ChIPQC 1.7.2
Tom Carroll , Rory Stark
| Snapshot Date: 2016-04-20 17:20:35 -0700 (Wed, 20 Apr 2016) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ChIPQC | | Last Changed Rev: 110662 / Revision: 116626 | | Last Changed Date: 2015-11-17 09:22:42 -0800 (Tue, 17 Nov 2015) |
| zin2 | Linux (Ubuntu 14.04.2 LTS) / x86_64 | NotNeeded | OK | WARNINGS | |  |
| moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | NotNeeded | OK | WARNINGS | OK | |
| morelia | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | [ WARNINGS ] | OK | |
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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_1.7.2.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.3-bioc/meat/ChIPQC.Rcheck’
* using R version 3.3.0 beta (2016-04-06 r70435)
* 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 ‘1.7.2’
* 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 ... [33s/37s] 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 ... NOTE
'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.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.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’
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 : <anonymous>: no visible global function
definition for ‘boxplot.stats’
plotRap,ChIPQCexperiment: no visible global function definition for
‘coord_cartesian’
plotSSD,ChIPQCexperiment: no visible binding for global variable
‘shiftlength’
plotSSD,ChIPQCexperiment: no visible binding for global variable
‘ccvector’
plotSSD,ChIPQCexperiment: no visible binding for global variable
‘readlen’
Undefined global functions or variables:
CC_Score CountsInPeaks Depth Distance FRIBL FRIP GenomicIntervals
Reads Sample Shift_Size Signal TxDb.Celegans.UCSC.ce6.ensGene
TxDb.Dmelanogaster.UCSC.dm3.ensGene TxDb.Hsapiens.UCSC.hg18.knownGene
TxDb.Hsapiens.UCSC.hg19.knownGene TxDb.Mmusculus.UCSC.mm10.knownGene
TxDb.Mmusculus.UCSC.mm9.knownGene TxDb.Rnorvegicus.UCSC.rn4.ensGene
boxplot.stats ccvector cdsBy coord_cartesian fiveUTRsByTranscript
intronsByTranscript log10_bp log2_Enrichment readlen seqlengths
seqlengths<- seqlevels<- shiftlength threeUTRsByTranscript
transcripts
Consider adding
importFrom("grDevices", "boxplot.stats")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... WARNING
Missing link or links in documentation object 'plotCC-methods.Rd':
‘ggplot2’
Missing link or links in documentation object 'plotCoverageHist-methods.Rd':
‘ggplot2’
Missing link or links in documentation object 'plotFribl-methods.Rd':
‘ggplot2’
Missing link or links in documentation object 'plotFrip-methods.Rd':
‘ggplot2’
Missing link or links in documentation object 'plotPeakProfile-methods.Rd':
‘ggplot2’
Missing link or links in documentation object 'plotRap-methods.Rd':
‘ggplot2’
Missing link or links in documentation object 'plotRegi-methods.Rd':
‘ggplot2’
See section 'Cross-references' in the 'Writing R Extensions' manual.
* 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 ... [78s/82s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
ChIPQCreport 42.838 1.612 48.218
* 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, 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
No methods found in "BiocGenerics" for requests: as.vector, unlist
No methods found in "IRanges" for requests: shiftApply, t
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
No methods found in "BiocGenerics" for requests: as.vector, unlist
No methods found in "IRanges" for requests: shiftApply, t
* DONE (ChIPQC)