BioC 2.13: CHECK report for BiSeq on zin1

Package: BiSeq

Version: 1.2.5

Command: /home/biocbuild/bbs-2.13-bioc/R/bin/R CMD check --no-vignettes --timings BiSeq_1.2.5.tar.gz

StartedAt: 2014-04-04 23:55:56 -0700 (Fri, 04 Apr 2014)

EndedAt: 2014-04-05 00:00:46 -0700 (Sat, 05 Apr 2014)

EllapsedTime: 290.2 seconds

RetCode: 0

Status:  OK

CheckDir: BiSeq.Rcheck

Warnings: 0

* using log directory ‘/home/biocbuild/bbs-2.13-bioc/meat/BiSeq.Rcheck’
* using R version 3.0.3 (2014-03-06)
* using platform: x86_64-unknown-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 ‘1.2.5’
* 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’ ‘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.
‘:::’ call which should be ‘::’: ‘IRanges:::width’
  See the note in ?`:::` about the use of this operator.
See the information on DESCRIPTION files in the chapter ‘Creating R
packages’ of the ‘Writing R Extensions’ manual.
* 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’ ... NOTE
The following files should probably not be installed:
  ‘unsrturl.bst’

Consider the use of a .Rinstignore file: see ‘Writing R Extensions’,
or move the vignette sources from ‘inst/doc’ to ‘vignettes’.
* checking for old-style vignette sources ... NOTE
Vignette sources only in ‘inst/doc’:
  ‘BiSeq.Rnw’
A ‘vignettes’ directory will be required as from R 3.1.0
* checking examples ... [94s/95s] OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
globalTest        25.993  0.004  26.135
estLocCor         12.177  0.024  12.447
betaRegression    10.825  0.388  11.385
makeVariogram     10.636  0.028  10.732
compareTwoSamples  4.020  1.108   4.879
* 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

NOTE: There were 4 notes.
See
  ‘/home/biocbuild/bbs-2.13-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	0.384	0.000	0.384
BSrel-class	0.332	0.008	0.344
DMRs	0.064	0.000	0.063
annotateGRanges	0.576	0.020	0.595
betaRegression	10.825	0.388	11.385
betaResults	0.004	0.008	0.012
betaResultsNull	0.008	0.004	0.009
binomLikelihoodSmooth	0.016	0.000	0.016
clusterSites	0.728	0.116	0.918
clusterSitesToGR	0.668	0.128	0.803
compareTwoSamples	4.020	1.108	4.879
covBoxplots	0.096	0.000	0.097
covStatistics	0.040	0.004	0.046
estLocCor	12.177	0.024	12.447
filterByCov	0.404	0.000	0.405
filterBySharedRegions	0.144	0.000	0.144
findDMRs	0.752	0.008	0.778
globalTest	25.993	0.004	26.135
limitCov	0.433	0.108	0.676
logisticRegression	1.760	0.012	1.777
makeVariogram	10.636	0.028	10.732
plotBindingSites	3.368	0.004	3.446
plotMeth	0.357	0.000	0.357
plotMethMap	0.644	0.000	0.648
plotSmoothMeth	0.224	0.004	0.235
predictMeth	1.332	0.328	1.524
predictedMeth	0.012	0.004	0.017
promoters	0.088	0.000	0.086
rawToRel	0.360	0.028	0.386
readBismark	0.084	0.000	0.087
rrbs	0.036	0.000	0.036
smoothVariogram	0.028	0.000	0.029
summarizeRegions	3.572	0.224	3.885
testClusters	0.112	0.004	0.117
trimClusters	0.664	0.000	0.664
vario	0.004	0.000	0.003
writeBED	0.536	0.000	0.537