BioC 3.4: CHECK report for ChIPQC on moscato1

Package: ChIPQC

Version: 1.9.2

Command: rm -rf ChIPQC.buildbin-libdir ChIPQC.Rcheck && mkdir ChIPQC.buildbin-libdir ChIPQC.Rcheck && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=ChIPQC.buildbin-libdir ChIPQC_1.9.2.tar.gz >ChIPQC.Rcheck\00install.out 2>&1 && cp ChIPQC.Rcheck\00install.out ChIPQC-install.out && D:\biocbld\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_1.9.2.tar.gz

StartedAt: 2016-09-20 05:31:07 -0700 (Tue, 20 Sep 2016)

EndedAt: 2016-09-20 05:40:43 -0700 (Tue, 20 Sep 2016)

EllapsedTime: 576.0 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 && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=ChIPQC.buildbin-libdir ChIPQC_1.9.2.tar.gz >ChIPQC.Rcheck\00install.out 2>&1 && cp ChIPQC.Rcheck\00install.out ChIPQC-install.out  && D:\biocbld\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_1.9.2.tar.gz
###
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* using log directory 'D:/biocbld/bbs-3.4-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 '1.9.2'
* 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
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> ... .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 28.71  16.11    45.1
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
              user system elapsed
ChIPQCreport 33.15  17.29   50.82
* 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
  'D:/biocbld/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_1.9.2.zip
* DONE (ChIPQC)

name	user	system	elapsed
ChIPQC-data	2.33	0.03	2.48
ChIPQC	0.89	0.01	0.90
ChIPQCexperiment-class	1.14	0.02	1.15
ChIPQCreport	28.71	16.11	45.10
ChIPQCsample-class	1.37	0.02	1.41
FragmentLengthCrossCoverage-methods	0.08	0.01	0.09
Normalisedaveragepeaksignal-methods	0.03	0.00	0.03
QCannotation-methods	0.01	0.02	0.03
QCcontrol-methods	0.24	0.00	0.24
QCdba-methods	0.14	0.02	0.15
QCmetadata-methods	0.17	0.00	0.18
QCmetrics-methods	0.53	0.01	0.54
QCsample-methods	0.06	0.00	0.06
ReadLengthCrossCoverage-methods	0.03	0.00	0.04
RelativeCrossCoverage-methods	0.08	0.00	0.07
averagepeaksignal-methods	0.05	0.00	0.05
coveragehistogram-methods	0.03	0.00	0.03
crosscoverage-methods	0.03	0.02	0.05
duplicateRate-methods	0.02	0.00	0.01
duplicates-methods	0.01	0.01	0.04
flagtagcounts-methods	0.03	0.00	0.03
fragmentlength-methods	0.08	0.00	0.07
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	0.94	0.00	0.94
plotCorHeatmap-methods	0.29	0.02	0.31
plotCoverageHist-methods	0.67	0.00	0.67
plotFribl-methods	1.10	0.00	1.09
plotFrip-methods	0.67	0.01	0.69
plotPeakProfile-methods	1.60	0.02	1.62
plotPrincomp-methods	0.33	0.00	0.33
plotRap-methods	0.84	0.01	0.86
plotRegi-methods	1.41	0.02	1.42
readlength-methods	0.03	0.00	0.03
reads-methods	0.01	0.00	0.02
regi-methods	0.05	0.02	0.06
ribl-methods	0.02	0.01	0.03
rip-methods	0.03	0.00	0.03
ssd-methods	0.01	0.00	0.02

name	user	system	elapsed
ChIPQC-data	1.65	0.00	1.65
ChIPQC	1.10	0.01	1.11
ChIPQCexperiment-class	0.64	0.05	0.69
ChIPQCreport	33.15	17.29	50.82
ChIPQCsample-class	1.62	0.00	1.62
FragmentLengthCrossCoverage-methods	0.10	0.00	0.09
Normalisedaveragepeaksignal-methods	0.03	0.00	0.03
QCannotation-methods	0.01	0.01	0.04
QCcontrol-methods	0.21	0.05	0.25
QCdba-methods	0.14	0.00	0.14
QCmetadata-methods	0.12	0.01	0.14
QCmetrics-methods	0.66	0.02	0.67
QCsample-methods	0.06	0.00	0.06
ReadLengthCrossCoverage-methods	0.02	0.00	0.02
RelativeCrossCoverage-methods	0.08	0.00	0.08
averagepeaksignal-methods	0.04	0.00	0.04
coveragehistogram-methods	0.03	0.00	0.03
crosscoverage-methods	0.03	0.00	0.03
duplicateRate-methods	0.01	0.02	0.03
duplicates-methods	0.02	0.00	0.01
flagtagcounts-methods	0.03	0.00	0.04
fragmentlength-methods	0.09	0.01	0.11
frip-methods	0.04	0.00	0.03
mapped-methods	0.01	0.00	0.01
peaks-methods	0.06	0.02	0.08
plotCC-methods	1.69	0.00	1.68
plotCorHeatmap-methods	0.28	0.03	0.32
plotCoverageHist-methods	0.79	0.00	0.82
plotFribl-methods	0.94	0.00	0.94
plotFrip-methods	0.86	0.00	0.86
plotPeakProfile-methods	1.90	0.04	1.95
plotPrincomp-methods	0.41	0.02	0.42
plotRap-methods	1.01	0.00	1.01
plotRegi-methods	1.62	0.02	1.64
readlength-methods	0.03	0.00	0.03
reads-methods	0.02	0.00	0.01
regi-methods	0.04	0.01	0.07
ribl-methods	0.01	0.00	0.02
rip-methods	0.05	0.00	0.04
ssd-methods	0.02	0.02	0.03