BioC 3.2: CHECK report for BiSeq on perceval

Package: BiSeq

Version: 1.9.2

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings BiSeq_1.9.2.tar.gz

StartedAt: 2015-08-23 22:40:01 -0700 (Sun, 23 Aug 2015)

EndedAt: 2015-08-23 22:45:46 -0700 (Sun, 23 Aug 2015)

EllapsedTime: 345.0 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_1.9.2.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 (2015-08-14 r69078)
* 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 ‘1.9.2’
* 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 ... [25s/25s] 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 ... [91s/91s] OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
globalTest        23.350  0.061  23.439
betaRegression     9.811  0.928  10.842
makeVariogram      8.576  0.127   8.731
estLocCor          8.143  0.179   8.803
compareTwoSamples  3.546  4.244   7.081
* 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	0.263	0.014	0.279
BSrel-class	0.629	0.012	0.642
DMRs	0.053	0.001	0.055
annotateGRanges	0.196	0.012	0.209
betaRegression	9.811	0.928	10.842
betaResults	0.008	0.001	0.010
betaResultsNull	0.007	0.001	0.008
binomLikelihoodSmooth	0.007	0.002	0.009
clusterSites	0.457	0.366	1.060
clusterSitesToGR	0.723	0.650	1.272
compareTwoSamples	3.546	4.244	7.081
covBoxplots	0.820	0.147	0.972
covStatistics	0.110	0.021	0.130
estLocCor	8.143	0.179	8.803
filterByCov	0.178	0.013	0.201
filterBySharedRegions	0.762	0.020	0.844
findDMRs	0.604	0.006	0.638
globalTest	23.350	0.061	23.439
limitCov	1.204	0.705	2.334
logisticRegression	1.511	0.009	1.536
makeVariogram	8.576	0.127	8.731
plotBindingSites	2.427	0.056	2.484
plotMeth	0.259	0.023	0.303
plotMethMap	0.282	0.032	0.314
plotSmoothMeth	0.133	0.011	0.145
predictMeth	1.434	1.607	2.530
predictedMeth	0.025	0.012	0.036
promoters	0.080	0.020	0.098
rawToRel	0.096	0.027	0.123
readBismark	0.073	0.019	0.093
rrbs	0.056	0.008	0.063
smoothVariogram	0.038	0.006	0.045
summarizeRegions	2.526	0.854	3.597
testClusters	0.103	0.005	0.109
trimClusters	0.560	0.018	0.580
vario	0.003	0.000	0.004
writeBED	0.225	0.016	0.269