BioC 2.12: CHECK report for segmentSeq on george2

Package: segmentSeq

Version: 1.12.1

Command: /home/biocbuild/bbs-2.12-bioc/R/bin/R CMD check --no-vignettes --timings segmentSeq_1.12.1.tar.gz

StartedAt: 2013-10-09 04:53:16 -0700 (Wed, 09 Oct 2013)

EndedAt: 2013-10-09 05:03:17 -0700 (Wed, 09 Oct 2013)

EllapsedTime: 601.4 seconds

RetCode: 0

Status:  OK

CheckDir: segmentSeq.Rcheck

Warnings: 0

* using log directory ‘/home/biocbuild/bbs-2.12-bioc/meat/segmentSeq.Rcheck’
* using R version 3.0.1 (2013-05-16)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* 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 ... [29s/30s] 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 installed files from ‘inst/doc’ ... OK
* checking examples ... [290s/302s] OK
Examples with CPU or elapsed time > 5s
                      user system elapsed
classifySeg         72.361  0.136  74.446
lociLikelihoods     40.555  0.060  42.480
heuristicSeg        36.658  0.120  38.745
processAD           23.901  0.052  25.366
segmentSeq-package  22.666  0.072  23.966
segData-class       22.217  0.032  23.112
plotGenome          18.921  0.020  20.158
alignmentData-class  9.425  0.012   9.499
findChunks           7.560  0.004   7.693
getCounts            7.032  0.016   7.717
getOverlaps          7.009  0.004   7.072
readMethods          6.353  0.004   6.643
* 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
  ‘/home/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	9.425	0.012	9.499
classifySeg	72.361	0.136	74.446
findChunks	7.560	0.004	7.693
getCounts	7.032	0.016	7.717
getOverlaps	7.009	0.004	7.072
heuristicSeg	36.658	0.120	38.745
lociLikelihoods	40.555	0.060	42.480
plotGenome	18.921	0.020	20.158
processAD	23.901	0.052	25.366
readMethods	6.353	0.004	6.643
segData-class	22.217	0.032	23.112
segmentSeq-package	22.666	0.072	23.966