BioC 3.2: CHECK report for BiSeq on oaxaca

Package: BiSeq

Version: 1.9.2

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings BiSeq_1.9.2.tar.gz

StartedAt: 2015-08-23 22:05:21 -0700 (Sun, 23 Aug 2015)

EndedAt: 2015-08-23 22:10:36 -0700 (Sun, 23 Aug 2015)

EllapsedTime: 314.8 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 BiSeq_1.9.2.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/BiSeq.Rcheck’
* using R version 3.2.2 (2015-08-14)
* 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 ‘1.9.2’
* 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 ... [22s/23s] 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’ ‘SummarizedExperiment’ ‘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 ... [83s/83s] OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
globalTest        26.818  0.078  27.196
betaRegression     9.322  0.557  10.008
makeVariogram      6.623  0.205   6.915
estLocCor          6.257  0.168   6.534
compareTwoSamples  3.276  2.243   5.163
* 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-3.2-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	0.182	0.007	0.189
BSrel-class	0.134	0.007	0.141
DMRs	0.060	0.001	0.061
annotateGRanges	0.419	0.007	0.426
betaRegression	9.322	0.557	10.008
betaResults	0.007	0.001	0.008
betaResultsNull	0.006	0.000	0.006
binomLikelihoodSmooth	0.008	0.001	0.009
clusterSites	0.419	0.197	1.289
clusterSitesToGR	1.171	0.569	1.091
compareTwoSamples	3.276	2.243	5.163
covBoxplots	0.386	0.055	0.440
covStatistics	0.067	0.005	0.073
estLocCor	6.257	0.168	6.534
filterByCov	0.160	0.009	0.172
filterBySharedRegions	0.170	0.007	0.182
findDMRs	0.928	0.009	0.996
globalTest	26.818	0.078	27.196
limitCov	0.842	0.365	1.473
logisticRegression	1.652	0.020	1.676
makeVariogram	6.623	0.205	6.915
plotBindingSites	2.582	0.041	2.641
plotMeth	0.288	0.012	0.303
plotMethMap	0.301	0.028	0.331
plotSmoothMeth	0.149	0.009	0.160
predictMeth	1.275	0.708	1.734
predictedMeth	0.018	0.010	0.029
promoters	0.082	0.014	0.097
rawToRel	0.112	0.044	0.157
readBismark	0.073	0.005	0.078
rrbs	0.060	0.012	0.072
smoothVariogram	0.027	0.002	0.029
summarizeRegions	2.301	0.380	2.784
testClusters	0.126	0.004	0.130
trimClusters	0.606	0.013	0.626
vario	0.002	0.001	0.003
writeBED	0.254	0.012	0.266