BioC 2.12: CHECK report for segmentSeq on moscato2

Package: segmentSeq

Version: 1.12.1

Command: rm -rf segmentSeq.buildbin-libdir && mkdir segmentSeq.buildbin-libdir && E:\biocbld\bbs-2.12-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=segmentSeq.buildbin-libdir segmentSeq_1.12.1.tar.gz >segmentSeq-install.out 2>&1 && E:\biocbld\bbs-2.12-bioc\R\bin\R.exe CMD check --library=segmentSeq.buildbin-libdir --install="check:segmentSeq-install.out" --force-multiarch --no-vignettes --timings segmentSeq_1.12.1.tar.gz && mv segmentSeq.buildbin-libdir/* segmentSeq.Rcheck/ && rmdir segmentSeq.buildbin-libdir

StartedAt: 2013-10-09 04:10:28 -0700 (Wed, 09 Oct 2013)

EndedAt: 2013-10-09 04:22:16 -0700 (Wed, 09 Oct 2013)

EllapsedTime: 708.1 seconds

RetCode: 0

Status:  OK

CheckDir: segmentSeq.Rcheck

Warnings: 0

* using log directory 'E:/biocbld/bbs-2.12-bioc/meat/segmentSeq.Rcheck'
* using R version 3.0.1 (2013-05-16)
* using platform: i386-w64-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'segmentSeq/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'segmentSeq' version '1.12.1'
* 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 whether package 'segmentSeq' can be installed ... OK
* checking installed package size ... OK
* checking package 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
* 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
* 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 for unstated 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 ... NOTE
.partheuristicSeg: no visible global function definition for
  '.methFunction'
.partheuristicSeg: no visible global function definition for
  '.constructMethNulls'
.partheuristicSeg: no visible global function definition for
  'getMethylatedCounts'
.squeezeAlign: no visible global function definition for
  'findMethChunks'
.stratifySample: no visible binding for global variable 'sD'
.stratifySample: no visible binding for global variable 'lensameFlag'
.stratifySample: no visible binding for global variable 'seglens'
processAD : partCounts: no visible global function definition for
  'getMethylatedCounts'
* 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 installed files from 'inst/doc' ... OK
* checking examples ...
** running examples for arch 'i386' ... [214s] OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
classifySeg        56.79   0.03   56.81
lociLikelihoods    29.62   0.00   29.64
heuristicSeg       27.77   0.00   27.79
processAD          18.90   0.00   18.90
segData-class      18.44   0.00   18.45
segmentSeq-package 18.03   0.00   18.05
plotGenome         13.40   0.00   13.40
** running examples for arch 'x64' ... [227s] OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
classifySeg        56.00   0.07   56.10
heuristicSeg       32.16   0.00   32.17
lociLikelihoods    30.25   0.02   30.27
processAD          20.65   0.00   20.67
segData-class      19.94   0.00   19.94
plotGenome         18.46   0.00   18.47
segmentSeq-package 18.39   0.02   18.41
getCounts           4.99   0.03    5.02
* 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 vignettes ... SKIPPED
* checking PDF version of manual ... OK

NOTE: There was 1 note.
See
  'E:/biocbld/bbs-2.12-bioc/meat/segmentSeq.Rcheck/00check.log'
for details.

install for i386

* 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

install for x64

* installing *source* package 'segmentSeq' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'segmentSeq' as segmentSeq_1.12.1.zip
* DONE (segmentSeq)