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BioC 3.0: CHECK report for MEDIPS on moscato1

This page was generated on 2015-04-10 09:46:42 -0700 (Fri, 10 Apr 2015).

Package 523/933HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MEDIPS 1.16.0
Lukas Chavez
Snapshot Date: 2015-04-09 16:20:12 -0700 (Thu, 09 Apr 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_0/madman/Rpacks/MEDIPS
Last Changed Rev: 95439 / Revision: 102249
Last Changed Date: 2014-10-13 14:38:33 -0700 (Mon, 13 Oct 2014)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  NotNeeded  OK  OK 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK [ OK ] OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK  OK  OK 
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK 

Summary

Package: MEDIPS
Version: 1.16.0
Command: rm -rf MEDIPS.buildbin-libdir MEDIPS.Rcheck && mkdir MEDIPS.buildbin-libdir MEDIPS.Rcheck && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=MEDIPS.buildbin-libdir MEDIPS_1.16.0.tar.gz >MEDIPS.Rcheck\00install.out 2>&1 && cp MEDIPS.Rcheck\00install.out MEDIPS-install.out && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD check --library=MEDIPS.buildbin-libdir --install="check:MEDIPS-install.out" --force-multiarch --no-vignettes --timings MEDIPS_1.16.0.tar.gz
StartedAt: 2015-04-10 02:49:13 -0700 (Fri, 10 Apr 2015)
EndedAt: 2015-04-10 03:01:40 -0700 (Fri, 10 Apr 2015)
EllapsedTime: 746.7 seconds
RetCode: 0
Status:  OK  
CheckDir: MEDIPS.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf MEDIPS.buildbin-libdir MEDIPS.Rcheck && mkdir MEDIPS.buildbin-libdir MEDIPS.Rcheck && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=MEDIPS.buildbin-libdir MEDIPS_1.16.0.tar.gz >MEDIPS.Rcheck\00install.out 2>&1 && cp MEDIPS.Rcheck\00install.out MEDIPS-install.out  && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD check --library=MEDIPS.buildbin-libdir --install="check:MEDIPS-install.out" --force-multiarch --no-vignettes --timings MEDIPS_1.16.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbld/bbs-3.0-bioc/meat/MEDIPS.Rcheck'
* using R version 3.1.3 (2015-03-09)
* using platform: i386-w64-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'MEDIPS/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'MEDIPS' version '1.16.0'
* 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 'MEDIPS' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  'BSgenome' 'DNAcopy'
A package should be listed in only one of these fields.
* 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
Namespaces in Imports field not imported from:
  'GenomicFeatures' 'GenomicRanges'
  All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
MEDIPS.CpGenrich: no visible global function definition for 'seqlevels'
MEDIPS.CpGenrich: no visible global function definition for
  'seqlengths'
MEDIPS.GenomicCoordinates: no visible global function definition for
  'GRanges'
MEDIPS.addCNV: no visible global function definition for 'seqnames'
MEDIPS.couplingVector: no visible global function definition for
  'countOverlaps'
MEDIPS.createROIset: no visible global function definition for
  'seqlevels'
MEDIPS.createROIset: no visible global function definition for
  'seqlengths'
MEDIPS.createROIset: no visible global function definition for
  'countOverlaps'
MEDIPS.createSet: no visible global function definition for 'seqlevels'
MEDIPS.createSet: no visible global function definition for
  'seqlengths'
MEDIPS.createSet: no visible global function definition for
  'countOverlaps'
MEDIPS.exportWIG: no visible global function definition for 'seqnames'
MEDIPS.getPositions: no visible global function definition for
  'GRanges'
MEDIPS.meth: no visible global function definition for 'seqnames'
MEDIPS.plotCalibrationPlot: no visible global function definition for
  'seqnames'
MEDIPS.saturation: no visible global function definition for
  'seqlevels'
MEDIPS.saturation: no visible global function definition for
  'seqlengths'
MEDIPS.saturation: no visible global function definition for
  'countOverlaps'
MEDIPS.selectROIs: no visible global function definition for 'GRanges'
MEDIPS.selectROIs: no visible global function definition for
  'elementMetadata<-'
MEDIPS.selectROIs: no visible global function definition for
  'elementMetadata'
MEDIPS.selectROIs: no visible global function definition for
  'findOverlaps'
MEDIPS.selectROIs: no visible global function definition for 'seqnames'
MEDIPS.seqCoverage: no visible global function definition for
  'seqlevels'
MEDIPS.seqCoverage: no visible global function definition for
  'seqlengths'
MEDIPS.seqCoverage: no visible global function definition for
  'countOverlaps'
MEDIPS.setAnnotation: no visible global function definition for
  'GRanges'
MEDIPS.setAnnotation: no visible global function definition for
  'findOverlaps'
bin.ROIs: no visible global function definition for 'GRanges'
getGRange: no visible global function definition for 'GRanges'
getGRange: no visible global function definition for 'strand<-'
getMObjectFromWIG: no visible global function definition for 'GRanges'
getMObjectFromWIG: no visible global function definition for
  'seqlengths'
getMObjectFromWIG: no visible global function definition for
  'runLength'
getMObjectFromWIG: no visible global function definition for 'seqnames'
getMObjectFromWIG: no visible global function definition for 'runValue'
getPairedGRange: no visible global function definition for 'GRanges'
getPairedGRange: no visible global function definition for 'strand<-'
scanBamToGRanges: no visible global function definition for 'GRanges'
* 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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... [203s] OK
Examples with CPU or elapsed time > 5s
                        user system elapsed
MEDIPS.meth            63.22   0.25   63.56
MEDIPS.addCNV          42.81   0.44   47.72
MEDIPS.saturation      11.53   0.03   11.56
MEDIPS.plotSaturation  10.67   0.05   10.72
MEDIPS.plotSeqCoverage  7.11   0.08    7.19
MEDIPS.selectROIs       6.49   0.01    6.51
MEDIPS.seqCoverage      5.35   0.15    5.51
MEDIPS.selectSig        4.99   0.13    5.13
MEDIPS.setAnnotation    4.36   0.08    8.17
MEDIPS.getAnnotation    0.50   0.10    7.20
** running examples for arch 'x64' ... [193s] OK
Examples with CPU or elapsed time > 5s
                        user system elapsed
MEDIPS.meth            65.50   0.29   65.79
MEDIPS.addCNV          40.08   0.45   40.53
MEDIPS.saturation      10.78   0.02   10.79
MEDIPS.plotSaturation  10.21   0.02   10.33
MEDIPS.plotSeqCoverage  7.30   0.06    7.36
MEDIPS.selectSig        5.99   0.08    6.07
MEDIPS.seqCoverage      5.34   0.16    5.49
MEDIPS.selectROIs       5.43   0.01    5.45
MEDIPS.setAnnotation    4.80   0.10    8.73
MEDIPS.getAnnotation    0.44   0.04    6.79
* 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

NOTE: There were 3 notes.
See
  'D:/biocbld/bbs-3.0-bioc/meat/MEDIPS.Rcheck/00check.log'
for details.

MEDIPS.Rcheck/00install.out:


install for i386

* installing *source* package 'MEDIPS' ...
** R
** 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 'MEDIPS' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'MEDIPS' as MEDIPS_1.16.0.zip
* DONE (MEDIPS)

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

nameusersystemelapsed
COUPLINGset-class000
MEDIPS.CpGenrich0.130.010.17
MEDIPS.addCNV42.81 0.4447.72
MEDIPS.annotate000
MEDIPS.correlation0.400.031.51
MEDIPS.couplingVector4.040.114.15
MEDIPS.coverageAnalysis000
MEDIPS.createROIset1.060.033.14
MEDIPS.createSet1.130.001.12
MEDIPS.exportWIG1.790.032.00
MEDIPS.genomeVector000
MEDIPS.getAnnotation0.50.17.2
MEDIPS.mergeFrames000
MEDIPS.mergeSets0.360.020.78
MEDIPS.meth63.22 0.2563.56
MEDIPS.methylProfiling000
MEDIPS.normalize000
MEDIPS.plotCalibrationPlot4.150.094.24
MEDIPS.plotCoverage000
MEDIPS.plotSaturation10.67 0.0510.72
MEDIPS.plotSeqCoverage7.110.087.19
MEDIPS.readAlignedSequences000
MEDIPS.saturation11.53 0.0311.56
MEDIPS.saturationAnalysis000
MEDIPS.selectROIs6.490.016.51
MEDIPS.selectSig4.990.135.13
MEDIPS.selectSignificants000
MEDIPS.seqCoverage5.350.155.51
MEDIPS.setAnnotation4.360.088.17
MEDIPSroiSet-class000
MEDIPSset-class000

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

nameusersystemelapsed
COUPLINGset-class000
MEDIPS.CpGenrich0.110.000.10
MEDIPS.addCNV40.08 0.4540.53
MEDIPS.annotate000
MEDIPS.correlation0.450.050.50
MEDIPS.couplingVector3.960.144.12
MEDIPS.coverageAnalysis000
MEDIPS.createROIset0.830.030.86
MEDIPS.createSet1.220.011.25
MEDIPS.exportWIG2.050.022.08
MEDIPS.genomeVector000
MEDIPS.getAnnotation0.440.046.79
MEDIPS.mergeFrames000
MEDIPS.mergeSets0.360.000.36
MEDIPS.meth65.50 0.2965.79
MEDIPS.methylProfiling000
MEDIPS.normalize000
MEDIPS.plotCalibrationPlot4.390.044.43
MEDIPS.plotCoverage000
MEDIPS.plotSaturation10.21 0.0210.33
MEDIPS.plotSeqCoverage7.300.067.36
MEDIPS.readAlignedSequences000
MEDIPS.saturation10.78 0.0210.79
MEDIPS.saturationAnalysis000
MEDIPS.selectROIs5.430.015.45
MEDIPS.selectSig5.990.086.07
MEDIPS.selectSignificants000
MEDIPS.seqCoverage5.340.165.49
MEDIPS.setAnnotation4.800.108.73
MEDIPSroiSet-class000
MEDIPSset-class000