BioC 3.1: CHECK report for BiSeq on petty

Package: BiSeq

Version: 1.8.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings BiSeq_1.8.0.tar.gz

StartedAt: 2015-10-08 21:46:12 -0700 (Thu, 08 Oct 2015)

EndedAt: 2015-10-08 21:52:57 -0700 (Thu, 08 Oct 2015)

EllapsedTime: 404.9 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 BiSeq_1.8.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.1-bioc/meat/BiSeq.Rcheck’
* using R version 3.2.2 Patched (2015-08-14 r69078)
* 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 ‘1.8.0’
* 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 ... [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.
* 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 ... [116s/116s] OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
globalTest        33.968  0.053  34.044
betaRegression    14.758  2.062  16.972
estLocCor         11.497  0.172  11.693
makeVariogram     10.024  0.188  10.216
compareTwoSamples  4.746  4.019   8.353
* 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
  ‘/Users/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	0.181	0.005	0.187
BSrel-class	0.124	0.005	0.129
DMRs	0.089	0.001	0.090
annotateGRanges	0.240	0.008	0.248
betaRegression	14.758	2.062	16.972
betaResults	0.013	0.002	0.015
betaResultsNull	0.010	0.001	0.012
binomLikelihoodSmooth	0.012	0.002	0.014
clusterSites	0.576	0.352	1.042
clusterSitesToGR	0.821	0.478	1.250
compareTwoSamples	4.746	4.019	8.353
covBoxplots	0.173	0.015	0.189
covStatistics	0.076	0.003	0.079
estLocCor	11.497	0.172	11.693
filterByCov	0.197	0.004	0.201
filterBySharedRegions	0.154	0.007	0.161
findDMRs	1.285	0.006	1.333
globalTest	33.968	0.053	34.044
limitCov	0.610	0.355	1.341
logisticRegression	2.396	0.090	2.488
makeVariogram	10.024	0.188	10.216
plotBindingSites	3.157	0.038	3.197
plotMeth	0.354	0.006	0.364
plotMethMap	0.351	0.008	0.361
plotSmoothMeth	0.195	0.003	0.198
predictMeth	1.715	1.363	2.654
predictedMeth	0.023	0.005	0.028
promoters	0.087	0.017	0.104
rawToRel	0.066	0.010	0.077
readBismark	0.08	0.02	0.10
rrbs	0.062	0.008	0.070
smoothVariogram	0.04	0.01	0.05
summarizeRegions	3.183	0.746	4.102
testClusters	0.161	0.006	0.167
trimClusters	0.709	0.006	0.716
vario	0.003	0.000	0.003
writeBED	0.246	0.005	0.250