BioC 3.5: CHECK report for ChIPQC on oaxaca

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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_1.11.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/ChIPQC.Rcheck’
* using R Under development (unstable) (2016-10-21 r71549)
* 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 ‘1.11.0’
* 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 ... OK
* checking installed package size ... OK
* 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 loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
Unexported object imported by a ':::' call: ‘S4Vectors:::tabulate2’
  See the note in ?`:::` about the use of this operator.
* 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: 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.hg20.knownGene’
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’
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’
Undefined global functions or variables:
  CC_Score CountsInPeaks Depth Distance FRIBL FRIP GenomicIntervals
  Reads Sample Shift_Size Signal TxDb.Hsapiens.UCSC.hg20.knownGene
  log10_bp log2_Enrichment seqlengths seqlengths<- seqlevels<-
* 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 ... NOTE
  Error : .onLoad failed in loadNamespace() for 'TxDb.Hsapiens.UCSC.hg19.knownGene', details:
    call: initialize(value, ...)
    error: attempt to apply non-function
  Error in .requirePackage(package) : 
    unable to find required package 'ChIPQC'
  Calls: <Anonymous> ... getClass -> getClassDef -> .classEnv -> .requirePackage
  Execution halted
* 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 ... OK
Examples with CPU or elapsed time > 5s
               user system elapsed
ChIPQCreport 37.406  1.398  39.062
* 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-3.5-bioc/meat/ChIPQC.Rcheck/00check.log’
for details.

name	user	system	elapsed
ChIPQC-data	2.115	0.069	2.263
ChIPQC	0.615	0.019	0.634
ChIPQCexperiment-class	0.576	0.021	0.596
ChIPQCreport	37.406	1.398	39.062
ChIPQCsample-class	1.142	0.023	1.293
FragmentLengthCrossCoverage-methods	0.064	0.004	0.068
Normalisedaveragepeaksignal-methods	0.024	0.006	0.031
QCannotation-methods	0.016	0.004	0.021
QCcontrol-methods	0.236	0.013	0.249
QCdba-methods	0.136	0.009	0.145
QCmetadata-methods	0.159	0.010	0.170
QCmetrics-methods	0.598	0.016	0.614
QCsample-methods	0.061	0.008	0.069
ReadLengthCrossCoverage-methods	0.019	0.008	0.026
RelativeCrossCoverage-methods	0.075	0.007	0.082
averagepeaksignal-methods	0.027	0.006	0.042
coveragehistogram-methods	0.029	0.008	0.038
crosscoverage-methods	0.025	0.008	0.033
duplicateRate-methods	0.020	0.007	0.027
duplicates-methods	0.019	0.006	0.026
flagtagcounts-methods	0.020	0.007	0.026
fragmentlength-methods	0.088	0.008	0.095
frip-methods	0.021	0.007	0.028
mapped-methods	0.020	0.008	0.028
peaks-methods	0.064	0.007	0.071
plotCC-methods	0.773	0.010	0.786
plotCorHeatmap-methods	0.305	0.012	0.317
plotCoverageHist-methods	0.718	0.009	0.728
plotFribl-methods	0.861	0.011	0.873
plotFrip-methods	0.771	0.010	0.798
plotPeakProfile-methods	1.787	0.041	1.830
plotPrincomp-methods	0.332	0.012	0.346
plotRap-methods	1.539	0.018	1.558
plotRegi-methods	1.577	0.025	1.604
readlength-methods	0.020	0.007	0.028
reads-methods	0.019	0.006	0.026
regi-methods	0.063	0.007	0.070
ribl-methods	0.020	0.007	0.027
rip-methods	0.020	0.006	0.025
ssd-methods	0.021	0.007	0.027

BioC 3.5: CHECK report for ChIPQC on oaxaca

Summary

Command output