BioC 3.2: CHECK report for BiSeq on zin1

Package: BiSeq

Version: 1.9.2

Command: /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings BiSeq_1.9.2.tar.gz

StartedAt: 2015-08-23 22:05:50 -0700 (Sun, 23 Aug 2015)

EndedAt: 2015-08-23 22:09:34 -0700 (Sun, 23 Aug 2015)

EllapsedTime: 223.9 seconds

RetCode: 0

Status:  OK

CheckDir: BiSeq.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings BiSeq_1.9.2.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/BiSeq.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-pc-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 ‘1.9.2’
* 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 ... [16s/16s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘methods’ ‘S4Vectors’ ‘IRanges’ ‘GenomicRanges’ ‘SummarizedExperiment’ ‘Formula’
A package should be listed in only one of these fields.
* 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 dependencies in R code ... NOTE
Namespace in Imports field not imported from: ‘Formula’
  All declared Imports should be used.
Package in Depends field not imported from: ‘Formula’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* 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’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [62s/62s] OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
globalTest     19.628  0.017  19.674
betaRegression  8.391  0.209   8.670
makeVariogram   5.046  0.004   5.131
* 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 vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.2-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	0.130	0.000	0.129
BSrel-class	0.1	0.0	0.1
DMRs	0.041	0.000	0.041
annotateGRanges	0.427	0.000	0.430
betaRegression	8.391	0.209	8.670
betaResults	0.007	0.000	0.007
betaResultsNull	0.006	0.000	0.005
binomLikelihoodSmooth	0.013	0.000	0.013
clusterSites	0.325	0.085	0.814
clusterSitesToGR	1.008	0.219	0.813
compareTwoSamples	2.338	1.045	3.051
covBoxplots	0.405	0.032	0.438
covStatistics	0.056	0.000	0.056
estLocCor	4.940	0.004	4.949
filterByCov	0.098	0.000	0.098
filterBySharedRegions	0.111	0.000	0.111
findDMRs	0.461	0.000	0.461
globalTest	19.628	0.017	19.674
limitCov	0.932	0.273	1.703
logisticRegression	1.217	0.000	1.217
makeVariogram	5.046	0.004	5.131
plotBindingSites	2.039	0.004	2.044
plotMeth	0.202	0.000	0.203
plotMethMap	0.221	0.000	0.221
plotSmoothMeth	0.106	0.000	0.106
predictMeth	1.097	0.428	0.954
predictedMeth	0.012	0.004	0.016
promoters	0.077	0.000	0.077
rawToRel	0.058	0.004	0.063
readBismark	0.058	0.004	0.063
rrbs	0.048	0.000	0.048
smoothVariogram	0.027	0.000	0.027
summarizeRegions	1.714	0.141	1.916
testClusters	0.101	0.000	0.100
trimClusters	0.485	0.000	0.485
vario	0.002	0.000	0.003
writeBED	0.19	0.00	0.19