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: 2015-10-27 05:54:35 -0400 (Tue, 27 Oct 2015)

EndedAt: 2015-10-27 06:00:00 -0400 (Tue, 27 Oct 2015)

EllapsedTime: 324.6 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 ... [23s/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 ... [89s/89s] OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
globalTest        24.633  0.028  24.661
betaRegression    10.592  0.679  11.370
makeVariogram      8.014  0.090   8.104
estLocCor          7.746  0.071   7.829
compareTwoSamples  3.856  3.280   6.605
* 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	0.008	0.232
BSrel-class	0.488	0.008	0.496
DMRs	0.053	0.001	0.054
annotateGRanges	0.185	0.009	0.194
betaRegression	10.592	0.679	11.370
betaResults	0.013	0.002	0.015
betaResultsNull	0.008	0.001	0.009
binomLikelihoodSmooth	0.011	0.002	0.012
clusterSites	0.502	0.274	1.067
clusterSitesToGR	0.810	0.507	1.261
compareTwoSamples	3.856	3.280	6.605
covBoxplots	0.586	0.112	0.758
covStatistics	0.062	0.007	0.191
estLocCor	7.746	0.071	7.829
filterByCov	0.140	0.007	0.146
filterBySharedRegions	0.150	0.009	0.159
findDMRs	0.570	0.003	0.573
globalTest	24.633	0.028	24.661
limitCov	0.911	0.402	2.479
logisticRegression	1.649	0.010	1.660
makeVariogram	8.014	0.090	8.104
plotBindingSites	2.890	0.040	2.931
plotMeth	0.260	0.011	0.274
plotMethMap	0.280	0.013	0.295
plotSmoothMeth	0.130	0.005	0.135
predictMeth	1.717	1.458	1.985
predictedMeth	0.023	0.010	0.035
promoters	0.091	0.018	0.109
rawToRel	0.094	0.028	0.122
readBismark	0.088	0.021	0.109
rrbs	0.058	0.009	0.067
smoothVariogram	0.027	0.004	0.033
summarizeRegions	2.309	0.594	3.137
testClusters	0.096	0.002	0.098
trimClusters	0.536	0.003	0.538
vario	0.003	0.000	0.004
writeBED	0.214	0.008	0.222