BioC 3.2: CHECK report for BiSeq on zin1

Package: BiSeq

Version: 1.10.0

Command: /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings BiSeq_1.10.0.tar.gz

StartedAt: 2016-04-22 22:35:30 -0700 (Fri, 22 Apr 2016)

EndedAt: 2016-04-22 22:39:45 -0700 (Fri, 22 Apr 2016)

EllapsedTime: 254.6 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_1.10.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/BiSeq.Rcheck’
* using R version 3.2.4 Revised (2016-03-16 r70336)
* 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 ‘1.10.0’
* 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 ... [19s/19s] 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 ... [66s/66s] OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
globalTest     20.092  0.012  20.220
betaRegression 11.979  0.265  12.272
estLocCor       5.626  0.059   5.723
* 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	0.137	0.000	0.138
BSrel-class	0.089	0.004	0.093
DMRs	0.044	0.000	0.044
annotateGRanges	0.181	0.004	0.185
betaRegression	11.979	0.265	12.272
betaResults	0.006	0.000	0.006
betaResultsNull	0.005	0.000	0.005
binomLikelihoodSmooth	0.005	0.000	0.006
clusterSites	0.328	0.059	0.414
clusterSitesToGR	0.388	0.119	0.498
compareTwoSamples	2.265	1.146	2.967
covBoxplots	0.105	0.000	0.105
covStatistics	0.101	0.000	0.100
estLocCor	5.626	0.059	5.723
filterByCov	0.108	0.004	0.122
filterBySharedRegions	0.118	0.000	0.118
findDMRs	0.513	0.000	0.515
globalTest	20.092	0.012	20.220
limitCov	0.304	0.080	0.477
logisticRegression	1.414	0.020	1.443
makeVariogram	4.274	0.016	4.359
plotBindingSites	2.029	0.008	2.046
plotMeth	0.184	0.000	0.184
plotMethMap	0.209	0.000	0.209
plotSmoothMeth	0.108	0.000	0.113
predictMeth	0.881	0.361	1.128
predictedMeth	0.012	0.004	0.016
promoters	0.061	0.004	0.064
rawToRel	0.061	0.000	0.062
readBismark	0.055	0.004	0.059
rrbs	0.054	0.000	0.054
smoothVariogram	0.026	0.004	0.031
summarizeRegions	1.247	0.123	1.379
testClusters	0.075	0.008	0.083
trimClusters	0.875	0.028	0.906
vario	0.003	0.000	0.002
writeBED	0.179	0.008	0.187