BioC 2.14: CHECK report for BiSeq on morelia

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 21:33:42 -0700 (Tue, 07 Oct 2014)

EndedAt: 2014-10-07 21:40:04 -0700 (Tue, 07 Oct 2014)

EllapsedTime: 381.8 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-darwin13.1.0 (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 ... [26s/26s] 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 ... [108s/109s] OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
globalTest        30.080  0.051  30.154
estLocCor         14.574  0.191  14.778
makeVariogram     11.974  0.432  13.003
betaRegression    10.281  0.712  11.150
compareTwoSamples  4.876  2.277   6.770
* 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	0.153	0.009	0.161
BSrel-class	0.091	0.004	0.096
DMRs	0.069	0.001	0.070
annotateGRanges	0.577	0.018	0.594
betaRegression	10.281	0.712	11.150
betaResults	0.008	0.001	0.009
betaResultsNull	0.006	0.000	0.006
binomLikelihoodSmooth	0.008	0.001	0.008
clusterSites	0.598	0.239	0.967
clusterSitesToGR	0.811	0.351	1.144
compareTwoSamples	4.876	2.277	6.770
covBoxplots	0.438	0.052	0.498
covStatistics	0.050	0.002	0.051
estLocCor	14.574	0.191	14.778
filterByCov	0.124	0.002	0.125
filterBySharedRegions	0.134	0.004	0.137
findDMRs	0.852	0.006	0.859
globalTest	30.080	0.051	30.154
limitCov	0.919	0.197	1.403
logisticRegression	2.306	0.032	2.360
makeVariogram	11.974	0.432	13.003
plotBindingSites	3.556	0.025	3.651
plotMeth	0.361	0.002	0.367
plotMethMap	0.327	0.005	0.349
plotSmoothMeth	0.530	0.004	0.534
predictMeth	1.710	0.760	2.244
predictedMeth	0.016	0.002	0.017
promoters	0.098	0.017	0.116
rawToRel	0.048	0.005	0.053
readBismark	0.099	0.005	0.104
rrbs	0.040	0.002	0.042
smoothVariogram	0.022	0.001	0.024
summarizeRegions	2.847	0.360	3.337
testClusters	0.155	0.005	0.161
trimClusters	0.731	0.015	0.747
vario	0.003	0.001	0.004
writeBED	0.257	0.007	0.265