Package: ChIPQC

Version: 1.18.2

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:ChIPQC.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings ChIPQC_1.18.2.tar.gz

StartedAt: 2019-04-15 22:55:53 -0400 (Mon, 15 Apr 2019)

EndedAt: 2019-04-15 23:03:12 -0400 (Mon, 15 Apr 2019)

EllapsedTime: 438.4 seconds

RetCode: 0

Status:  OK

CheckDir: ChIPQC.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:ChIPQC.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings ChIPQC_1.18.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/ChIPQC.Rcheck’
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘1.18.2’
* 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 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 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.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 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 46.744  3.142  50.499
* 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-3.8-bioc/meat/ChIPQC.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL ChIPQC
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘ChIPQC’ ...
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
   ‘ChIPQC.Rnw’ 
** testing if installed package can be loaded
* DONE (ChIPQC)

name	user	system	elapsed
ChIPQC-data	1.809	0.070	1.949
ChIPQC	0.622	0.020	0.647
ChIPQCexperiment-class	0.633	0.029	0.665
ChIPQCreport	46.744	3.142	50.499
ChIPQCsample-class	1.537	0.029	1.583
FragmentLengthCrossCoverage-methods	0.079	0.004	0.085
Normalisedaveragepeaksignal-methods	0.031	0.007	0.037
QCannotation-methods	0.019	0.005	0.026
QCcontrol-methods	0.272	0.013	0.289
QCdba-methods	0.162	0.009	0.171
QCmetadata-methods	0.178	0.009	0.188
QCmetrics-methods	0.611	0.017	0.631
QCsample-methods	0.076	0.009	0.087
ReadLengthCrossCoverage-methods	0.022	0.006	0.028
RelativeCrossCoverage-methods	0.082	0.007	0.090
averagepeaksignal-methods	0.032	0.008	0.040
coveragehistogram-methods	0.027	0.006	0.033
crosscoverage-methods	0.036	0.008	0.043
duplicateRate-methods	0.018	0.007	0.024
duplicates-methods	0.019	0.005	0.023
flagtagcounts-methods	0.020	0.007	0.027
fragmentlength-methods	0.070	0.008	0.077
frip-methods	0.017	0.005	0.022
mapped-methods	0.017	0.007	0.023
peaks-methods	0.157	0.006	0.163
plotCC-methods	2.078	0.014	2.115
plotCorHeatmap-methods	0.309	0.010	0.321
plotCoverageHist-methods	0.943	0.011	0.959
plotFribl-methods	0.997	0.009	1.012
plotFrip-methods	0.990	0.010	1.005
plotPeakProfile-methods	3.753	0.052	3.828
plotPrincomp-methods	0.365	0.017	0.399
plotRap-methods	1.486	0.015	1.517
plotRegi-methods	2.690	0.030	2.743
plotSSD-methods	2.060	0.025	2.101
readlength-methods	0.018	0.006	0.026
reads-methods	0.023	0.006	0.030
regi-methods	0.054	0.007	0.062
ribl-methods	0.017	0.007	0.024
rip-methods	0.020	0.007	0.029
ssd-methods	0.022	0.008	0.030