BioC 3.1: CHECK report for BiSeq on morelia

Package: BiSeq

Version: 1.8.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings BiSeq_1.8.0.tar.gz

StartedAt: 2015-10-08 23:41:49 -0700 (Thu, 08 Oct 2015)

EndedAt: 2015-10-08 23:46:01 -0700 (Thu, 08 Oct 2015)

EllapsedTime: 252.1 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_1.8.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.1-bioc/meat/BiSeq.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-apple-darwin13.4.0 (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 ‘1.8.0’
* 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 ... [18s/18s] 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’ ‘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 ... [67s/67s] OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
globalTest     21.886  0.634  22.539
betaRegression  8.483  0.722   9.316
estLocCor       5.323  0.512   5.873
* 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-3.1-bioc/meat/BiSeq.Rcheck/00check.log’
for details.

* installing *source* package ‘BiSeq’ ...
** R
** data
** inst
** preparing package for lazy loading
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
* DONE (BiSeq)

name	user	system	elapsed
BSraw-class	0.114	0.006	0.119
BSrel-class	0.059	0.003	0.062
DMRs	0.044	0.001	0.045
annotateGRanges	0.204	0.041	0.246
betaRegression	8.483	0.722	9.316
betaResults	0.009	0.002	0.010
betaResultsNull	0.004	0.000	0.005
binomLikelihoodSmooth	0.005	0.000	0.005
clusterSites	0.359	0.141	0.633
clusterSitesToGR	0.471	0.250	0.674
compareTwoSamples	2.872	2.127	4.646
covBoxplots	0.084	0.006	0.091
covStatistics	0.051	0.003	0.053
estLocCor	5.323	0.512	5.873
filterByCov	0.146	0.002	0.148
filterBySharedRegions	0.385	0.030	0.415
findDMRs	0.419	0.011	0.432
globalTest	21.886	0.634	22.539
limitCov	0.605	0.206	0.954
logisticRegression	1.491	0.123	1.618
makeVariogram	4.491	0.289	4.783
plotBindingSites	1.575	0.045	1.620
plotMeth	0.155	0.002	0.159
plotMethMap	0.159	0.003	0.161
plotSmoothMeth	0.168	0.037	0.205
predictMeth	0.833	0.532	1.233
predictedMeth	0.009	0.001	0.010
promoters	0.052	0.006	0.058
rawToRel	0.029	0.003	0.032
readBismark	0.037	0.005	0.043
rrbs	0.034	0.004	0.039
smoothVariogram	0.017	0.002	0.019
summarizeRegions	1.407	0.292	1.860
testClusters	0.076	0.010	0.087
trimClusters	0.343	0.016	0.359
vario	0.002	0.000	0.002
writeBED	0.149	0.005	0.154