BioC 2.12: CHECK report for segmentSeq on petty

Package: segmentSeq

Version: 1.12.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch segmentSeq_1.12.1.tar.gz

StartedAt: 2013-10-08 23:53:43 -0700 (Tue, 08 Oct 2013)

EndedAt: 2013-10-09 00:03:24 -0700 (Wed, 09 Oct 2013)

EllapsedTime: 580.7 seconds

RetCode: 0

Status:  OK

CheckDir: segmentSeq.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/segmentSeq.Rcheck'
* using R version 3.0.1 (2013-05-16)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: ASCII
* 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 for sufficient/correct file permissions ... OK
* checking whether package 'segmentSeq' can be installed ... [28s/29s] 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
* 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 sizes of PDF files under 'inst/doc' ... OK
* checking installed files from 'inst/doc' ... OK
* checking examples ... [292s/297s] OK
Examples with CPU or elapsed time > 5s
                      user system elapsed
classifySeg         80.045  0.477  82.284
lociLikelihoods     38.379  0.151  38.918
heuristicSeg        37.234  0.187  38.181
processAD           24.481  0.146  24.915
segData-class       24.083  0.166  24.598
segmentSeq-package  23.770  0.204  24.189
plotGenome          18.975  0.070  19.232
alignmentData-class  6.863  0.118   7.059
getCounts            5.927  0.037   6.057
findChunks           5.859  0.036   6.010
getOverlaps          5.498  0.032   5.605
readMethods          5.087  0.055   5.187
* 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
  '/Users/biocbuild/bbs-2.12-bioc/meat/segmentSeq.Rcheck/00check.log'
for details.

* 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
* DONE (segmentSeq)

name	user	system	elapsed
alignmentData-class	6.863	0.118	7.059
classifySeg	80.045	0.477	82.284
findChunks	5.859	0.036	6.010
getCounts	5.927	0.037	6.057
getOverlaps	5.498	0.032	5.605
heuristicSeg	37.234	0.187	38.181
lociLikelihoods	38.379	0.151	38.918
plotGenome	18.975	0.070	19.232
processAD	24.481	0.146	24.915
readMethods	5.087	0.055	5.187
segData-class	24.083	0.166	24.598
segmentSeq-package	23.770	0.204	24.189