BioC 3.3: CHECK report for ChIPQC on oaxaca

Package: ChIPQC

Version: 1.8.9

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings ChIPQC_1.8.9.tar.gz

StartedAt: 2016-10-13 00:04:16 -0700 (Thu, 13 Oct 2016)

EndedAt: 2016-10-13 00:11:05 -0700 (Thu, 13 Oct 2016)

EllapsedTime: 409.6 seconds

RetCode: 0

Status:  OK

CheckDir: ChIPQC.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings ChIPQC_1.8.9.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.3-bioc/meat/ChIPQC.Rcheck’
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-apple-darwin13.4.0 (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 ‘1.8.9’
* 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 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
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 sizes of PDF files under ‘inst/doc’ ... 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 36.043  1.424  43.947
* 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
  ‘/Users/biocbuild/bbs-3.3-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	2.180	0.070	2.405
ChIPQC	1.023	0.018	1.043
ChIPQCexperiment-class	1.004	0.018	1.023
ChIPQCreport	36.043	1.424	43.947
ChIPQCsample-class	1.927	0.065	2.062
FragmentLengthCrossCoverage-methods	0.085	0.008	0.092
Normalisedaveragepeaksignal-methods	0.030	0.007	0.038
QCannotation-methods	0.021	0.007	0.027
QCcontrol-methods	0.245	0.013	0.258
QCdba-methods	0.142	0.009	0.151
QCmetadata-methods	0.162	0.008	0.169
QCmetrics-methods	0.611	0.017	0.640
QCsample-methods	0.059	0.007	0.067
ReadLengthCrossCoverage-methods	0.018	0.005	0.099
RelativeCrossCoverage-methods	0.079	0.006	0.085
averagepeaksignal-methods	0.029	0.007	0.036
coveragehistogram-methods	0.028	0.006	0.035
crosscoverage-methods	0.026	0.007	0.033
duplicateRate-methods	0.017	0.006	0.024
duplicates-methods	0.016	0.006	0.022
flagtagcounts-methods	0.019	0.006	0.025
fragmentlength-methods	0.112	0.016	0.128
frip-methods	0.018	0.006	0.024
mapped-methods	0.020	0.006	0.026
peaks-methods	0.066	0.007	0.073
plotCC-methods	1.698	0.012	1.789
plotCorHeatmap-methods	0.741	0.015	1.004
plotCoverageHist-methods	0.755	0.014	0.770
plotFribl-methods	0.845	0.018	0.864
plotFrip-methods	0.893	0.011	0.906
plotPeakProfile-methods	1.855	0.056	2.044
plotPrincomp-methods	0.372	0.012	0.385
plotRap-methods	0.988	0.009	1.011
plotRegi-methods	1.542	0.022	1.578
plotSSD-methods	1.934	0.020	2.000
readlength-methods	0.018	0.007	0.026
reads-methods	0.019	0.006	0.026
regi-methods	0.062	0.008	0.070
ribl-methods	0.017	0.005	0.022
rip-methods	0.020	0.006	0.025
ssd-methods	0.018	0.007	0.025