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

Package: deltaGseg

Version: 1.10.0

Command: rm -rf deltaGseg.buildbin-libdir deltaGseg.Rcheck && mkdir deltaGseg.buildbin-libdir deltaGseg.Rcheck && C:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=deltaGseg.buildbin-libdir deltaGseg_1.10.0.tar.gz >deltaGseg.Rcheck\00install.out 2>&1 && cp deltaGseg.Rcheck\00install.out deltaGseg-install.out && C:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=deltaGseg.buildbin-libdir --install="check:deltaGseg-install.out" --force-multiarch --no-vignettes --timings deltaGseg_1.10.0.tar.gz

StartedAt: 2015-10-27 01:11:17 -0400 (Tue, 27 Oct 2015)

EndedAt: 2015-10-27 01:25:00 -0400 (Tue, 27 Oct 2015)

EllapsedTime: 823.6 seconds

RetCode: 0

Status:  OK

CheckDir: deltaGseg.Rcheck

Warnings: 0

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### Running command:
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###   rm -rf deltaGseg.buildbin-libdir deltaGseg.Rcheck && mkdir deltaGseg.buildbin-libdir deltaGseg.Rcheck && C:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=deltaGseg.buildbin-libdir deltaGseg_1.10.0.tar.gz >deltaGseg.Rcheck\00install.out 2>&1 && cp deltaGseg.Rcheck\00install.out deltaGseg-install.out  && C:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=deltaGseg.buildbin-libdir --install="check:deltaGseg-install.out" --force-multiarch --no-vignettes --timings deltaGseg_1.10.0.tar.gz
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* using log directory 'C:/biocbld/bbs-3.2-bioc/meat/deltaGseg.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 'deltaGseg/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'deltaGseg' version '1.10.0'
* 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 whether package 'deltaGseg' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* 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 ... 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 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 ...
** running examples for arch 'i386' ... [340s] OK
Examples with CPU or elapsed time > 5s
            user system elapsed
clusterPV 300.05  33.53  335.26
** running examples for arch 'x64' ... [417s] OK
Examples with CPU or elapsed time > 5s
            user system elapsed
clusterPV 380.57  31.77  412.41
* 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: 3 NOTEs
See
  'C:/biocbld/bbs-3.2-bioc/meat/deltaGseg.Rcheck/00check.log'
for details.

install for i386

* 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

install for x64

* installing *source* package 'deltaGseg' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'deltaGseg' as deltaGseg_1.10.0.zip
* DONE (deltaGseg)

name	user	system	elapsed
SegSeriesTrajectories-class	0.02	0.00	0.01
SegTrajectories-class	0	0	0
Trajectories-class	0	0	0
TransTrajectories-class	0	0	0
chooseBreaks	0.18	0.00	0.19
clusterPV-methods	0	0	0
clusterPV	300.05	33.53	335.26
clusterSegments-methods	0	0	0
clusterSegments	0	0	0
denoiseSegments-methods	0	0	0
denoiseSegments	0.67	0.03	0.71
diagnosticPlots-methods	0	0	0
diagnosticPlots	0.44	0.02	0.45
getAVD	0.04	0.01	0.06
getBreaks-methods	0	0	0
getBreaks	0.07	0.00	0.06
getIntervals-methods	0	0	0
getIntervals	0.04	0.02	0.06
getSegments-methods	0	0	0
getSegments	0.08	0.00	0.08
getTNames-methods	0	0	0
getTNames	0.05	0.01	0.06
getTraj	0.06	0.00	0.07
parseTraj	0.16	0.00	0.15
plotDiff-methods	0	0	0
plotDiff	0.31	0.02	0.33
splitTraj-methods	0	0	0
splitTraj	0.06	0.00	0.06
transformSeries-methods	0	0	0
transformSeries	0.08	0.00	0.08

name	user	system	elapsed
SegSeriesTrajectories-class	0	0	0
SegTrajectories-class	0.00	0.02	0.02
Trajectories-class	0	0	0
TransTrajectories-class	0	0	0
chooseBreaks	0.18	0.01	0.20
clusterPV-methods	0	0	0
clusterPV	380.57	31.77	412.41
clusterSegments-methods	0	0	0
clusterSegments	0	0	0
denoiseSegments-methods	0	0	0
denoiseSegments	0.90	0.04	0.95
diagnosticPlots-methods	0	0	0
diagnosticPlots	0.47	0.02	0.49
getAVD	0.06	0.00	0.06
getBreaks-methods	0	0	0
getBreaks	0.07	0.00	0.06
getIntervals-methods	0	0	0
getIntervals	0.06	0.00	0.06
getSegments-methods	0	0	0
getSegments	0.04	0.00	0.05
getTNames-methods	0	0	0
getTNames	0.13	0.02	0.14
getTraj	0.04	0.00	0.04
parseTraj	0.11	0.00	0.11
plotDiff-methods	0	0	0
plotDiff	0.28	0.01	0.30
splitTraj-methods	0	0	0
splitTraj	0.08	0.00	0.08
transformSeries-methods	0	0	0
transformSeries	0.08	0.00	0.08