BioC 3.2: CHECK report for deltaGseg on moscato1

Package: deltaGseg

Version: 1.10.1

Command: rm -rf deltaGseg.buildbin-libdir deltaGseg.Rcheck && mkdir deltaGseg.buildbin-libdir deltaGseg.Rcheck && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=deltaGseg.buildbin-libdir deltaGseg_1.10.1.tar.gz >deltaGseg.Rcheck\00install.out 2>&1 && cp deltaGseg.Rcheck\00install.out deltaGseg-install.out && D:\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_1.10.1.tar.gz

StartedAt: 2016-04-23 01:32:59 -0700 (Sat, 23 Apr 2016)

EndedAt: 2016-04-23 01:52:21 -0700 (Sat, 23 Apr 2016)

EllapsedTime: 1162.1 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 && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=deltaGseg.buildbin-libdir deltaGseg_1.10.1.tar.gz >deltaGseg.Rcheck\00install.out 2>&1 && cp deltaGseg.Rcheck\00install.out deltaGseg-install.out  && D:\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_1.10.1.tar.gz
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* using log directory 'D:/biocbld/bbs-3.2-bioc/meat/deltaGseg.Rcheck'
* using R version 3.2.4 (2016-03-10)
* 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 '1.10.1'
* 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' ... [483s] OK
Examples with CPU or elapsed time > 5s
            user system elapsed
clusterPV 440.19  36.27  477.51
** running examples for arch 'x64' ... [537s] OK
Examples with CPU or elapsed time > 5s
            user system elapsed
clusterPV 494.33  33.64  528.86
* 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
  'D:/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_1.10.1.zip
* DONE (deltaGseg)

name	user	system	elapsed
SegSeriesTrajectories-class	0	0	0
SegTrajectories-class	0	0	0
Trajectories-class	0.00	0.02	0.02
TransTrajectories-class	0	0	0
chooseBreaks	0.25	0.01	0.26
clusterPV-methods	0	0	0
clusterPV	440.19	36.27	477.51
clusterSegments-methods	0	0	0
clusterSegments	0	0	0
denoiseSegments-methods	0	0	0
denoiseSegments	0.95	0.00	0.95
diagnosticPlots-methods	0	0	0
diagnosticPlots	0.67	0.00	1.17
getAVD	0.08	0.03	0.10
getBreaks-methods	0	0	0
getBreaks	0.10	0.00	0.09
getIntervals-methods	0	0	0
getIntervals	0.10	0.02	0.13
getSegments-methods	0	0	0
getSegments	0.13	0.02	0.14
getTNames-methods	0	0	0
getTNames	0.08	0.01	0.10
getTraj	0.11	0.02	0.12
parseTraj	0.17	0.00	0.17
plotDiff-methods	0.01	0.00	0.02
plotDiff	0.44	0.00	0.49
splitTraj-methods	0	0	0
splitTraj	0.1	0.0	0.1
transformSeries-methods	0.01	0.00	0.01
transformSeries	0.11	0.00	0.11

name	user	system	elapsed
SegSeriesTrajectories-class	0	0	0
SegTrajectories-class	0	0	0
Trajectories-class	0	0	0
TransTrajectories-class	0	0	0
chooseBreaks	0.25	0.01	0.26
clusterPV-methods	0	0	0
clusterPV	494.33	33.64	528.86
clusterSegments-methods	0	0	0
clusterSegments	0	0	0
denoiseSegments-methods	0	0	0
denoiseSegments	1.06	0.06	1.13
diagnosticPlots-methods	0	0	0
diagnosticPlots	1.08	0.00	1.17
getAVD	0.09	0.03	0.12
getBreaks-methods	0.02	0.00	0.02
getBreaks	0.12	0.00	0.12
getIntervals-methods	0	0	0
getIntervals	0.12	0.00	0.12
getSegments-methods	0.02	0.00	0.02
getSegments	0.09	0.01	0.11
getTNames-methods	0	0	0
getTNames	0.11	0.00	0.11
getTraj	0.10	0.02	0.10
parseTraj	0.40	0.00	0.41
plotDiff-methods	0	0	0
plotDiff	0.64	0.02	1.95
splitTraj-methods	0	0	0
splitTraj	0.11	0.00	0.10
transformSeries-methods	0	0	0
transformSeries	0.14	0.02	0.16