BioC 2.12: CHECK report for BiSeq on george2

Package: BiSeq

Version: 1.0.3

Command: /home/biocbuild/bbs-2.12-bioc/R/bin/R CMD check --no-vignettes --timings BiSeq_1.0.3.tar.gz

StartedAt: 2013-10-09 00:31:06 -0700 (Wed, 09 Oct 2013)

EndedAt: 2013-10-09 00:39:30 -0700 (Wed, 09 Oct 2013)

EllapsedTime: 504.1 seconds

RetCode: 0

Status:  OK

CheckDir: BiSeq.Rcheck

Warnings: 0

* using log directory ‘/home/biocbuild/bbs-2.12-bioc/meat/BiSeq.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 ‘BiSeq/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘BiSeq’ version ‘1.0.3’
* 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 ‘BiSeq’ can be installed ... [35s/36s] 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 ... 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:
  ‘unsrturl.bst’

Consider the use of a .Rinstignore file: see ‘Writing R Extensions’,
or move the vignette sources from ‘inst/doc’ to ‘vignettes’.
* checking examples ... [143s/146s] OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
makeVariogram     23.853  0.036  24.335
estLocCor         23.161  0.032  23.611
betaRegression    19.257  1.176  20.735
compareTwoSamples  8.064  3.936  10.963
summarizeRegions  10.541  0.492  12.379
plotBindingSites   6.593  0.008   6.616
predictMeth        4.377  1.220   4.706
* 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/BiSeq.Rcheck/00check.log’
for details.

* installing *source* package ‘BiSeq’ ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (BiSeq)

name	user	system	elapsed
BSraw-class	0.849	0.012	0.863
BSrel-class	0.724	0.000	0.727
DMRs	0.068	0.004	0.071
annotateGRanges	1.008	0.032	1.038
betaRegression	19.257	1.176	20.735
betaResults	0.040	0.008	0.049
betaResultsNull	0.028	0.000	0.028
binomLikelihoodSmooth	0.040	0.000	0.039
clusterSites	1.660	0.476	3.260
clusterSitesToGR	3.548	0.544	4.044
compareTwoSamples	8.064	3.936	10.963
covBoxplots	0.960	0.036	1.040
covStatistics	0.080	0.004	0.089
estLocCor	23.161	0.032	23.611
filterByCov	0.240	0.000	0.241
filterBySharedRegions	0.297	0.000	0.296
findDMRs	1.136	0.008	1.145
limitCov	1.616	0.416	3.267
logisticRegression	3.376	0.008	3.386
makeVariogram	23.853	0.036	24.335
plotBindingSites	6.593	0.008	6.616
plotMeth	0.428	0.008	0.435
plotMethMap	1.296	0.016	1.422
plotSmoothMeth	0.312	0.004	0.343
predictMeth	4.377	1.220	4.706
predictedMeth	0.036	0.004	0.040
promoters	0.132	0.012	0.142
rawToRel	0.864	0.052	0.917
readBismark	0.116	0.004	0.121
rrbs	0.064	0.000	0.066
smoothVariogram	0.06	0.00	0.06
summarizeRegions	10.541	0.492	12.379
testClusters	0.192	0.000	0.232
trimClusters	1.068	0.000	1.173
vario	0.008	0.000	0.008
writeBED	0.892	0.000	0.953