BioC 3.0: CHECK report for BiSeq on oaxaca

Package: BiSeq

Version: 1.6.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch BiSeq_1.6.0.tar.gz

StartedAt: 2015-04-09 21:49:13 -0700 (Thu, 09 Apr 2015)

EndedAt: 2015-04-09 21:55:35 -0700 (Thu, 09 Apr 2015)

EllapsedTime: 382.3 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_1.6.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.0-bioc/meat/BiSeq.Rcheck’
* using R version 3.1.3 (2015-03-09)
* 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 ‘1.6.0’
* 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 ... [29s/29s] 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.
':::' call which should be '::': ‘IRanges:::width’
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.predictMeth: no visible global function definition for ‘seqlevels<-’
.predictMeth: no visible global function definition for ‘seqlevels’
.predictMeth : predict.cluster: no visible global function definition
  for ‘seqlevels<-’
.predictMeth : predict.cluster: no visible global function definition
  for ‘seqlevels’
predictMeth,BSraw-numeric-numeric-numeric: no visible global function
  definition for ‘seqlevels<-’
predictMeth,BSraw-numeric-numeric-numeric: no visible global function
  definition for ‘seqlevels’
predictMeth,BSraw-numeric-numeric-numeric : predict.cluster: no visible
  global function definition for ‘seqlevels<-’
predictMeth,BSraw-numeric-numeric-numeric : predict.cluster: no visible
  global function definition for ‘seqlevels’
* 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 ... [95s/96s] OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
globalTest        31.234  0.045  31.612
betaRegression    10.322  0.561  11.512
estLocCor          7.605  0.158   7.837
makeVariogram      6.878  0.322   7.238
compareTwoSamples  3.447  1.890   5.044
* 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

NOTE: There were 3 notes.
See
  ‘/Users/biocbuild/bbs-3.0-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	0.146	0.003	0.164
BSrel-class	0.094	0.004	0.103
DMRs	0.078	0.001	0.080
annotateGRanges	0.608	0.016	0.687
betaRegression	10.322	0.561	11.512
betaResults	0.008	0.001	0.008
betaResultsNull	0.007	0.001	0.008
binomLikelihoodSmooth	0.008	0.001	0.010
clusterSites	0.450	0.181	0.796
clusterSitesToGR	0.939	0.305	1.238
compareTwoSamples	3.447	1.890	5.044
covBoxplots	0.132	0.008	0.141
covStatistics	0.061	0.002	0.069
estLocCor	7.605	0.158	7.837
filterByCov	0.135	0.003	0.139
filterBySharedRegions	0.158	0.007	0.166
findDMRs	0.677	0.012	0.697
globalTest	31.234	0.045	31.612
limitCov	1.113	0.776	2.091
logisticRegression	2.082	0.040	2.129
makeVariogram	6.878	0.322	7.238
plotBindingSites	2.857	0.024	2.885
plotMeth	0.329	0.004	0.334
plotMethMap	0.342	0.005	0.347
plotSmoothMeth	0.208	0.002	0.210
predictMeth	1.355	0.693	1.861
predictedMeth	0.015	0.002	0.017
promoters	0.089	0.011	0.100
rawToRel	0.056	0.005	0.061
readBismark	0.093	0.009	0.103
rrbs	0.043	0.001	0.045
smoothVariogram	0.026	0.003	0.030
summarizeRegions	2.573	0.363	3.094
testClusters	0.148	0.008	0.160
trimClusters	0.625	0.032	0.659
vario	0.003	0.000	0.004
writeBED	0.225	0.006	0.231