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BioC 2.14: CHECK report for segmentSeq on morelia

This page was generated on 2014-10-08 09:04:13 -0700 (Wed, 08 Oct 2014).

Package 713/824HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
segmentSeq 1.16.0
Thomas J. Hardcastle
Snapshot Date: 2014-10-07 17:20:37 -0700 (Tue, 07 Oct 2014)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_14/madman/Rpacks/segmentSeq
Last Changed Rev: 88838 / Revision: 95116
Last Changed Date: 2014-04-11 14:07:21 -0700 (Fri, 11 Apr 2014)
zin2 Linux (Ubuntu 12.04.4 LTS) / x86_64  NotNeeded  OK  OK 
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK  OK  OK 
petty Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK  OK  OK 
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK [ OK ] OK 

Summary

Package: segmentSeq
Version: 1.16.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch segmentSeq_1.16.0.tar.gz
StartedAt: 2014-10-08 01:29:57 -0700 (Wed, 08 Oct 2014)
EndedAt: 2014-10-08 01:37:00 -0700 (Wed, 08 Oct 2014)
EllapsedTime: 422.8 seconds
RetCode: 0
Status:  OK 
CheckDir: segmentSeq.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch segmentSeq_1.16.0.tar.gz
###
##############################################################################
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* using log directory ‘/Users/biocbuild/bbs-2.14-bioc/meat/segmentSeq.Rcheck’
* using R version 3.1.1 (2014-07-10)
* using platform: x86_64-apple-darwin13.1.0 (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 ‘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 ‘segmentSeq’ can be installed ... [22s/22s] 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 ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘baySeq’ ‘IRanges’ ‘methods’ ‘GenomicRanges’
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
'library' or 'require' call to ‘GenomicRanges’ which was already attached by Depends.
  Please remove these calls from your code.
Package in Depends field not imported from: ‘ShortRead’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
See the information on DESCRIPTION files in the chapter ‘Creating R
packages’ of the ‘Writing R Extensions’ manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.partheuristicSeg : <anonymous>: warning in Rle(-Inf, length =
  length(emptyPD@coordinates)): partial argument match of 'length' to
  'lengths'
.constructNulls: no visible binding for global variable ‘cl’
.getMethylatedCounts : <anonymous> : createIntervals: no visible
  binding for global variable ‘dupTags’
.methLikelihoods : <anonymous>: possible error in getLikelihoods.BB(cD
  = repD, bootStraps = bootStraps, nullData = TRUE, verbose = FALSE, cl
  = cl): unused argument (nullData = TRUE)
.stratifySample: no visible binding for global variable ‘sD’
.stratifySample: no visible binding for global variable ‘lensameFlag’
.stratifySample: no visible binding for global variable ‘seglens’
plotAverageProfile: no visible binding for global variable
  ‘profCHH.DMR’
* checking Rd files ... NOTE
prepare_Rd: averageMethylationRegions.Rd:104-105: Dropping empty section \examples
prepare_Rd: summariseLoci.Rd:22-24: Dropping empty section \details
* 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 ... [195s/195s] OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
classifySeg        61.115  0.162  61.427
heuristicSeg       23.855  0.065  23.936
lociLikelihoods    23.505  0.073  23.591
readMeths          16.114  0.758  16.889
plotGenome         16.215  0.055  16.282
processAD           9.004  0.044   9.055
segData-class       8.124  0.070   8.210
segmentSeq-package  8.057  0.055   8.121
* 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

NOTE: There were 5 notes.
See
  ‘/Users/biocbuild/bbs-2.14-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-class3.1190.0313.156
classifySeg61.115 0.16261.427
findChunks2.8010.0152.819
getCounts4.1920.0274.219
getOverlaps3.9840.0174.005
heuristicSeg23.855 0.06523.936
lociLikelihoods23.505 0.07323.591
plotGenome16.215 0.05516.282
processAD9.0040.0449.055
readMethods3.1910.0323.224
readMeths16.114 0.75816.889
segData-class8.1240.0708.210
segmentSeq-package8.0570.0558.121