BioC 3.2: CHECK report for BiSeq on linux1.bioconductor.org

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: 2015-10-27 01:30:51 -0400 (Tue, 27 Oct 2015)

EndedAt: 2015-10-27 01:34:27 -0400 (Tue, 27 Oct 2015)

EllapsedTime: 215.7 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 3.2.2 (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 ‘1.10.0’
* 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 ... [14s/14s] 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [56s/56s] OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
globalTest     16.542  0.008  16.550
betaRegression  8.615  0.308   8.930
makeVariogram   5.461  0.024   5.493
* 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	0.116	0.000	0.117
BSrel-class	0.359	0.003	0.363
DMRs	0.036	0.000	0.036
annotateGRanges	0.128	0.004	0.133
betaRegression	8.615	0.308	8.930
betaResults	0.003	0.004	0.007
betaResultsNull	0.004	0.000	0.003
binomLikelihoodSmooth	0.012	0.000	0.012
clusterSites	0.237	0.072	0.366
clusterSitesToGR	0.345	0.138	0.432
compareTwoSamples	2.078	1.030	2.698
covBoxplots	0.513	0.028	0.540
covStatistics	0.072	0.000	0.072
estLocCor	4.278	0.000	4.278
filterByCov	0.093	0.000	0.092
filterBySharedRegions	0.099	0.004	0.104
findDMRs	0.402	0.000	0.402
globalTest	16.542	0.008	16.550
limitCov	0.570	0.129	0.776
logisticRegression	1.003	0.004	1.007
makeVariogram	5.461	0.024	5.493
plotBindingSites	1.825	0.000	1.827
plotMeth	0.167	0.000	0.167
plotMethMap	0.171	0.004	0.175
plotSmoothMeth	0.083	0.000	0.083
predictMeth	0.819	0.343	1.013
predictedMeth	0.020	0.004	0.023
promoters	0.082	0.004	0.086
rawToRel	0.077	0.004	0.081
readBismark	0.060	0.004	0.064
rrbs	0.073	0.000	0.073
smoothVariogram	0.035	0.000	0.035
summarizeRegions	1.788	0.175	2.077
testClusters	0.117	0.000	0.117
trimClusters	0.463	0.000	0.462
vario	0.000	0.000	0.002
writeBED	0.457	0.000	0.458