BioC 2.14: CHECK report for BiSeq on petty

Package: BiSeq

Version: 1.4.2

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch BiSeq_1.4.2.tar.gz

StartedAt: 2014-10-07 20:58:45 -0700 (Tue, 07 Oct 2014)

EndedAt: 2014-10-07 21:10:52 -0700 (Tue, 07 Oct 2014)

EllapsedTime: 727.0 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 --no-multiarch BiSeq_1.4.2.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-2.14-bioc/meat/BiSeq.Rcheck’
* using R version 3.1.1 (2014-07-10)
* 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 ‘1.4.2’
* 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 ... [47s/52s] 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 loading without being on the library search path ... 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 ... NOTE
  'BiocParallel' did not register default BiocParallelParams
* 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 ... [210s/212s] OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
globalTest        54.382  0.107  54.772
estLocCor         29.695  0.208  30.634
makeVariogram     26.438  0.365  26.904
betaRegression    20.136  2.446  23.058
compareTwoSamples  9.453  6.530  15.437
plotBindingSites   5.776  0.046   5.843
summarizeRegions   4.901  0.686   5.946
* 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 3 notes.
See
  ‘/Users/biocbuild/bbs-2.14-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	0.266	0.016	0.283
BSrel-class	0.164	0.009	0.173
DMRs	0.130	0.001	0.132
annotateGRanges	1.096	0.028	1.127
betaRegression	20.136	2.446	23.058
betaResults	0.015	0.002	0.018
betaResultsNull	0.012	0.002	0.013
binomLikelihoodSmooth	0.016	0.002	0.018
clusterSites	1.093	0.580	1.997
clusterSitesToGR	1.580	0.837	2.370
compareTwoSamples	9.453	6.530	15.437
covBoxplots	0.767	0.136	0.906
covStatistics	0.081	0.003	0.084
estLocCor	29.695	0.208	30.634
filterByCov	0.261	0.004	0.264
filterBySharedRegions	0.287	0.009	0.297
findDMRs	1.614	0.008	1.624
globalTest	54.382	0.107	54.772
limitCov	1.548	0.507	2.434
logisticRegression	3.742	0.089	3.847
makeVariogram	26.438	0.365	26.904
plotBindingSites	5.776	0.046	5.843
plotMeth	0.653	0.007	0.664
plotMethMap	1.132	0.011	1.147
plotSmoothMeth	0.448	0.004	0.454
predictMeth	2.946	1.717	4.254
predictedMeth	0.029	0.013	0.042
promoters	0.149	0.031	0.182
rawToRel	0.079	0.012	0.092
readBismark	0.173	0.010	0.183
rrbs	0.072	0.002	0.074
smoothVariogram	0.041	0.007	0.052
summarizeRegions	4.901	0.686	5.946
testClusters	0.244	0.006	0.251
trimClusters	1.431	0.015	1.450
vario	0.005	0.001	0.006
writeBED	0.425	0.014	0.442