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BioC 3.2: CHECK report for segmentSeq on windows1.bioconductor.org

This page was generated on 2015-10-27 17:29:05 -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: rm -rf segmentSeq.buildbin-libdir segmentSeq.Rcheck && mkdir segmentSeq.buildbin-libdir segmentSeq.Rcheck && C:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=segmentSeq.buildbin-libdir segmentSeq_2.4.0.tar.gz >segmentSeq.Rcheck\00install.out 2>&1 && cp segmentSeq.Rcheck\00install.out segmentSeq-install.out && C:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=segmentSeq.buildbin-libdir --install="check:segmentSeq-install.out" --force-multiarch --no-vignettes --timings segmentSeq_2.4.0.tar.gz
StartedAt: 2015-10-27 05:28:29 -0400 (Tue, 27 Oct 2015)
EndedAt: 2015-10-27 05:34:47 -0400 (Tue, 27 Oct 2015)
EllapsedTime: 378.4 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: segmentSeq.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf segmentSeq.buildbin-libdir segmentSeq.Rcheck && mkdir segmentSeq.buildbin-libdir segmentSeq.Rcheck && C:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=segmentSeq.buildbin-libdir segmentSeq_2.4.0.tar.gz >segmentSeq.Rcheck\00install.out 2>&1 && cp segmentSeq.Rcheck\00install.out segmentSeq-install.out  && C:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=segmentSeq.buildbin-libdir --install="check:segmentSeq-install.out" --force-multiarch --no-vignettes --timings segmentSeq_2.4.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/biocbld/bbs-3.2-bioc/meat/segmentSeq.Rcheck'
* using R version 3.2.2 Patched (2015-08-16 r69094)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* 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 whether package 'segmentSeq' can be installed ... 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
* 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
'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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... [78s] OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
classifySeg     27.15   0.09   27.25
readMeths        9.48   0.52   10.00
lociLikelihoods  9.21   0.00    9.20
heuristicSeg     7.72   0.01    7.74
** running examples for arch 'x64' ... [98s] OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
classifySeg     33.50   0.02   33.51
heuristicSeg    11.34   0.00   11.34
lociLikelihoods 10.94   0.02   10.95
readMeths        9.75   0.42   10.17
plotGenome       6.97   0.00    6.97
* 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
  'C:/biocbld/bbs-3.2-bioc/meat/segmentSeq.Rcheck/00check.log'
for details.

segmentSeq.Rcheck/00install.out:


install for i386

* 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

install for x64

* installing *source* package 'segmentSeq' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'segmentSeq' as segmentSeq_2.4.0.zip
* DONE (segmentSeq)

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

nameusersystemelapsed
alignmentData-class1.370.001.39
classifySeg27.15 0.0927.25
findChunks1.350.001.34
getCounts2.250.022.27
getOverlaps1.530.001.53
heuristicSeg7.720.017.74
lociLikelihoods9.210.009.20
plotGenome4.250.004.25
processAD2.150.002.16
readMethods1.330.001.32
readMeths 9.48 0.5210.00
segData-class1.750.011.77
segmentSeq-package1.970.001.96

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

nameusersystemelapsed
alignmentData-class1.790.001.80
classifySeg33.50 0.0233.51
findChunks1.620.001.63
getCounts3.280.003.28
getOverlaps1.880.001.87
heuristicSeg11.34 0.0011.34
lociLikelihoods10.94 0.0210.95
plotGenome6.970.006.97
processAD2.440.002.44
readMethods1.870.001.88
readMeths 9.75 0.4210.17
segData-class2.660.022.67
segmentSeq-package2.270.012.28