BioC 3.3: CHECK report for ChIPQC on windows2.bioconductor.org
This page was generated on 2015-10-27 12:15:34 -0400 (Tue, 27 Oct 2015).
ChIPQC 1.7.0
Tom Carroll , Rory Stark
| Snapshot Date: 2015-10-26 20:20:04 -0400 (Mon, 26 Oct 2015) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ChIPQC | | Last Changed Rev: 109592 / Revision: 109948 | | Last Changed Date: 2015-10-13 15:59:53 -0400 (Tue, 13 Oct 2015) |
| linux2.bioconductor.org | Linux (Ubuntu 14.04.2 LTS) / x86_64 | NotNeeded | OK | OK | |  |
| windows2.bioconductor.org | Windows Server 2012 R2 Enterprise SP1 (64-bit) / x64 | NotNeeded | OK | [ OK ] | OK | |
Summary
| Package: ChIPQC
|
| Version: 1.7.0
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| Command: rm -rf ChIPQC.buildbin-libdir ChIPQC.Rcheck && mkdir ChIPQC.buildbin-libdir ChIPQC.Rcheck && c:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=ChIPQC.buildbin-libdir ChIPQC_1.7.0.tar.gz >ChIPQC.Rcheck\00install.out 2>&1 && cp ChIPQC.Rcheck\00install.out ChIPQC-install.out && c:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD check --library=ChIPQC.buildbin-libdir --install="check:ChIPQC-install.out" --force-multiarch --no-vignettes --timings ChIPQC_1.7.0.tar.gz
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| StartedAt: 2015-10-27 01:16:08 -0400 (Tue, 27 Oct 2015)
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| EndedAt: 2015-10-27 01:23:44 -0400 (Tue, 27 Oct 2015)
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| EllapsedTime: 455.5 seconds
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| RetCode: 0
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| Status: OK
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| CheckDir: ChIPQC.Rcheck
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| Warnings: 0
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Command output
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###
### Running command:
###
### rm -rf ChIPQC.buildbin-libdir ChIPQC.Rcheck && mkdir ChIPQC.buildbin-libdir ChIPQC.Rcheck && c:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=ChIPQC.buildbin-libdir ChIPQC_1.7.0.tar.gz >ChIPQC.Rcheck\00install.out 2>&1 && cp ChIPQC.Rcheck\00install.out ChIPQC-install.out && c:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD check --library=ChIPQC.buildbin-libdir --install="check:ChIPQC-install.out" --force-multiarch --no-vignettes --timings ChIPQC_1.7.0.tar.gz
###
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* using log directory 'c:/biocbld/bbs-3.3-bioc/meat/ChIPQC.Rcheck'
* using R Under development (unstable) (2015-09-22 r69418)
* 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 '1.7.0'
* 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 ... 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
* 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
'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: 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
ccvector cdsBy coord_cartesian fiveUTRsByTranscript
intronsByTranscript log10_bp log2_Enrichment readlen seqlengths
seqlengths<- seqlevels<- shiftlength threeUTRsByTranscript
transcripts
* 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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... [63s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
ChIPQCreport 28.42 11.89 40.32
** running examples for arch 'x64' ... [71s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
ChIPQCreport 33.86 11.14 45.04
* 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
'c:/biocbld/bbs-3.3-bioc/meat/ChIPQC.Rcheck/00check.log'
for details.
ChIPQC.Rcheck/00install.out:
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_1.7.0.zip
* DONE (ChIPQC)
ChIPQC.Rcheck/examples_i386/ChIPQC-Ex.timings:
| name | user | system | elapsed
|
| ChIPQC-data | 1.26 | 0.02 | 1.28 |
|
| ChIPQC | 0.35 | 0.05 | 0.39 |
|
| ChIPQCexperiment-class | 0.39 | 0.00 | 0.39 |
|
| ChIPQCreport | 28.42 | 11.89 | 40.32 |
|
| ChIPQCsample-class | 0.55 | 0.00 | 0.54 |
|
| FragmentLengthCrossCoverage-methods | 0.06 | 0.00 | 0.07 |
|
| Normalisedaveragepeaksignal-methods | 0.03 | 0.00 | 0.03 |
|
| QCannotation-methods | 0.02 | 0.00 | 0.01 |
|
| QCcontrol-methods | 0.18 | 0.01 | 0.21 |
|
| QCdba-methods | 0.10 | 0.02 | 0.11 |
|
| QCmetadata-methods | 0.11 | 0.00 | 0.10 |
|
| QCmetrics-methods | 0.37 | 0.01 | 0.40 |
|
| QCsample-methods | 0.05 | 0.00 | 0.04 |
|
| ReadLengthCrossCoverage-methods | 0.00 | 0.02 | 0.02 |
|
| RelativeCrossCoverage-methods | 0.07 | 0.00 | 0.07 |
|
| averagepeaksignal-methods | 0.01 | 0.00 | 0.01 |
|
| coveragehistogram-methods | 0.02 | 0.02 | 0.03 |
|
| crosscoverage-methods | 0.03 | 0.00 | 0.03 |
|
| duplicateRate-methods | 0.01 | 0.00 | 0.02 |
|
| duplicates-methods | 0.02 | 0.00 | 0.02 |
|
| flagtagcounts-methods | 0.02 | 0.00 | 0.01 |
|
| fragmentlength-methods | 0.06 | 0.00 | 0.06 |
|
| frip-methods | 0.01 | 0.00 | 0.02 |
|
| mapped-methods | 0.02 | 0.00 | 0.01 |
|
| peaks-methods | 0.03 | 0.01 | 0.05 |
|
| plotCC-methods | 0.59 | 0.02 | 0.61 |
|
| plotCorHeatmap-methods | 1.74 | 0.06 | 1.80 |
|
| plotCoverageHist-methods | 0.37 | 0.00 | 0.37 |
|
| plotFribl-methods | 0.43 | 0.00 | 0.42 |
|
| plotFrip-methods | 0.43 | 0.00 | 0.44 |
|
| plotPeakProfile-methods | 1.22 | 0.03 | 1.25 |
|
| plotPrincomp-methods | 1.90 | 0.02 | 1.92 |
|
| plotRap-methods | 0.64 | 0.00 | 0.64 |
|
| plotRegi-methods | 1.07 | 0.03 | 1.09 |
|
| readlength-methods | 0.01 | 0.00 | 0.02 |
|
| reads-methods | 0.02 | 0.00 | 0.02 |
|
| regi-methods | 0.05 | 0.00 | 0.04 |
|
| ribl-methods | 0.01 | 0.00 | 0.02 |
|
| rip-methods | 0.02 | 0.00 | 0.01 |
|
| ssd-methods | 0.00 | 0.01 | 0.02 |
|
ChIPQC.Rcheck/examples_x64/ChIPQC-Ex.timings:
| name | user | system | elapsed
|
| ChIPQC-data | 1.08 | 0.05 | 1.13 |
|
| ChIPQC | 0.92 | 0.01 | 0.93 |
|
| ChIPQCexperiment-class | 0.44 | 0.02 | 0.46 |
|
| ChIPQCreport | 33.86 | 11.14 | 45.04 |
|
| ChIPQCsample-class | 0.68 | 0.02 | 0.71 |
|
| FragmentLengthCrossCoverage-methods | 0.08 | 0.00 | 0.07 |
|
| Normalisedaveragepeaksignal-methods | 0.02 | 0.00 | 0.02 |
|
| QCannotation-methods | 0.00 | 0.01 | 0.02 |
|
| QCcontrol-methods | 0.17 | 0.02 | 0.18 |
|
| QCdba-methods | 0.08 | 0.01 | 0.10 |
|
| QCmetadata-methods | 0.09 | 0.00 | 0.09 |
|
| QCmetrics-methods | 0.45 | 0.00 | 0.45 |
|
| QCsample-methods | 0.05 | 0.00 | 0.05 |
|
| ReadLengthCrossCoverage-methods | 0.00 | 0.02 | 0.01 |
|
| RelativeCrossCoverage-methods | 0.08 | 0.00 | 0.08 |
|
| averagepeaksignal-methods | 0.03 | 0.00 | 0.03 |
|
| coveragehistogram-methods | 0.01 | 0.00 | 0.02 |
|
| crosscoverage-methods | 0.02 | 0.00 | 0.01 |
|
| duplicateRate-methods | 0.01 | 0.00 | 0.02 |
|
| duplicates-methods | 0 | 0 | 0 |
|
| flagtagcounts-methods | 0.01 | 0.00 | 0.02 |
|
| fragmentlength-methods | 0.08 | 0.00 | 0.08 |
|
| frip-methods | 0 | 0 | 0 |
|
| mapped-methods | 0 | 0 | 0 |
|
| peaks-methods | 0.06 | 0.00 | 0.07 |
|
| plotCC-methods | 0.64 | 0.01 | 0.65 |
|
| plotCorHeatmap-methods | 2.35 | 0.05 | 2.39 |
|
| plotCoverageHist-methods | 0.39 | 0.02 | 0.41 |
|
| plotFribl-methods | 0.75 | 0.01 | 0.76 |
|
| plotFrip-methods | 0.57 | 0.00 | 0.58 |
|
| plotPeakProfile-methods | 1.25 | 0.03 | 1.28 |
|
| plotPrincomp-methods | 2.30 | 0.07 | 2.36 |
|
| plotRap-methods | 0.64 | 0.01 | 0.66 |
|
| plotRegi-methods | 0.92 | 0.05 | 0.97 |
|
| readlength-methods | 0.02 | 0.00 | 0.01 |
|
| reads-methods | 0.01 | 0.00 | 0.02 |
|
| regi-methods | 0.05 | 0.00 | 0.05 |
|
| ribl-methods | 0.02 | 0.00 | 0.01 |
|
| rip-methods | 0.01 | 0.00 | 0.02 |
|
| ssd-methods | 0.02 | 0.00 | 0.01 |
|