BioC 3.2: CHECK report for ChIPQC on oaxaca

Package: ChIPQC

Version: 1.6.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings ChIPQC_1.6.1.tar.gz

StartedAt: 2015-10-27 02:10:37 -0400 (Tue, 27 Oct 2015)

EndedAt: 2015-10-27 02:18:08 -0400 (Tue, 27 Oct 2015)

EllapsedTime: 451.5 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: ChIPQC.Rcheck

Warnings: 1

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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_1.6.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/ChIPQC.Rcheck’
* using R version 3.2.2 (2015-08-14)
* 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 ‘1.6.1’
* 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 ... [38s/39s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* 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 ... WARNING
'library' or 'require' call not declared from: ‘TxDb.Hsapiens.UCSC.hg38.knownGene’
'library' or 'require' calls in package code:
  ‘TxDb.Celegans.UCSC.ce6.ensGene’
  ‘TxDb.Dmelanogaster.UCSC.dm3.ensGene’
  ‘TxDb.Hsapiens.UCSC.hg18.knownGene’
  ‘TxDb.Hsapiens.UCSC.hg19.knownGene’
  ‘TxDb.Hsapiens.UCSC.hg38.knownGene’
  ‘TxDb.Mmusculus.UCSC.mm10.knownGene’
  ‘TxDb.Mmusculus.UCSC.mm9.knownGene’
  ‘TxDb.Rnorvegicus.UCSC.rn4.ensGene’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
* 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: warning in read.delim(LoadFile, sep = sepr, header = TRUE,
  comment = "#"): partial argument match of 'comment' to 'comment.char'
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.hg19.knownGene’
getAnnotation: no visible binding for global variable
  ‘TxDb.Hsapiens.UCSC.hg18.knownGene’
getAnnotation: no visible binding for global variable
  ‘TxDb.Hsapiens.UCSC.hg38.knownGene’
getAnnotation: no visible binding for global variable
  ‘TxDb.Mmusculus.UCSC.mm10.knownGene’
getAnnotation: no visible binding for global variable
  ‘TxDb.Mmusculus.UCSC.mm9.knownGene’
getAnnotation: no visible binding for global variable
  ‘TxDb.Rnorvegicus.UCSC.rn4.ensGene’
getAnnotation: no visible binding for global variable
  ‘TxDb.Celegans.UCSC.ce6.ensGene’
getAnnotation: no visible binding for global variable
  ‘TxDb.Dmelanogaster.UCSC.dm3.ensGene’
getAnnotation: no visible global function definition for
  ‘fiveUTRsByTranscript’
getAnnotation: no visible global function definition for
  ‘threeUTRsByTranscript’
getAnnotation: no visible global function definition for ‘cdsBy’
getAnnotation: no visible global function definition for
  ‘intronsByTranscript’
getAnnotation: no visible global function definition for ‘transcripts’
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 global function definition for ‘geom_point’
sampleQC: no visible global function definition for ‘index’
sampleQC: no visible global function definition for ‘BamFile’
sampleQC: no visible global function definition for ‘indexBam’
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’
plotRap,ChIPQCexperiment: no visible global function definition for
  ‘coord_cartesian’
* 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 ... OK
* 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 ... [86s/86s] OK
Examples with CPU or elapsed time > 5s
               user system elapsed
ChIPQCreport 47.415  1.491   48.96
* 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: 1 WARNING, 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.2-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	1.447	0.032	1.480
ChIPQC	1.024	0.016	1.040
ChIPQCexperiment-class	0.519	0.019	0.539
ChIPQCreport	47.415	1.491	48.960
ChIPQCsample-class	1.050	0.031	1.160
FragmentLengthCrossCoverage-methods	0.098	0.007	0.105
Normalisedaveragepeaksignal-methods	0.023	0.012	0.035
QCannotation-methods	0.014	0.005	0.020
QCcontrol-methods	0.257	0.012	0.270
QCdba-methods	0.108	0.007	0.116
QCmetadata-methods	0.127	0.009	0.136
QCmetrics-methods	0.570	0.016	0.587
QCsample-methods	0.092	0.008	0.099
ReadLengthCrossCoverage-methods	0.014	0.006	0.021
RelativeCrossCoverage-methods	0.088	0.007	0.095
averagepeaksignal-methods	0.025	0.007	0.032
coveragehistogram-methods	0.023	0.008	0.032
crosscoverage-methods	0.022	0.009	0.030
duplicateRate-methods	0.014	0.006	0.019
duplicates-methods	0.014	0.007	0.020
flagtagcounts-methods	0.014	0.006	0.020
fragmentlength-methods	0.075	0.007	0.082
frip-methods	0.014	0.007	0.020
mapped-methods	0.014	0.006	0.020
peaks-methods	0.081	0.007	0.088
plotCC-methods	0.859	0.013	0.873
plotCorHeatmap-methods	2.484	0.074	2.560
plotCoverageHist-methods	0.640	0.013	0.654
plotFribl-methods	0.726	0.015	0.742
plotFrip-methods	0.742	0.013	0.762
plotPeakProfile-methods	1.560	0.061	1.621
plotPrincomp-methods	2.503	0.067	2.573
plotRap-methods	0.919	0.006	0.929
plotRegi-methods	1.358	0.017	1.382
plotSSD-methods	1.273	0.021	1.300
readlength-methods	0.015	0.004	0.019
reads-methods	0.015	0.004	0.018
regi-methods	0.060	0.005	0.066
ribl-methods	0.013	0.004	0.017
rip-methods	0.014	0.004	0.018
ssd-methods	0.014	0.004	0.018