BioC 3.2: CHECK report for ChIPQC on oaxaca

Package: ChIPQC

Version: 1.6.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings ChIPQC_1.6.1.tar.gz

StartedAt: 2016-04-22 22:37:45 -0700 (Fri, 22 Apr 2016)

EndedAt: 2016-04-22 22:45:16 -0700 (Fri, 22 Apr 2016)

EllapsedTime: 451.2 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: ChIPQC.Rcheck

Warnings: 2

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings ChIPQC_1.6.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/ChIPQC.Rcheck’
* using R version 3.2.4 (2016-03-10)
* 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 ‘1.6.1’
* 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 ... [33s/34s] 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 ... WARNING
'library' or 'require' call not declared from: ‘TxDb.Hsapiens.UCSC.hg38.knownGene’
'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 ... WARNING
Missing link or links in documentation object 'plotCC-methods.Rd':
  ‘ggplot2’

Missing link or links in documentation object 'plotCoverageHist-methods.Rd':
  ‘ggplot2’

Missing link or links in documentation object 'plotFribl-methods.Rd':
  ‘ggplot2’

Missing link or links in documentation object 'plotFrip-methods.Rd':
  ‘ggplot2’

Missing link or links in documentation object 'plotPeakProfile-methods.Rd':
  ‘ggplot2’

Missing link or links in documentation object 'plotRap-methods.Rd':
  ‘ggplot2’

Missing link or links in documentation object 'plotRegi-methods.Rd':
  ‘ggplot2’

Missing link or links in documentation object 'plotSSD-methods.Rd':
  ‘ggplot2’

See section 'Cross-references' in the 'Writing R Extensions' manual.

* 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 ... [96s/97s] OK
Examples with CPU or elapsed time > 5s
              user system elapsed
ChIPQCreport 54.36  1.759  56.555
* 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: 2 WARNINGs, 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.2-bioc/meat/ChIPQC.Rcheck/00check.log’
for details.

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

name	user	system	elapsed
ChIPQC-data	1.718	0.038	1.757
ChIPQC	1.051	0.023	1.075
ChIPQCexperiment-class	0.581	0.024	0.606
ChIPQCreport	54.360	1.759	56.555
ChIPQCsample-class	0.984	0.026	1.036
FragmentLengthCrossCoverage-methods	0.094	0.004	0.100
Normalisedaveragepeaksignal-methods	0.025	0.005	0.030
QCannotation-methods	0.014	0.005	0.018
QCcontrol-methods	0.246	0.009	0.256
QCdba-methods	0.118	0.006	0.125
QCmetadata-methods	0.129	0.008	0.137
QCmetrics-methods	0.612	0.013	0.625
QCsample-methods	0.070	0.006	0.075
ReadLengthCrossCoverage-methods	0.014	0.005	0.019
RelativeCrossCoverage-methods	0.078	0.006	0.085
averagepeaksignal-methods	0.023	0.006	0.030
coveragehistogram-methods	0.024	0.006	0.030
crosscoverage-methods	0.022	0.006	0.029
duplicateRate-methods	0.014	0.005	0.020
duplicates-methods	0.016	0.006	0.021
flagtagcounts-methods	0.015	0.006	0.021
fragmentlength-methods	0.074	0.005	0.080
frip-methods	0.015	0.006	0.020
mapped-methods	0.015	0.006	0.020
peaks-methods	0.088	0.006	0.095
plotCC-methods	0.950	0.010	0.961
plotCorHeatmap-methods	2.630	0.077	2.710
plotCoverageHist-methods	0.819	0.009	0.830
plotFribl-methods	0.879	0.005	0.885
plotFrip-methods	0.937	0.007	0.944
plotPeakProfile-methods	1.988	0.047	2.038
plotPrincomp-methods	3.108	0.080	3.192
plotRap-methods	1.148	0.009	1.159
plotRegi-methods	1.730	0.016	1.748
plotSSD-methods	1.656	0.015	1.673
readlength-methods	0.013	0.005	0.017
reads-methods	0.012	0.006	0.018
regi-methods	0.065	0.006	0.071
ribl-methods	0.015	0.006	0.021
rip-methods	0.012	0.005	0.018
ssd-methods	0.013	0.004	0.017