BioC 3.5: CHECK report for ChIPQC on malbec2

Package: ChIPQC

Version: 1.12.3

Command: /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings ChIPQC_1.12.3.tar.gz

StartedAt: 2017-10-17 21:54:40 -0400 (Tue, 17 Oct 2017)

EndedAt: 2017-10-17 22:00:18 -0400 (Tue, 17 Oct 2017)

EllapsedTime: 337.5 seconds

RetCode: 0

Status:  OK

CheckDir: ChIPQC.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings ChIPQC_1.12.3.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.5-bioc/meat/ChIPQC.Rcheck’
* using R version 3.4.2 (2017-09-28)
* using platform: x86_64-pc-linux-gnu (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 ‘1.12.3’
* 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
Namespace in Imports field not imported from: ‘TxDb.Hsapiens.UCSC.hg38.knownGene’
  All declared Imports should be used.
Unexported object imported by a ':::' call: ‘S4Vectors:::tabulate2’
  See the note in ?`:::` about the use of this operator.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘makeFripPlot’ ‘mergeMetadata’
* 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.hg38.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’
makeSSDPlot: no visible binding for global variable ‘Sample’
makeSSDPlot: no visible binding for global variable ‘SSD’
makeSSDPlot: no visible global function definition for ‘geom_point’
sampleQC: no visible global function definition for ‘seqlevels<-’
plotCC,ChIPQCexperiment: no visible binding for global variable
  ‘Sample’
plotCC,list: no visible binding for global variable ‘Sample’
plotPeakProfile,ChIPQCexperiment: no visible binding for global
  variable ‘Sample’
plotPeakProfile,list: no visible binding for global variable ‘Sample’
Undefined global functions or variables:
  CC_Score CountsInPeaks Depth Distance FRIBL FRIP GenomicIntervals
  Reads SSD Sample Shift_Size Signal TxDb.Hsapiens.UCSC.hg38.knownGene
  geom_point log10_bp log2_Enrichment seqlengths seqlengths<-
  seqlevels<-
Consider adding
  importFrom("stats", "SSD")
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 ... NOTE
  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 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 34.652  0.564  35.285
* 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
  ‘/home/biocbuild/bbs-3.5-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	2.492	0.032	2.523
ChIPQC	0.360	0.020	0.378
ChIPQCexperiment-class	0.532	0.012	0.544
ChIPQCreport	34.652	0.564	35.285
ChIPQCsample-class	1.856	0.040	2.209
FragmentLengthCrossCoverage-methods	0.076	0.000	0.076
Normalisedaveragepeaksignal-methods	0.028	0.004	0.034
QCannotation-methods	0.016	0.000	0.017
QCcontrol-methods	0.272	0.000	0.272
QCdba-methods	0.104	0.004	0.107
QCmetadata-methods	0.112	0.000	0.111
QCmetrics-methods	0.360	0.004	0.365
QCsample-methods	0.040	0.000	0.042
ReadLengthCrossCoverage-methods	0.016	0.000	0.016
RelativeCrossCoverage-methods	0.048	0.004	0.052
averagepeaksignal-methods	0.020	0.004	0.026
coveragehistogram-methods	0.024	0.000	0.026
crosscoverage-methods	0.020	0.004	0.024
duplicateRate-methods	0.012	0.004	0.016
duplicates-methods	0.012	0.000	0.015
flagtagcounts-methods	0.016	0.000	0.016
fragmentlength-methods	0.052	0.000	0.050
frip-methods	0.012	0.004	0.016
mapped-methods	0.016	0.000	0.015
peaks-methods	0.048	0.000	0.048
plotCC-methods	1.584	0.000	1.587
plotCorHeatmap-methods	0.216	0.000	0.217
plotCoverageHist-methods	0.612	0.000	0.615
plotFribl-methods	0.656	0.000	0.657
plotFrip-methods	0.744	0.000	0.743
plotPeakProfile-methods	1.696	0.008	1.706
plotPrincomp-methods	0.268	0.004	0.274
plotRap-methods	0.856	0.000	0.857
plotRegi-methods	1.308	0.000	1.310
plotSSD-methods	2.756	0.036	2.799
readlength-methods	0.012	0.004	0.016
reads-methods	0.016	0.000	0.015
regi-methods	0.036	0.004	0.041
ribl-methods	0.016	0.000	0.015
rip-methods	0.016	0.000	0.016
ssd-methods	0.012	0.004	0.015