BioC 3.5: CHECK report for ChIPQC on tokay2

Package: ChIPQC

Version: 1.12.3

Command: rm -rf ChIPQC.buildbin-libdir ChIPQC.Rcheck && mkdir ChIPQC.buildbin-libdir ChIPQC.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=ChIPQC.buildbin-libdir ChIPQC_1.12.3.tar.gz >ChIPQC.Rcheck\00install.out 2>&1 && cp ChIPQC.Rcheck\00install.out ChIPQC-install.out && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=ChIPQC.buildbin-libdir --install="check:ChIPQC-install.out" --force-multiarch --no-vignettes --timings ChIPQC_1.12.3.tar.gz

StartedAt: 2017-08-15 22:39:22 -0400 (Tue, 15 Aug 2017)

EndedAt: 2017-08-15 22:49:01 -0400 (Tue, 15 Aug 2017)

EllapsedTime: 579.0 seconds

RetCode: 0

Status:  OK

CheckDir: ChIPQC.Rcheck

Warnings: 0

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### Running command:
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###   rm -rf ChIPQC.buildbin-libdir ChIPQC.Rcheck && mkdir ChIPQC.buildbin-libdir ChIPQC.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=ChIPQC.buildbin-libdir ChIPQC_1.12.3.tar.gz >ChIPQC.Rcheck\00install.out 2>&1 && cp ChIPQC.Rcheck\00install.out ChIPQC-install.out  &&  C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=ChIPQC.buildbin-libdir --install="check:ChIPQC-install.out" --force-multiarch --no-vignettes --timings ChIPQC_1.12.3.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.5-bioc/meat/ChIPQC.Rcheck'
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* 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 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
              user system elapsed
ChIPQCreport 30.56   2.55   33.28
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
              user system elapsed
ChIPQCreport 39.58   2.61   42.34
* 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
  'C:/Users/biocbuild/bbs-3.5-bioc/meat/ChIPQC.Rcheck/00check.log'
for details.

install for i386

* 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

install for x64

* installing *source* package 'ChIPQC' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'ChIPQC' as ChIPQC_1.12.3.zip
* DONE (ChIPQC)

name	user	system	elapsed
ChIPQC-data	2.19	0.09	2.28
ChIPQC	0.50	0.05	0.55
ChIPQCexperiment-class	0.95	0.01	0.97
ChIPQCreport	30.56	2.55	33.28
ChIPQCsample-class	2.38	0.03	2.41
FragmentLengthCrossCoverage-methods	0.06	0.02	0.08
Normalisedaveragepeaksignal-methods	0.03	0.01	0.04
QCannotation-methods	0.00	0.03	0.04
QCcontrol-methods	0.33	0.02	0.34
QCdba-methods	0.14	0.00	0.14
QCmetadata-methods	0.20	0.01	0.22
QCmetrics-methods	0.69	0.02	0.70
QCsample-methods	0.08	0.00	0.08
ReadLengthCrossCoverage-methods	0.01	0.02	0.03
RelativeCrossCoverage-methods	0.09	0.00	0.09
averagepeaksignal-methods	0.05	0.01	0.06
coveragehistogram-methods	0.06	0.00	0.07
crosscoverage-methods	0.05	0.00	0.04
duplicateRate-methods	0.05	0.00	0.05
duplicates-methods	0.01	0.02	0.03
flagtagcounts-methods	0.03	0.01	0.05
fragmentlength-methods	0.10	0.02	0.11
frip-methods	0.01	0.01	0.03
mapped-methods	0.02	0.02	0.03
peaks-methods	0.05	0.00	0.05
plotCC-methods	2.2	0.0	2.2
plotCorHeatmap-methods	0.39	0.02	0.41
plotCoverageHist-methods	1.05	0.01	1.06
plotFribl-methods	1.04	0.02	1.06
plotFrip-methods	1.14	0.01	1.16
plotPeakProfile-methods	2.80	0.02	2.81
plotPrincomp-methods	0.47	0.00	0.47
plotRap-methods	0.94	0.01	0.95
plotRegi-methods	1.89	0.00	1.89
plotSSD-methods	1.92	0.05	1.97
readlength-methods	0.03	0.00	0.03
reads-methods	0.02	0.00	0.02
regi-methods	0.04	0.02	0.06
ribl-methods	0.02	0.00	0.02
rip-methods	0.02	0.01	0.03
ssd-methods	0.01	0.02	0.03

name	user	system	elapsed
ChIPQC-data	3.1	0.0	3.1
ChIPQC	0.45	0.00	0.45
ChIPQCexperiment-class	0.45	0.00	0.45
ChIPQCreport	39.58	2.61	42.34
ChIPQCsample-class	2.5	0.0	2.5
FragmentLengthCrossCoverage-methods	0.08	0.00	0.08
Normalisedaveragepeaksignal-methods	0.01	0.02	0.03
QCannotation-methods	0.02	0.01	0.03
QCcontrol-methods	0.28	0.00	0.29
QCdba-methods	0.11	0.02	0.12
QCmetadata-methods	0.11	0.03	0.14
QCmetrics-methods	0.56	0.00	0.56
QCsample-methods	0.06	0.00	0.07
ReadLengthCrossCoverage-methods	0.02	0.00	0.01
RelativeCrossCoverage-methods	0.06	0.01	0.08
averagepeaksignal-methods	0.03	0.02	0.05
coveragehistogram-methods	0.03	0.00	0.03
crosscoverage-methods	0.03	0.00	0.03
duplicateRate-methods	0.03	0.00	0.03
duplicates-methods	0.02	0.00	0.02
flagtagcounts-methods	0.02	0.02	0.03
fragmentlength-methods	0.06	0.00	0.06
frip-methods	0.01	0.01	0.03
mapped-methods	0.02	0.00	0.02
peaks-methods	0.05	0.02	0.06
plotCC-methods	1.65	0.01	1.67
plotCorHeatmap-methods	0.97	0.03	1.00
plotCoverageHist-methods	0.72	0.00	0.72
plotFribl-methods	0.77	0.00	0.77
plotFrip-methods	0.84	0.02	0.85
plotPeakProfile-methods	1.87	0.02	1.90
plotPrincomp-methods	0.33	0.00	0.32
plotRap-methods	0.99	0.00	0.99
plotRegi-methods	1.65	0.00	1.65
plotSSD-methods	2.05	0.00	2.05
readlength-methods	0.02	0.00	0.02
reads-methods	0.01	0.00	0.01
regi-methods	0.05	0.01	0.07
ribl-methods	0.02	0.00	0.01
rip-methods	0.00	0.02	0.02
ssd-methods	0.02	0.00	0.02