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BioC 3.0: CHECK report for segmentSeq on perceval

This page was generated on 2015-04-10 09:54:56 -0700 (Fri, 10 Apr 2015).

Package 806/933HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
segmentSeq 2.0.1
Thomas J. Hardcastle
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/segmentSeq
Last Changed Rev: 96616 / Revision: 102249
Last Changed Date: 2014-11-07 13:48:56 -0800 (Fri, 07 Nov 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: segmentSeq
Version: 2.0.1
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch segmentSeq_2.0.1.tar.gz
StartedAt: 2015-04-10 06:12:46 -0700 (Fri, 10 Apr 2015)
EndedAt: 2015-04-10 06:21:28 -0700 (Fri, 10 Apr 2015)
EllapsedTime: 521.4 seconds
RetCode: 0
Status:  OK 
CheckDir: segmentSeq.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch segmentSeq_2.0.1.tar.gz
###
##############################################################################
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* using log directory ‘/Users/biocbuild/bbs-3.0-bioc/meat/segmentSeq.Rcheck’
* using R version 3.1.3 (2015-03-09)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘segmentSeq/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘segmentSeq’ version ‘2.0.1’
* 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 ‘segmentSeq’ can be installed ... [35s/37s] OK
* checking installed package size ... NOTE
  installed size is  9.9Mb
  sub-directories of 1Mb or more:
    extdata   9.2Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* 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' call to ‘GenomicRanges’ which was already attached by Depends.
  Please remove these calls from your code.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.chrProcessing: no visible global function definition for ‘seqlengths’
.chrProcessing: no visible global function definition for ‘seqlevels’
.classifyNulls : <anonymous>: no visible global function definition for
  ‘seqlengths’
.constructMethNulls: no visible global function definition for
  ‘seqlevels’
.constructNullPriors: no visible global function definition for
  ‘seqlevels’
.constructNulls: no visible global function definition for ‘seqlevels’
.findMethChunks: no visible global function definition for ‘seqlevels’
.getCounts: no visible global function definition for ‘seqlevels’
.getCounts : <anonymous>: no visible global function definition for
  ‘clusterCall’
.getCounts : <anonymous>: no visible global function definition for
  ‘parLapply’
.getLocLikelihoods: no visible global function definition for
  ‘clusterCall’
.getLocLikelihoods: no visible global function definition for
  ‘parRapply’
.getMethylatedCounts: no visible global function definition for
  ‘seqlevels’
.getMethylatedCounts: no visible global function definition for
  ‘clusterEvalQ’
.getOverlaps: no visible global function definition for ‘seqlevels’
.getOverlaps : <anonymous>: no visible global function definition for
  ‘clusterCall’
.getOverlaps : <anonymous>: no visible global function definition for
  ‘parApply’
.getOverlaps: no visible global function definition for ‘clusterEvalQ’
.lociLikelihoods: no visible global function definition for ‘abind’
.partheuristicSeg: no visible global function definition for
  ‘seqlevels’
.partheuristicSeg : <anonymous>: no visible global function definition
  for ‘seqlengths’
.partheuristicSeg : <anonymous>: no visible global function definition
  for ‘seqlevels’
.plotSampleMeth: no visible global function definition for ‘seqlengths’
.processPosts: no visible global function definition for ‘clusterEvalQ’
.processPosts: no visible global function definition for ‘seqlevels’
.processPosts : <anonymous>: no visible global function definition for
  ‘seqlengths’
.processTags: no visible global function definition for ‘seqlevels’
.processTags: no visible global function definition for ‘seqlengths’
.processTags: no visible global function definition for ‘seqlengths<-’
.squeezeAlign: no visible global function definition for ‘seqlevels’
.subProfile: no visible global function definition for ‘seqlevels’
findChunks: no visible global function definition for ‘seqlevels’
plotGenome: no visible global function definition for ‘seqlevels’
plotGenome: no visible global function definition for ‘seqlevels<-’
processAD: no visible global function definition for ‘seqlevels’
readBAM: no visible global function definition for ‘Seqinfo’
readBAM : <anonymous>: no visible global function definition for
  ‘scanBam’
readBAM : <anonymous>: no visible global function definition for
  ‘ScanBamParam’
readBAM : <anonymous>: no visible global function definition for
  ‘seqlevels’
readGeneric: no visible global function definition for ‘Seqinfo’
readGeneric : <anonymous>: no visible global function definition for
  ‘seqlevels’
readMeths: no visible binding for global variable ‘seqlevels’
readMeths : <anonymous>: no visible global function definition for
  ‘seqlevels<-’
* 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 ... [176s/176s] OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
classifySeg     54.909  0.209  55.183
readMeths       22.771  1.230  24.047
lociLikelihoods 20.345  0.062  20.453
heuristicSeg    17.598  0.042  17.647
plotGenome       9.590  0.035   9.685
getCounts        5.053  0.018   5.072
* 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/segmentSeq.Rcheck/00check.log’
for details.

segmentSeq.Rcheck/00install.out:

* installing *source* package ‘segmentSeq’ ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (segmentSeq)

segmentSeq.Rcheck/segmentSeq-Ex.timings:

nameusersystemelapsed
alignmentData-class3.8320.0273.874
classifySeg54.909 0.20955.183
findChunks3.2320.0183.250
getCounts5.0530.0185.072
getOverlaps3.6880.0153.704
heuristicSeg17.598 0.04217.647
lociLikelihoods20.345 0.06220.453
plotGenome9.5900.0359.685
processAD4.2680.0174.291
readMethods3.8190.0233.845
readMeths22.771 1.23024.047
segData-class4.0780.0594.137
segmentSeq-package4.3260.0244.351