsByBins	0.332	0.109	3.551
summarizePatternInPeaks	0.754	0.073	0.828
toGRanges	0.035	0.003	0.063
translatePattern	0.001	0.000	0.001
wgEncodeTfbsV3	0.254	0.020	0.274
write2FASTA	0.018	0.001	0.020
xget	0.168	0.007	0.175