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BioC 3.0: CHECK report for deltaGseg on perceval

This page was generated on 2015-04-10 09:57:52 -0700 (Fri, 10 Apr 2015).

Package 233/933HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
deltaGseg 1.6.0
Diana Low
Snapshot Date: 2015-04-09 16:20:12 -0700 (Thu, 09 Apr 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_0/madman/Rpacks/deltaGseg
Last Changed Rev: 95439 / Revision: 102249
Last Changed Date: 2014-10-13 14:38:33 -0700 (Mon, 13 Oct 2014)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  NotNeeded  OK  OK 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK  OK  OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK [ OK ] OK 
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK 

Summary

Package: deltaGseg
Version: 1.6.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch deltaGseg_1.6.0.tar.gz
StartedAt: 2015-04-10 00:42:59 -0700 (Fri, 10 Apr 2015)
EndedAt: 2015-04-10 00:58:50 -0700 (Fri, 10 Apr 2015)
EllapsedTime: 951.2 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_1.6.0.tar.gz
###
##############################################################################
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* using log directory ‘/Users/biocbuild/bbs-3.0-bioc/meat/deltaGseg.Rcheck’
* using R version 3.1.3 (2015-03-09)
* 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 ‘1.6.0’
* 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 ... [9s/12s] 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 ... [14m/14m] OK
Examples with CPU or elapsed time > 5s
            user system elapsed
clusterPV 802.48 27.821 831.076
* 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

NOTE: There were 2 notes.
See
  ‘/Users/biocbuild/bbs-3.0-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-class0.0030.0010.003
SegTrajectories-class0.0020.0010.003
Trajectories-class0.0010.0000.001
TransTrajectories-class0.0020.0010.002
chooseBreaks0.4450.0360.496
clusterPV-methods0.0010.0000.001
clusterPV802.480 27.821831.076
clusterSegments-methods0.0010.0000.001
clusterSegments0.0010.0010.001
denoiseSegments-methods0.0000.0000.001
denoiseSegments1.2270.1981.454
diagnosticPlots-methods0.0010.0000.001
diagnosticPlots0.9560.0521.008
getAVD0.0690.0270.096
getBreaks-methods0.0000.0000.001
getBreaks0.0670.0180.085
getIntervals-methods0.0000.0000.001
getIntervals0.0710.0300.102
getSegments-methods0.0010.0000.000
getSegments0.0740.0250.100
getTNames-methods0.0010.0000.001
getTNames0.0730.0180.091
getTraj0.0680.0200.087
parseTraj0.1540.0190.173
plotDiff-methods0.0010.0000.000
plotDiff0.4350.0240.469
splitTraj-methods000
splitTraj0.0760.0130.089
transformSeries-methods0.0010.0000.001
transformSeries0.1240.0190.143