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BioC 3.3: CHECK report for ChIPpeakAnno on zin2

This page was generated on 2016-10-13 12:42:11 -0700 (Thu, 13 Oct 2016).

Package 177/1210HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ChIPpeakAnno 3.6.5
Lihua Julie Zhu , Jianhong Ou
Snapshot Date: 2016-10-12 17:20:15 -0700 (Wed, 12 Oct 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_3/madman/Rpacks/ChIPpeakAnno
Last Changed Rev: 119313 / Revision: 122332
Last Changed Date: 2016-07-12 07:18:50 -0700 (Tue, 12 Jul 2016)
zin2 Linux (Ubuntu 14.04.2 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: ChIPpeakAnno
Version: 3.6.5
Command: /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings ChIPpeakAnno_3.6.5.tar.gz
StartedAt: 2016-10-13 00:23:06 -0700 (Thu, 13 Oct 2016)
EndedAt: 2016-10-13 00:28:31 -0700 (Thu, 13 Oct 2016)
EllapsedTime: 324.9 seconds
RetCode: 0
Status:  OK 
CheckDir: ChIPpeakAnno.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings ChIPpeakAnno_3.6.5.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.3-bioc/meat/ChIPpeakAnno.Rcheck’
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-pc-linux-gnu (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 19.4Mb
  sub-directories of 1Mb or more:
    data     12.7Mb
    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 17.627  0.045  17.866
addGeneIDs     1.134  0.224   6.982
* 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
  ‘/home/biocbuild/bbs-3.3-bioc/meat/ChIPpeakAnno.Rcheck/00check.log’
for details.


ChIPpeakAnno.Rcheck/00install.out:

* 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)

ChIPpeakAnno.Rcheck/ChIPpeakAnno-Ex.timings:

nameusersystemelapsed
BED2RangedData0.0540.0000.055
ChIPpeakAnno-package0.0000.0000.001
ExonPlusUtr.human.GRCh374.1190.1764.301
GFF2RangedData0.0150.0000.015
HOT.spots0.6060.0080.614
IDRfilter0.0010.0000.001
Peaks.Ste12.Replicate10.0270.0000.028
Peaks.Ste12.Replicate20.0170.0080.024
Peaks.Ste12.Replicate30.0230.0000.024
TSS.human.GRCh370.1510.0040.154
TSS.human.GRCh380.4510.0120.463
TSS.human.NCBI360.1430.0010.146
TSS.mouse.GRCm380.1390.0040.144
TSS.mouse.NCBIM370.1210.0070.129
TSS.rat.RGSC3.40.10.00.1
TSS.rat.Rnor_5.00.0840.0080.092
TSS.zebrafish.Zv80.0940.0000.094
TSS.zebrafish.Zv90.1150.0040.119
addAncestors2.0820.0392.210
addGeneIDs1.1340.2246.982
addMetadata0.6910.0480.744
annoGR0.0010.0000.000
annoPeaks1.0660.0551.206
annotatePeakInBatch1.7930.0521.853
annotatedPeak0.1150.0000.115
assignChromosomeRegion0.0030.0000.003
bdp0.0010.0000.001
binOverFeature0.4310.0040.435
condenseMatrixByColnames0.0170.0000.017
convert2EntrezID0.3300.0080.338
countPatternInSeqs0.0970.0040.102
egOrgMap0.0010.0000.001
enrichedGO0.0020.0000.003
featureAlignedDistribution0.3890.0040.393
featureAlignedHeatmap0.5360.0000.537
featureAlignedSignal0.3510.0240.375
findEnhancers17.627 0.04517.866
findOverlappingPeaks0.0000.0040.003
findOverlapsOfPeaks0.4460.0000.486
getAllPeakSequence0.5880.0200.661
getAnnotation0.0010.0000.000
getEnrichedGO0.0120.0040.016
getEnrichedPATH0.0010.0000.001
getGeneSeq0.0030.0000.003
getUniqueGOidCount0.0020.0000.002
getVennCounts0.0020.0000.002
hyperGtest0.0020.0000.002
makeVennDiagram0.0050.0000.004
mergePlusMinusPeaks0.0020.0000.002
myPeakList0.0230.0000.023
oligoFrequency0.0020.0040.009
oligoSummary0.0010.0000.001
peakPermTest0.0030.0000.002
peaksNearBDP0.0020.0000.001
pie10.0130.0000.013
preparePool0.0010.0000.001
reCenterPeaks0.0190.0000.019
summarizeOverlapsByBins0.1530.0272.786
summarizePatternInPeaks0.5980.0200.631
toGRanges0.0230.0000.025
translatePattern0.0010.0000.001
wgEncodeTfbsV30.2510.0280.279
write2FASTA0.0110.0000.011
xget0.1600.0040.164