BioC 3.1: CHECK report for ChIPQC on morelia

Package: ChIPQC

Version: 1.4.4

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings ChIPQC_1.4.4.tar.gz

StartedAt: 2015-10-09 00:08:23 -0700 (Fri, 09 Oct 2015)

EndedAt: 2015-10-09 00:15:22 -0700 (Fri, 09 Oct 2015)

EllapsedTime: 418.6 seconds

RetCode: 0

Status:  OK

CheckDir: ChIPQC.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 ChIPQC_1.4.4.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.1-bioc/meat/ChIPQC.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ChIPQC/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ChIPQC’ version ‘1.4.4’
* 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 ‘ChIPQC’ can be installed ... [32s/35s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* 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
'library' or 'require' calls in package code:
  ‘TxDb.Celegans.UCSC.ce6.ensGene’
  ‘TxDb.Dmelanogaster.UCSC.dm3.ensGene’
  ‘TxDb.Hsapiens.UCSC.hg18.knownGene’
  ‘TxDb.Hsapiens.UCSC.hg19.knownGene’
  ‘TxDb.Hsapiens.UCSC.hg38.knownGene’
  ‘TxDb.Mmusculus.UCSC.mm10.knownGene’
  ‘TxDb.Mmusculus.UCSC.mm9.knownGene’
  ‘TxDb.Rnorvegicus.UCSC.rn4.ensGene’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... NOTE
Foreign function call to a different package:
  .Call("rle_sum_any", ..., PACKAGE = "chipseq")
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
* checking R code for possible problems ... NOTE
GetGRanges: warning in read.delim(LoadFile, sep = sepr, header = TRUE,
  comment = "#"): partial argument match of 'comment' to 'comment.char'
GetGRanges: no visible global function definition for ‘seqlevels<-’
findCovMaxPos: no visible global function definition for ‘seqlengths’
findCovMaxPos: no visible global function definition for ‘seqlengths<-’
getAnnotation: no visible binding for global variable
  ‘TxDb.Hsapiens.UCSC.hg19.knownGene’
getAnnotation: no visible binding for global variable
  ‘TxDb.Hsapiens.UCSC.hg18.knownGene’
getAnnotation: no visible binding for global variable
  ‘TxDb.Hsapiens.UCSC.hg38.knownGene’
getAnnotation: no visible binding for global variable
  ‘TxDb.Mmusculus.UCSC.mm10.knownGene’
getAnnotation: no visible binding for global variable
  ‘TxDb.Mmusculus.UCSC.mm9.knownGene’
getAnnotation: no visible binding for global variable
  ‘TxDb.Rnorvegicus.UCSC.rn4.ensGene’
getAnnotation: no visible binding for global variable
  ‘TxDb.Celegans.UCSC.ce6.ensGene’
getAnnotation: no visible binding for global variable
  ‘TxDb.Dmelanogaster.UCSC.dm3.ensGene’
getAnnotation: no visible global function definition for
  ‘fiveUTRsByTranscript’
getAnnotation: no visible global function definition for
  ‘threeUTRsByTranscript’
getAnnotation: no visible global function definition for ‘cdsBy’
getAnnotation: no visible global function definition for
  ‘intronsByTranscript’
getAnnotation: no visible global function definition for ‘transcripts’
getAnnotation: no visible global function definition for ‘seqlengths’
makeCCplot: no visible binding for global variable ‘Shift_Size’
makeCCplot: no visible binding for global variable ‘CC_Score’
makeCoveragePlot: no visible binding for global variable ‘Depth’
makeCoveragePlot: no visible binding for global variable ‘log10_bp’
makeCoveragePlot: no visible binding for global variable ‘Sample’
makeFriblPlot: no visible binding for global variable ‘Sample’
makeFriblPlot: no visible binding for global variable ‘FRIBL’
makeFriblPlot: no visible binding for global variable ‘Reads’
makeFripPlot: no visible binding for global variable ‘Sample’
makeFripPlot: no visible binding for global variable ‘FRIP’
makeFripPlot: no visible binding for global variable ‘Reads’
makePeakProfilePlot: no visible binding for global variable ‘Distance’
makePeakProfilePlot: no visible binding for global variable ‘Signal’
makeRapPlot: no visible binding for global variable ‘Sample’
makeRapPlot: no visible binding for global variable ‘CountsInPeaks’
makeRegiPlot: no visible binding for global variable ‘Sample’
makeRegiPlot: no visible binding for global variable ‘GenomicIntervals’
makeRegiPlot: no visible binding for global variable ‘log2_Enrichment’
makeSSDPlot: no visible binding for global variable ‘Sample’
makeSSDPlot: no visible global function definition for ‘geom_point’
sampleQC: no visible global function definition for ‘index’
sampleQC: no visible global function definition for ‘BamFile’
sampleQC: no visible global function definition for ‘indexBam’
sampleQC: no visible global function definition for ‘seqlevels<-’
plotCC,ChIPQCexperiment: no visible binding for global variable
  ‘Sample’
plotPeakProfile,ChIPQCexperiment: no visible binding for global
  variable ‘Sample’
plotRap,ChIPQCexperiment: no visible global function definition for
  ‘coord_cartesian’
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [80s/91s] OK
Examples with CPU or elapsed time > 5s
               user system elapsed
ChIPQCreport 42.302  3.517  54.938
* 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: 4 NOTEs
See
  ‘/Users/biocbuild/bbs-3.1-bioc/meat/ChIPQC.Rcheck/00check.log’
for details.

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

name	user	system	elapsed
ChIPQC-data	1.300	0.213	1.679
ChIPQC	0.787	0.018	0.806
ChIPQCexperiment-class	0.452	0.020	0.473
ChIPQCreport	42.302	3.517	54.938
ChIPQCsample-class	0.856	0.081	0.998
FragmentLengthCrossCoverage-methods	0.058	0.004	0.063
Normalisedaveragepeaksignal-methods	0.016	0.003	0.019
QCannotation-methods	0.013	0.003	0.015
QCcontrol-methods	0.237	0.008	0.246
QCdba-methods	0.100	0.031	0.131
QCmetadata-methods	0.115	0.007	0.122
QCmetrics-methods	0.431	0.011	0.441
QCsample-methods	0.052	0.004	0.057
ReadLengthCrossCoverage-methods	0.013	0.004	0.017
RelativeCrossCoverage-methods	0.072	0.004	0.076
averagepeaksignal-methods	0.029	0.006	0.035
coveragehistogram-methods	0.412	0.006	0.419
crosscoverage-methods	0.467	0.007	0.475
duplicateRate-methods	0.015	0.004	0.020
duplicates-methods	0.015	0.004	0.019
flagtagcounts-methods	0.011	0.004	0.015
fragmentlength-methods	0.091	0.006	0.096
frip-methods	0.015	0.004	0.018
mapped-methods	0.013	0.004	0.017
peaks-methods	0.066	0.004	0.069
plotCC-methods	0.727	0.063	0.890
plotCorHeatmap-methods	2.242	0.144	2.396
plotCoverageHist-methods	0.498	0.009	0.508
plotFribl-methods	0.462	0.009	0.470
plotFrip-methods	0.637	0.034	0.672
plotPeakProfile-methods	1.460	0.112	1.599
plotPrincomp-methods	2.780	0.245	3.068
plotRap-methods	0.761	0.105	0.934
plotRegi-methods	1.149	0.023	1.173
plotSSD-methods	1.100	0.077	1.179
readlength-methods	0.014	0.005	0.019
reads-methods	0.012	0.004	0.017
regi-methods	0.061	0.005	0.066
ribl-methods	0.015	0.005	0.019
rip-methods	0.012	0.004	0.016
ssd-methods	0.014	0.004	0.019