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BioC 3.0: CHECK report for MEDIPS on oaxaca

This page was generated on 2015-04-10 10:04:30 -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: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch MEDIPS_1.16.0.tar.gz
StartedAt: 2015-04-10 01:01:54 -0700 (Fri, 10 Apr 2015)
EndedAt: 2015-04-10 01:09:56 -0700 (Fri, 10 Apr 2015)
EllapsedTime: 481.8 seconds
RetCode: 0
Status:  OK 
CheckDir: MEDIPS.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch MEDIPS_1.16.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.0-bioc/meat/MEDIPS.Rcheck’
* using R version 3.1.3 (2015-03-09)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘MEDIPS’ can be installed ... [27s/30s] 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
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [172s/186s] OK
Examples with CPU or elapsed time > 5s
                         user system elapsed
MEDIPS.meth            60.235  0.892  61.842
MEDIPS.addCNV          32.851  0.860  34.271
MEDIPS.plotSaturation  11.068  0.805  11.937
MEDIPS.saturation      10.835  0.580  11.491
MEDIPS.selectSig        6.258  0.221   6.507
MEDIPS.setAnnotation    6.077  0.269  10.296
MEDIPS.plotSeqCoverage  5.380  0.426   5.823
MEDIPS.selectROIs       5.244  0.155   5.495
MEDIPS.getAnnotation    0.928  0.010   8.106
* 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
  ‘/Users/biocbuild/bbs-3.0-bioc/meat/MEDIPS.Rcheck/00check.log’
for details.

MEDIPS.Rcheck/00install.out:

* 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
* DONE (MEDIPS)

MEDIPS.Rcheck/MEDIPS-Ex.timings:

nameusersystemelapsed
COUPLINGset-class0.0020.0010.003
MEDIPS.CpGenrich0.1110.0130.574
MEDIPS.addCNV32.851 0.86034.271
MEDIPS.annotate0.0010.0000.001
MEDIPS.correlation0.4170.0730.513
MEDIPS.couplingVector3.0500.2863.583
MEDIPS.coverageAnalysis0.0010.0000.001
MEDIPS.createROIset0.8680.0910.989
MEDIPS.createSet1.1590.1411.308
MEDIPS.exportWIG1.8200.1741.995
MEDIPS.genomeVector0.0000.0000.001
MEDIPS.getAnnotation0.9280.0108.106
MEDIPS.mergeFrames0.0080.0000.008
MEDIPS.mergeSets0.3320.0080.370
MEDIPS.meth60.235 0.89261.842
MEDIPS.methylProfiling0.0010.0000.001
MEDIPS.normalize0.0000.0000.001
MEDIPS.plotCalibrationPlot3.5540.3213.904
MEDIPS.plotCoverage0.0010.0000.001
MEDIPS.plotSaturation11.068 0.80511.937
MEDIPS.plotSeqCoverage5.3800.4265.823
MEDIPS.readAlignedSequences000
MEDIPS.saturation10.835 0.58011.491
MEDIPS.saturationAnalysis0.0010.0000.001
MEDIPS.selectROIs5.2440.1555.495
MEDIPS.selectSig6.2580.2216.507
MEDIPS.selectSignificants0.0010.0000.001
MEDIPS.seqCoverage4.0130.4954.533
MEDIPS.setAnnotation 6.077 0.26910.296
MEDIPSroiSet-class0.0010.0000.002
MEDIPSset-class0.0020.0010.003