Package: BiSeq

Version: 1.0.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch BiSeq_1.0.1.tar.gz

StartedAt: 2013-05-01 03:01:38 -0700 (Wed, 01 May 2013)

EndedAt: 2013-05-01 03:08:58 -0700 (Wed, 01 May 2013)

EllapsedTime: 440.5 seconds

RetCode: 0

Status:  OK

CheckDir: BiSeq.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/BiSeq.Rcheck'
* using R version 3.0.0 Patched (2013-04-08 r62531)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'BiSeq/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'BiSeq' version '1.0.1'
* 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 'BiSeq' 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 ... 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 ... [137s/139s] OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
makeVariogram     22.688  0.659  23.781
estLocCor         21.930  0.541  22.757
betaRegression    17.538  1.739  19.939
compareTwoSamples  8.356  4.980  11.372
summarizeRegions   7.075  1.241   9.662
predictMeth        4.295  1.909   5.192
plotBindingSites   5.977  0.111   6.254
clusterSitesToGR   3.701  1.283   5.785
* 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/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	0.210	0.018	0.233
BSrel-class	0.149	0.024	0.180
DMRs	0.067	0.008	0.075
annotateGRanges	0.808	0.066	0.884
betaRegression	17.538	1.739	19.939
betaResults	0.019	0.004	0.026
betaResultsNull	0.014	0.003	0.017
binomLikelihoodSmooth	0.031	0.006	0.040
clusterSites	1.506	0.623	3.100
clusterSitesToGR	3.701	1.283	5.785
compareTwoSamples	8.356	4.980	11.372
covBoxplots	0.644	0.091	0.744
covStatistics	0.086	0.012	0.099
estLocCor	21.930	0.541	22.757
filterByCov	0.221	0.015	0.236
filterBySharedRegions	0.225	0.025	0.252
findDMRs	1.535	0.015	1.554
limitCov	1.490	0.574	3.312
logisticRegression	2.509	0.095	2.622
makeVariogram	22.688	0.659	23.781
plotBindingSites	5.977	0.111	6.254
plotMeth	0.366	0.012	0.385
plotMethMap	0.488	0.027	0.524
plotSmoothMeth	0.224	0.013	0.249
predictMeth	4.295	1.909	5.192
predictedMeth	0.027	0.007	0.035
promoters	0.109	0.014	0.124
rawToRel	0.13	0.03	0.16
readBismark	1.201	0.036	1.264
rrbs	0.070	0.006	0.087
smoothVariogram	0.053	0.011	0.070
summarizeRegions	7.075	1.241	9.662
testClusters	0.155	0.014	0.174
trimClusters	0.925	0.038	0.990
vario	0.006	0.003	0.009
writeBED	1.061	0.031	1.105