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BioC 3.2: CHECK report for segmentSeq on oaxaca

This page was generated on 2015-10-27 17:39:08 -0400 (Tue, 27 Oct 2015).

Package 950/1104HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
segmentSeq 2.4.0
Thomas J. Hardcastle
Snapshot Date: 2015-10-26 19:24:07 -0400 (Mon, 26 Oct 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/segmentSeq
Last Changed Rev: 109589 / Revision: 109947
Last Changed Date: 2015-10-13 15:36:05 -0400 (Tue, 13 Oct 2015)
linux1.bioconductor.org Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK  WARNINGS UNNEEDED, same version exists in internal repository
windows1.bioconductor.org Windows Server 2012 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository

Summary

Package: segmentSeq
Version: 2.4.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings segmentSeq_2.4.0.tar.gz
StartedAt: 2015-10-27 07:45:38 -0400 (Tue, 27 Oct 2015)
EndedAt: 2015-10-27 07:50:07 -0400 (Tue, 27 Oct 2015)
EllapsedTime: 268.6 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: segmentSeq.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings segmentSeq_2.4.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/segmentSeq.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-apple-darwin13.4.0 (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 ‘2.4.0’
* 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 ‘segmentSeq’ can be installed ... [15s/16s] 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
  ‘parLapplyLB’
.getLocLikelihoods: no visible global function definition for
  ‘clusterExport’
.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
  ‘clusterExport’
.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 ... WARNING
Codoc mismatches from documentation object 'plotMethDistribution':
plotMethDistribution
  Code: function(meth, samples, bw = 0.001, subtract, chrs,
                 centromeres, add = FALSE, col, ylim = NULL, legend =
                 TRUE, ...)
  Docs: function(meth, samples, bw = 0.001, subtract, chrs,
                 centromeres, add = FALSE, col, legend = TRUE, ...)
  Argument names in code not in docs:
    ylim
  Mismatches in argument names:
    Position: 9 Code: ylim Docs: legend
    Position: 10 Code: legend Docs: ...

* 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 ... [98s/99s] OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
classifySeg     33.704  0.188  33.906
lociLikelihoods 12.006  0.042  12.057
heuristicSeg    10.829  0.053  10.889
readMeths       10.219  0.547  10.772
plotGenome       6.413  0.027   6.444
* 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: 1 WARNING, 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.2-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-class1.5310.0261.557
classifySeg33.704 0.18833.906
findChunks1.8440.0131.857
getCounts2.9050.0142.919
getOverlaps2.2640.0132.277
heuristicSeg10.829 0.05310.889
lociLikelihoods12.006 0.04212.057
plotGenome6.4130.0276.444
processAD2.5250.0232.549
readMethods1.6380.0081.646
readMeths10.219 0.54710.772
segData-class2.5700.0302.601
segmentSeq-package2.3270.0352.363