Back to the "Multiple platform build/check report" A  B [C] D  E  F  G  H  I  J  K  L  M  N  O  P  Q  R  S  T  U  V  W  X  Y  Z 

BioC 3.1: CHECK report for ChIPQC on moscato2

This page was generated on 2015-10-09 09:31:06 -0700 (Fri, 09 Oct 2015).

Package 158/1024HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ChIPQC 1.4.4
Tom Carroll , Rory Stark
Snapshot Date: 2015-10-08 17:20:21 -0700 (Thu, 08 Oct 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_1/madman/Rpacks/ChIPQC
Last Changed Rev: 105879 / Revision: 109384
Last Changed Date: 2015-07-07 10:07:59 -0700 (Tue, 07 Jul 2015)
zin2 Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository
petty Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: ChIPQC
Version: 1.4.4
Command: rm -rf ChIPQC.buildbin-libdir ChIPQC.Rcheck && mkdir ChIPQC.buildbin-libdir ChIPQC.Rcheck && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=ChIPQC.buildbin-libdir ChIPQC_1.4.4.tar.gz >ChIPQC.Rcheck\00install.out 2>&1 && cp ChIPQC.Rcheck\00install.out ChIPQC-install.out && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD check --library=ChIPQC.buildbin-libdir --install="check:ChIPQC-install.out" --force-multiarch --no-vignettes --timings ChIPQC_1.4.4.tar.gz
StartedAt: 2015-10-09 00:13:33 -0700 (Fri, 09 Oct 2015)
EndedAt: 2015-10-09 00:24:32 -0700 (Fri, 09 Oct 2015)
EllapsedTime: 659.3 seconds
RetCode: 0
Status:  OK  
CheckDir: ChIPQC.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf ChIPQC.buildbin-libdir ChIPQC.Rcheck && mkdir ChIPQC.buildbin-libdir ChIPQC.Rcheck && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=ChIPQC.buildbin-libdir ChIPQC_1.4.4.tar.gz >ChIPQC.Rcheck\00install.out 2>&1 && cp ChIPQC.Rcheck\00install.out ChIPQC-install.out  && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD check --library=ChIPQC.buildbin-libdir --install="check:ChIPQC-install.out" --force-multiarch --no-vignettes --timings ChIPQC_1.4.4.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'E:/biocbld/bbs-3.1-bioc/meat/ChIPQC.Rcheck'
* using R version 3.2.2 (2015-08-14)
* 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 '1.4.4'
* 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.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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... [86s] OK
Examples with CPU or elapsed time > 5s
              user system elapsed
ChIPQCreport 37.55  15.12    53.2
** running examples for arch 'x64' ... [100s] OK
Examples with CPU or elapsed time > 5s
              user system elapsed
ChIPQCreport 41.76  15.45   59.78
* 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
  'E:/biocbld/bbs-3.1-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
Creating a generic function for 'nchar' from package 'base' in package 'S4Vectors'
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Creating a generic function for 'nchar' from package 'base' in package 'S4Vectors'

install for x64

* installing *source* package 'ChIPQC' ...
** testing if installed package can be loaded
Creating a generic function for 'nchar' from package 'base' in package 'S4Vectors'
* MD5 sums
packaged installation of 'ChIPQC' as ChIPQC_1.4.4.zip
* DONE (ChIPQC)

ChIPQC.Rcheck/examples_i386/ChIPQC-Ex.timings:

nameusersystemelapsed
ChIPQC-data1.730.031.76
ChIPQC0.50.00.5
ChIPQCexperiment-class0.510.000.51
ChIPQCreport37.5515.1253.20
ChIPQCsample-class0.720.010.73
FragmentLengthCrossCoverage-methods0.080.000.08
Normalisedaveragepeaksignal-methods0.030.000.03
QCannotation-methods0.020.020.03
QCcontrol-methods0.200.010.22
QCdba-methods0.120.000.13
QCmetadata-methods0.130.000.12
QCmetrics-methods0.530.000.53
QCsample-methods0.080.000.08
ReadLengthCrossCoverage-methods0.010.020.03
RelativeCrossCoverage-methods0.100.000.09
averagepeaksignal-methods0.030.010.04
coveragehistogram-methods0.560.000.57
crosscoverage-methods0.630.020.64
duplicateRate-methods0.010.000.01
duplicates-methods0.000.010.02
flagtagcounts-methods0.030.000.03
fragmentlength-methods0.080.000.08
frip-methods0.020.000.01
mapped-methods0.010.000.02
peaks-methods0.080.000.07
plotCC-methods0.80.00.8
plotCorHeatmap-methods2.060.002.06
plotCoverageHist-methods0.50.00.5
plotFribl-methods0.540.000.54
plotFrip-methods0.80.00.8
plotPeakProfile-methods2.600.002.61
plotPrincomp-methods2.370.022.38
plotRap-methods0.710.010.72
plotRegi-methods1.040.001.05
plotSSD-methods1.030.001.02
readlength-methods0.020.000.02
reads-methods0.010.000.02
regi-methods0.060.000.06
ribl-methods0.020.000.01
rip-methods0.020.000.02
ssd-methods0.010.000.02

ChIPQC.Rcheck/examples_x64/ChIPQC-Ex.timings:

nameusersystemelapsed
ChIPQC-data1.530.041.57
ChIPQC1.130.001.14
ChIPQCexperiment-class0.860.000.86
ChIPQCreport41.7615.4559.78
ChIPQCsample-class0.970.001.20
FragmentLengthCrossCoverage-methods0.110.010.12
Normalisedaveragepeaksignal-methods0.010.000.02
QCannotation-methods0.030.000.03
QCcontrol-methods0.250.020.26
QCdba-methods0.100.020.11
QCmetadata-methods0.100.000.11
QCmetrics-methods0.770.010.78
QCsample-methods0.090.000.10
ReadLengthCrossCoverage-methods0.020.000.01
RelativeCrossCoverage-methods0.090.000.10
averagepeaksignal-methods0.060.000.06
coveragehistogram-methods0.660.000.65
crosscoverage-methods0.970.000.97
duplicateRate-methods0.010.000.02
duplicates-methods0.020.000.01
flagtagcounts-methods0.010.000.02
fragmentlength-methods0.080.020.09
frip-methods0.010.000.01
mapped-methods0.020.000.02
peaks-methods0.080.000.08
plotCC-methods1.040.001.04
plotCorHeatmap-methods2.930.012.95
plotCoverageHist-methods0.880.000.87
plotFribl-methods0.790.000.80
plotFrip-methods0.670.000.67
plotPeakProfile-methods1.660.001.65
plotPrincomp-methods3.910.063.98
plotRap-methods0.910.020.92
plotRegi-methods1.540.001.55
plotSSD-methods1.410.021.42
readlength-methods0.010.000.01
reads-methods0.030.000.03
regi-methods0.070.000.06
ribl-methods0.010.000.02
rip-methods0.000.010.02
ssd-methods0.030.000.03