BioC 3.2: CHECK report for BiSeq on perceval

Package: BiSeq

Version: 1.10.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings BiSeq_1.10.0.tar.gz

StartedAt: 2015-11-10 02:40:22 -0800 (Tue, 10 Nov 2015)

EndedAt: 2015-11-10 02:45:37 -0800 (Tue, 10 Nov 2015)

EllapsedTime: 315.3 seconds

RetCode: 0

Status:  OK

CheckDir: BiSeq.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings BiSeq_1.10.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/BiSeq.Rcheck’
* using R version 3.2.2 Patched (2015-10-08 r69496)
* using platform: x86_64-apple-darwin10.8.0 (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 ‘1.10.0’
* 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 ... [22s/23s] 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 ... [87s/87s] OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
globalTest        24.926  0.024  24.951
betaRegression    10.433  0.681  11.212
makeVariogram      8.052  0.075   8.127
estLocCor          8.016  0.073   8.255
compareTwoSamples  3.307  2.752   5.633
* 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
  ‘/Users/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	0.223	0.010	0.274
BSrel-class	0.500	0.011	0.511
DMRs	0.054	0.001	0.055
annotateGRanges	0.218	0.013	0.230
betaRegression	10.433	0.681	11.212
betaResults	0.008	0.001	0.009
betaResultsNull	0.006	0.001	0.007
binomLikelihoodSmooth	0.008	0.001	0.009
clusterSites	0.424	0.232	0.892
clusterSitesToGR	0.667	0.419	1.011
compareTwoSamples	3.307	2.752	5.633
covBoxplots	0.591	0.113	0.704
covStatistics	0.060	0.007	0.068
estLocCor	8.016	0.073	8.255
filterByCov	0.146	0.008	0.154
filterBySharedRegions	0.154	0.011	0.164
findDMRs	0.597	0.003	0.601
globalTest	24.926	0.024	24.951
limitCov	0.929	0.397	2.475
logisticRegression	1.529	0.031	1.560
makeVariogram	8.052	0.075	8.127
plotBindingSites	2.453	0.036	2.490
plotMeth	0.252	0.009	0.263
plotMethMap	0.264	0.008	0.273
plotSmoothMeth	0.549	0.006	0.556
predictMeth	1.696	1.403	1.932
predictedMeth	0.019	0.007	0.026
promoters	0.083	0.015	0.098
rawToRel	0.074	0.014	0.090
readBismark	0.073	0.014	0.087
rrbs	0.056	0.007	0.063
smoothVariogram	0.026	0.004	0.032
summarizeRegions	1.888	0.475	2.506
testClusters	0.106	0.007	0.113
trimClusters	0.571	0.004	0.574
vario	0.003	0.000	0.004
writeBED	0.240	0.012	0.252