BioC 3.4: CHECK report for ChIPQC on tokay1

Package: ChIPQC

Version: 1.10.3

Command: rm -rf ChIPQC.buildbin-libdir ChIPQC.Rcheck && mkdir ChIPQC.buildbin-libdir ChIPQC.Rcheck && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=ChIPQC.buildbin-libdir ChIPQC_1.10.3.tar.gz >ChIPQC.Rcheck\00install.out 2>&1 && cp ChIPQC.Rcheck\00install.out ChIPQC-install.out && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD check --library=ChIPQC.buildbin-libdir --install="check:ChIPQC-install.out" --force-multiarch --no-vignettes --timings ChIPQC_1.10.3.tar.gz

StartedAt: 2017-04-14 21:28:21 -0400 (Fri, 14 Apr 2017)

EndedAt: 2017-04-14 21:36:27 -0400 (Fri, 14 Apr 2017)

EllapsedTime: 486.1 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-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=ChIPQC.buildbin-libdir ChIPQC_1.10.3.tar.gz >ChIPQC.Rcheck\00install.out 2>&1 && cp ChIPQC.Rcheck\00install.out ChIPQC-install.out  && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD check --library=ChIPQC.buildbin-libdir --install="check:ChIPQC-install.out" --force-multiarch --no-vignettes --timings ChIPQC_1.10.3.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.4-bioc/meat/ChIPQC.Rcheck'
* using R version 3.3.3 (2017-03-06)
* 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 '1.10.3'
* 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
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
findCovMaxPos: no visible global function definition for 'seqlengths'
findCovMaxPos: no visible global function definition for 'seqlengths<-'
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'
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 geom_point log10_bp
  log2_Enrichment seqlengths seqlengths<-
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 : .onLoad failed in loadNamespace() for 'TxDb.Hsapiens.UCSC.hg38.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 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 31.67   2.64   34.32
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
              user system elapsed
ChIPQCreport 31.62   2.33   34.14
* 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-3.4-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_1.10.3.zip
* DONE (ChIPQC)

name	user	system	elapsed
ChIPQC-data	1.85	0.07	1.92
ChIPQC	0.53	0.13	0.65
ChIPQCexperiment-class	0.42	0.05	0.47
ChIPQCreport	31.67	2.64	34.32
ChIPQCsample-class	1.70	0.01	1.71
FragmentLengthCrossCoverage-methods	0.08	0.02	0.10
Normalisedaveragepeaksignal-methods	0.03	0.01	0.05
QCannotation-methods	0.01	0.00	0.02
QCcontrol-methods	0.22	0.00	0.22
QCdba-methods	0.22	0.00	0.21
QCmetadata-methods	0.17	0.00	0.18
QCmetrics-methods	0.43	0.02	0.43
QCsample-methods	0.05	0.00	0.05
ReadLengthCrossCoverage-methods	0.01	0.00	0.01
RelativeCrossCoverage-methods	0.05	0.01	0.06
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	0.02	0.00	0.01
duplicates-methods	0.03	0.00	0.04
flagtagcounts-methods	0.01	0.00	0.01
fragmentlength-methods	0.07	0.00	0.06
frip-methods	0.01	0.02	0.04
mapped-methods	0.02	0.01	0.03
peaks-methods	0.07	0.00	0.07
plotCC-methods	1.6	0.0	1.6
plotCorHeatmap-methods	0.87	0.02	0.89
plotCoverageHist-methods	0.78	0.00	0.79
plotFribl-methods	0.72	0.03	0.75
plotFrip-methods	0.7	0.0	0.7
plotPeakProfile-methods	1.74	0.01	1.75
plotPrincomp-methods	0.29	0.00	0.30
plotRap-methods	1.18	0.03	1.20
plotRegi-methods	1.26	0.00	1.26
plotSSD-methods	1.61	0.00	1.61
readlength-methods	0.03	0.00	0.04
reads-methods	0.02	0.00	0.01
regi-methods	0.03	0.02	0.05
ribl-methods	0.01	0.02	0.03
rip-methods	0.02	0.00	0.01
ssd-methods	0.01	0.00	0.02

name	user	system	elapsed
ChIPQC-data	2.26	0.00	2.26
ChIPQC	0.61	0.05	0.66
ChIPQCexperiment-class	0.42	0.03	0.45
ChIPQCreport	31.62	2.33	34.14
ChIPQCsample-class	1.29	0.01	1.30
FragmentLengthCrossCoverage-methods	0.06	0.00	0.06
Normalisedaveragepeaksignal-methods	0.05	0.00	0.05
QCannotation-methods	0.01	0.00	0.01
QCcontrol-methods	0.24	0.00	0.24
QCdba-methods	0.1	0.0	0.1
QCmetadata-methods	0.11	0.02	0.13
QCmetrics-methods	0.47	0.00	0.47
QCsample-methods	0.05	0.01	0.06
ReadLengthCrossCoverage-methods	0.02	0.00	0.02
RelativeCrossCoverage-methods	0.06	0.00	0.06
averagepeaksignal-methods	0.01	0.02	0.03
coveragehistogram-methods	0.02	0.01	0.03
crosscoverage-methods	0.01	0.02	0.03
duplicateRate-methods	0.02	0.02	0.03
duplicates-methods	0.02	0.00	0.02
flagtagcounts-methods	0.01	0.01	0.03
fragmentlength-methods	0.06	0.00	0.06
frip-methods	0.02	0.00	0.02
mapped-methods	0.03	0.00	0.03
peaks-methods	0.06	0.00	0.06
plotCC-methods	1.82	0.02	1.83
plotCorHeatmap-methods	0.86	0.01	0.88
plotCoverageHist-methods	0.76	0.00	0.76
plotFribl-methods	0.88	0.00	0.88
plotFrip-methods	0.79	0.00	0.79
plotPeakProfile-methods	1.89	0.03	1.93
plotPrincomp-methods	0.30	0.00	0.29
plotRap-methods	1.11	0.02	1.13
plotRegi-methods	2.47	0.03	2.50
plotSSD-methods	2.75	0.02	2.76
readlength-methods	0.02	0.00	0.01
reads-methods	0.02	0.00	0.02
regi-methods	0.04	0.01	0.06
ribl-methods	0.02	0.00	0.02
rip-methods	0.01	0.00	0.01
ssd-methods	0.02	0.02	0.03