BioC 3.3: CHECK report for ChIPQC on moscato2

Package: ChIPQC

Version: 1.8.9

Command: rm -rf ChIPQC.buildbin-libdir ChIPQC.Rcheck && mkdir ChIPQC.buildbin-libdir ChIPQC.Rcheck && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=ChIPQC.buildbin-libdir ChIPQC_1.8.9.tar.gz >ChIPQC.Rcheck\00install.out 2>&1 && cp ChIPQC.Rcheck\00install.out ChIPQC-install.out && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD check --library=ChIPQC.buildbin-libdir --install="check:ChIPQC-install.out" --force-multiarch --no-vignettes --timings ChIPQC_1.8.9.tar.gz

StartedAt: 2016-10-13 01:59:28 -0700 (Thu, 13 Oct 2016)

EndedAt: 2016-10-13 02:11:09 -0700 (Thu, 13 Oct 2016)

EllapsedTime: 701.2 seconds

RetCode: 0

Status:  OK

CheckDir: ChIPQC.Rcheck

Warnings: 0

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### Running command:
###
###   rm -rf ChIPQC.buildbin-libdir ChIPQC.Rcheck && mkdir ChIPQC.buildbin-libdir ChIPQC.Rcheck && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=ChIPQC.buildbin-libdir ChIPQC_1.8.9.tar.gz >ChIPQC.Rcheck\00install.out 2>&1 && cp ChIPQC.Rcheck\00install.out ChIPQC-install.out  && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD check --library=ChIPQC.buildbin-libdir --install="check:ChIPQC-install.out" --force-multiarch --no-vignettes --timings ChIPQC_1.8.9.tar.gz
###
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* using log directory 'E:/biocbld/bbs-3.3-bioc/meat/ChIPQC.Rcheck'
* using R version 3.3.1 (2016-06-21)
* 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 '1.8.9'
* 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.
* 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> ... .findInheritedMethods -> getClass -> getClassDef -> .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 38.57   2.82    41.5
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
              user system elapsed
ChIPQCreport 38.75   2.51   45.78
* 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
  'E:/biocbld/bbs-3.3-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_1.8.9.zip
* DONE (ChIPQC)

name	user	system	elapsed
ChIPQC-data	2.60	0.05	2.65
ChIPQC	0.73	0.00	0.73
ChIPQCexperiment-class	1.42	0.03	1.45
ChIPQCreport	38.57	2.82	41.50
ChIPQCsample-class	1.92	0.00	1.93
FragmentLengthCrossCoverage-methods	0.12	0.00	0.13
Normalisedaveragepeaksignal-methods	0.06	0.00	0.06
QCannotation-methods	0.03	0.02	0.05
QCcontrol-methods	0.39	0.00	0.39
QCdba-methods	0.21	0.00	0.20
QCmetadata-methods	0.26	0.00	0.27
QCmetrics-methods	1.25	0.01	1.27
QCsample-methods	0.06	0.00	0.06
ReadLengthCrossCoverage-methods	0.01	0.00	0.01
RelativeCrossCoverage-methods	0.08	0.00	0.08
averagepeaksignal-methods	0.04	0.00	0.04
coveragehistogram-methods	0.05	0.00	0.05
crosscoverage-methods	0.05	0.02	0.06
duplicateRate-methods	0.03	0.00	0.03
duplicates-methods	0.03	0.00	0.04
flagtagcounts-methods	0.02	0.01	0.03
fragmentlength-methods	0.06	0.02	0.08
frip-methods	0.01	0.01	0.03
mapped-methods	0.03	0.00	0.03
peaks-methods	0.07	0.00	0.06
plotCC-methods	1.85	0.00	1.86
plotCorHeatmap-methods	0.32	0.02	0.32
plotCoverageHist-methods	0.71	0.00	0.72
plotFribl-methods	0.81	0.01	0.83
plotFrip-methods	0.80	0.00	0.79
plotPeakProfile-methods	2.71	0.00	2.72
plotPrincomp-methods	0.44	0.00	0.44
plotRap-methods	0.97	0.00	0.96
plotRegi-methods	1.67	0.00	1.67
plotSSD-methods	2.87	0.02	3.26
readlength-methods	0.01	0.02	0.03
reads-methods	0.02	0.01	0.03
regi-methods	0.07	0.00	0.06
ribl-methods	0.01	0.02	0.03
rip-methods	0.05	0.00	0.05
ssd-methods	0.03	0.01	0.05

name	user	system	elapsed
ChIPQC-data	2.48	0.00	2.48
ChIPQC	1.45	0.00	1.45
ChIPQCexperiment-class	1.78	0.00	1.78
ChIPQCreport	38.75	2.51	45.78
ChIPQCsample-class	2.09	0.01	2.11
FragmentLengthCrossCoverage-methods	0.11	0.00	0.11
Normalisedaveragepeaksignal-methods	0.03	0.02	0.04
QCannotation-methods	0.02	0.00	0.02
QCcontrol-methods	0.34	0.00	0.34
QCdba-methods	0.17	0.00	0.17
QCmetadata-methods	0.3	0.0	0.3
QCmetrics-methods	1.00	0.01	1.02
QCsample-methods	0.09	0.02	0.10
ReadLengthCrossCoverage-methods	0.77	0.02	0.78
RelativeCrossCoverage-methods	0.15	0.00	0.16
averagepeaksignal-methods	0.05	0.01	0.06
coveragehistogram-methods	0.05	0.00	0.05
crosscoverage-methods	0.03	0.00	0.03
duplicateRate-methods	0.03	0.00	0.03
duplicates-methods	0.01	0.02	0.03
flagtagcounts-methods	0.02	0.00	0.02
fragmentlength-methods	0.11	0.00	0.10
frip-methods	0.01	0.01	0.03
mapped-methods	0.02	0.02	0.03
peaks-methods	0.08	0.00	0.08
plotCC-methods	2.82	0.00	2.82
plotCorHeatmap-methods	0.53	0.01	0.55
plotCoverageHist-methods	1.05	0.03	1.07
plotFribl-methods	1.12	0.00	1.13
plotFrip-methods	1.33	0.02	1.73
plotPeakProfile-methods	2.52	0.05	2.57
plotPrincomp-methods	0.44	0.00	0.44
plotRap-methods	1.23	0.00	1.23
plotRegi-methods	2.12	0.00	2.12
plotSSD-methods	2.87	0.00	2.87
readlength-methods	0.04	0.00	0.04
reads-methods	0.03	0.01	0.04
regi-methods	0.09	0.00	0.10
ribl-methods	0.03	0.00	0.03
rip-methods	0.03	0.02	0.05
ssd-methods	0.03	0.00	0.03