BioC 3.5: CHECK report for metagenomeSeq on oaxaca

Package: metagenomeSeq

Version: 1.17.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings metagenomeSeq_1.17.0.tar.gz

StartedAt: 2017-03-04 05:35:21 -0800 (Sat, 04 Mar 2017)

EndedAt: 2017-03-04 05:39:48 -0800 (Sat, 04 Mar 2017)

EllapsedTime: 267.2 seconds

RetCode: 0

Status:  OK

CheckDir: metagenomeSeq.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 metagenomeSeq_1.17.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/metagenomeSeq.Rcheck’
* using R Under development (unstable) (2017-02-15 r72177)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘metagenomeSeq/DESCRIPTION’ ... OK
* this is package ‘metagenomeSeq’ version ‘1.17.0’
* 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 ‘metagenomeSeq’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* 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 ... OK
* 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 ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* 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: OK

* installing *source* package ‘metagenomeSeq’ ...
** 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 (metagenomeSeq)

name	user	system	elapsed
MRcoefs	3.155	0.107	3.292
MRcounts	0.337	0.019	0.356
MRexperiment-class	0.000	0.000	0.001
MRfulltable	2.194	0.043	2.236
MRtable	1.276	0.033	1.310
aggregateBySample	0.317	0.025	0.343
aggregateByTaxonomy	0.353	0.023	0.377
biom2MRexperiment	0.600	0.010	0.673
calcNormFactors	0.673	0.110	0.783
correctIndices	0.181	0.024	0.206
correlationTest	0.366	0.034	0.399
cumNorm	0.581	0.064	0.644
cumNormMat	0.752	0.090	0.842
cumNormStat	0.634	0.060	0.695
cumNormStatFast	0.266	0.030	0.296
expSummary	0.141	0.011	0.152
exportMat	1.377	1.205	2.585
exportStats	0.644	0.059	0.704
extractMR	2.543	0.653	3.198
filterData	0.243	0.022	0.265
fitDO	0.710	0.051	4.055
fitFeatureModel	1.316	0.078	1.395
fitLogNormal	1.858	0.256	2.116
fitMultipleTimeSeries	4.605	0.165	4.864
fitPA	0.483	0.032	3.662
fitSSTimeSeries	1.013	0.110	1.122
fitTimeSeries	1.127	0.078	1.206
fitZig	2.311	0.341	2.653
libSize-set	0.424	0.021	0.446
libSize	0.391	0.009	0.400
loadBiom	0.273	0.001	0.276
loadMeta	0.059	0.001	0.061
loadMetaQ	0.000	0.000	0.001
loadPhenoData	0.032	0.006	0.038
makeLabels	0.000	0.000	0.001
mergeMRexperiments	2.352	0.451	2.802
newMRexperiment	0.045	0.000	0.045
normFactors-set	0.390	0.018	0.408
normFactors	0.318	0.013	0.332
plotBubble	0.746	0.170	3.815
plotClassTimeSeries	1.144	0.083	1.227
plotCorr	0.633	0.087	0.720
plotFeature	0.187	0.014	0.209
plotGenus	0.171	0.016	0.188
plotMRheatmap	4.845	0.096	4.949
plotOTU	0.201	0.017	0.220
plotOrd	0.284	0.036	0.321
plotRare	0.175	0.017	0.194
plotTimeSeries	1.035	0.094	1.716
posteriorProbs	1.627	0.302	1.928
returnAppropriateObj	0.334	0.019	0.353
ssFit	0.000	0.000	0.001
ssIntervalCandidate	0	0	0
ssPerm	0.001	0.000	0.000
ssPermAnalysis	0.000	0.000	0.001
trapz	0.001	0.000	0.001
ts2MRexperiment	1.926	0.209	2.136
uniqueFeatures	0.137	0.014	0.152
zigControl	0	0	0