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BioC 2.14: CHECK report for deltaGseg on petty

This page was generated on 2014-10-08 09:00:45 -0700 (Wed, 08 Oct 2014).

Package 220/824HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
deltaGseg 1.4.0
Diana Low
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/deltaGseg
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: deltaGseg
Version: 1.4.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch deltaGseg_1.4.0.tar.gz
StartedAt: 2014-10-07 21:38:34 -0700 (Tue, 07 Oct 2014)
EndedAt: 2014-10-07 21:56:53 -0700 (Tue, 07 Oct 2014)
EllapsedTime: 1098.8 seconds
RetCode: 0
Status:  OK 
CheckDir: deltaGseg.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch deltaGseg_1.4.0.tar.gz
###
##############################################################################
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* using log directory ‘/Users/biocbuild/bbs-2.14-bioc/meat/deltaGseg.Rcheck’
* using R version 3.1.1 (2014-07-10)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘deltaGseg/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘deltaGseg’ version ‘1.4.0’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  ‘ggplot2’ ‘changepoint’ ‘wavethresh’ ‘tseries’ ‘pvclust’ ‘fBasics’
  ‘grid’ ‘reshape’ ‘scales’
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 ‘deltaGseg’ can be installed ... [14s/14s] OK
* checking installed package size ... OK
* 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... NOTE
The following files should probably not be installed:
  ‘diagplots.png’, ‘simclust.png’, ‘simtraj.png’, ‘simtrajtr.png’,
  ‘simtrajtr2.png’, ‘traj1.png’, ‘traj1break.png’, ‘traj1ss0.png’,
  ‘traj1ss1.png’, ‘traj1tr.png’

Consider the use of a .Rinstignore file: see ‘Writing R Extensions’,
or move the vignette sources from ‘inst/doc’ to ‘vignettes’.
* checking files in ‘vignettes’ ... OK
* checking examples ... [16m/16m] OK
Examples with CPU or elapsed time > 5s
             user system elapsed
clusterPV 893.719  27.22 933.525
* 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 2 notes.
See
  ‘/Users/biocbuild/bbs-2.14-bioc/meat/deltaGseg.Rcheck/00check.log’
for details.

deltaGseg.Rcheck/00install.out:

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

deltaGseg.Rcheck/deltaGseg-Ex.timings:

nameusersystemelapsed
SegSeriesTrajectories-class0.0040.0010.005
SegTrajectories-class0.0020.0000.003
Trajectories-class0.0020.0000.003
TransTrajectories-class0.0020.0010.003
chooseBreaks0.4330.0350.469
clusterPV-methods0.0010.0000.001
clusterPV893.719 27.220933.525
clusterSegments-methods0.0010.0010.001
clusterSegments0.0010.0000.002
denoiseSegments-methods0.0010.0000.001
denoiseSegments1.7430.1751.942
diagnosticPlots-methods0.0010.0000.002
diagnosticPlots1.2150.0411.426
getAVD0.1040.0150.120
getBreaks-methods0.0010.0000.001
getBreaks0.1220.0210.143
getIntervals-methods0.0010.0000.001
getIntervals0.2600.0250.285
getSegments-methods0.0010.0000.002
getSegments0.1110.0140.125
getTNames-methods0.0010.0000.001
getTNames0.1070.0140.122
getTraj0.1060.0150.121
parseTraj0.2350.0280.281
plotDiff-methods0.0010.0000.001
plotDiff0.6720.0250.709
splitTraj-methods0.0020.0000.002
splitTraj0.1120.0170.130
transformSeries-methods0.0010.0000.001
transformSeries0.1770.0250.204