BioC 3.1: CHECK report for BiSeq on zin2

Package: BiSeq

Version: 1.8.0

Command: /home/biocbuild/bbs-3.1-bioc/R/bin/R CMD check --no-vignettes --timings BiSeq_1.8.0.tar.gz

StartedAt: 2015-10-08 22:54:30 -0700 (Thu, 08 Oct 2015)

EndedAt: 2015-10-08 22:57:59 -0700 (Thu, 08 Oct 2015)

EllapsedTime: 209.0 seconds

RetCode: 0

Status:  OK

CheckDir: BiSeq.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.1-bioc/R/bin/R CMD check --no-vignettes --timings BiSeq_1.8.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.1-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 ‘1.8.0’
* 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 ... [15s/15s] 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 ... [60s/59s] OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
globalTest     19.245  0.004  19.295
betaRegression  8.418  0.359   8.808
estLocCor       5.550  0.016   5.563
* 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-3.1-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	0.098	0.004	0.102
BSrel-class	0.058	0.000	0.058
DMRs	0.048	0.000	0.048
annotateGRanges	0.189	0.000	0.189
betaRegression	8.418	0.359	8.808
betaResults	0.007	0.000	0.007
betaResultsNull	0.008	0.000	0.008
binomLikelihoodSmooth	0.008	0.000	0.007
clusterSites	0.27	0.07	0.37
clusterSitesToGR	0.402	0.056	0.437
compareTwoSamples	2.139	0.976	2.787
covBoxplots	0.085	0.004	0.090
covStatistics	0.046	0.000	0.046
estLocCor	5.550	0.016	5.563
filterByCov	0.091	0.000	0.090
filterBySharedRegions	0.093	0.000	0.092
findDMRs	0.868	0.000	0.867
globalTest	19.245	0.004	19.295
limitCov	0.570	0.091	1.118
logisticRegression	1.310	0.004	1.334
makeVariogram	4.815	0.020	4.884
plotBindingSites	2.080	0.004	2.112
plotMeth	0.164	0.000	0.175
plotMethMap	0.180	0.000	0.188
plotSmoothMeth	0.105	0.000	0.106
predictMeth	1.022	0.358	0.874
predictedMeth	0.013	0.000	0.013
promoters	0.065	0.004	0.069
rawToRel	0.047	0.004	0.051
readBismark	0.044	0.000	0.044
rrbs	0.037	0.000	0.038
smoothVariogram	0.016	0.012	0.028
summarizeRegions	1.501	0.136	1.652
testClusters	0.086	0.000	0.087
trimClusters	0.474	0.004	0.479
vario	0.003	0.000	0.002
writeBED	0.159	0.000	0.159