BioC 2.12: CHECK report for BiSeq on petty

Package: BiSeq

Version: 1.0.3

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch BiSeq_1.0.3.tar.gz

StartedAt: 2013-10-08 21:45:21 -0700 (Tue, 08 Oct 2013)

EndedAt: 2013-10-08 21:54:12 -0700 (Tue, 08 Oct 2013)

EllapsedTime: 531.1 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 3.0.1 (2013-05-16)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file '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 sizes of PDF files under 'inst/doc' ... 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 ... [171s/173s] OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
makeVariogram     30.007  0.602  31.297
estLocCor         29.602  0.623  30.393
betaRegression    22.703  1.656  25.074
compareTwoSamples 10.555  6.206  14.930
summarizeRegions   7.701  1.315  10.654
predictMeth        5.838  2.234   6.682
plotBindingSites   7.019  0.074   7.296
* 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	0.632	0.015	0.666
BSrel-class	0.979	0.017	1.000
DMRs	0.090	0.003	0.093
annotateGRanges	0.499	0.046	0.552
betaRegression	22.703	1.656	25.074
betaResults	0.025	0.004	0.029
betaResultsNull	0.017	0.004	0.021
binomLikelihoodSmooth	0.039	0.009	0.049
clusterSites	1.989	0.672	4.188
clusterSitesToGR	3.767	1.019	4.758
compareTwoSamples	10.555	6.206	14.930
covBoxplots	0.225	0.022	0.247
covStatistics	0.091	0.013	0.105
estLocCor	29.602	0.623	30.393
filterByCov	0.243	0.011	0.258
filterBySharedRegions	0.276	0.023	0.299
findDMRs	1.950	0.021	1.983
limitCov	1.929	0.657	4.145
logisticRegression	3.573	0.080	3.691
makeVariogram	30.007	0.602	31.297
plotBindingSites	7.019	0.074	7.296
plotMeth	0.503	0.012	0.521
plotMethMap	0.998	0.025	1.027
plotSmoothMeth	0.339	0.007	0.349
predictMeth	5.838	2.234	6.682
predictedMeth	0.032	0.005	0.037
promoters	0.148	0.017	0.165
rawToRel	0.103	0.018	0.121
readBismark	0.148	0.008	0.157
rrbs	0.076	0.006	0.082
smoothVariogram	0.058	0.010	0.080
summarizeRegions	7.701	1.315	10.654
testClusters	0.207	0.011	0.218
trimClusters	1.331	0.034	1.368
vario	0.007	0.004	0.010
writeBED	1.279	0.023	1.326