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BioC 3.2: CHECK report for segmentSeq on zin1

This page was generated on 2015-08-24 10:47:45 -0700 (Mon, 24 Aug 2015).

Package 922/1071HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
segmentSeq 2.3.2
Thomas J. Hardcastle
Snapshot Date: 2015-08-23 16:24:14 -0700 (Sun, 23 Aug 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/segmentSeq
Last Changed Rev: 107067 / Revision: 107696
Last Changed Date: 2015-08-04 03:46:22 -0700 (Tue, 04 Aug 2015)
zin1 Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK [ WARNINGS ]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: 2.3.2
Command: /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings segmentSeq_2.3.2.tar.gz
StartedAt: 2015-08-24 03:37:12 -0700 (Mon, 24 Aug 2015)
EndedAt: 2015-08-24 03:41:07 -0700 (Mon, 24 Aug 2015)
EllapsedTime: 235.2 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: segmentSeq.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings segmentSeq_2.3.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/segmentSeq.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-pc-linux-gnu (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 ‘2.3.2’
* 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 ... [14s/14s] OK
* checking installed package size ... NOTE
  installed size is 10.0Mb
  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 ... [90s/90s] OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
classifySeg     32.250  0.035  32.388
lociLikelihoods 10.256  0.000  10.268
readMeths        9.455  0.056   9.515
heuristicSeg     9.339  0.004   9.351
plotGenome       5.309  0.000   5.336
* 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
  ‘/home/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-class1.7150.0041.720
classifySeg32.250 0.03532.388
findChunks1.6350.0041.640
getCounts2.9840.0002.988
getOverlaps1.9140.0001.915
heuristicSeg9.3390.0049.351
lociLikelihoods10.256 0.00010.268
plotGenome5.3090.0005.336
processAD2.2450.0002.249
readMethods1.6680.0001.667
readMeths9.4550.0569.515
segData-class2.2580.0162.275
segmentSeq-package2.2150.0082.221