BioC 3.5: CHECK report for metagenomeSeq on veracruz2

Package: metagenomeSeq

Version: 1.18.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings metagenomeSeq_1.18.0.tar.gz

StartedAt: 2017-08-16 05:06:20 -0400 (Wed, 16 Aug 2017)

EndedAt: 2017-08-16 05:09:06 -0400 (Wed, 16 Aug 2017)

EllapsedTime: 166.3 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_1.18.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/metagenomeSeq.Rcheck’
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘metagenomeSeq/DESCRIPTION’ ... OK
* this is package ‘metagenomeSeq’ version ‘1.18.0’
* 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	2.832	0.112	3.036
MRcounts	0.404	0.022	0.434
MRexperiment-class	0.001	0.000	0.001
MRfulltable	2.143	0.057	2.260
MRtable	1.236	0.042	1.309
aggregateBySample	0.243	0.014	0.265
aggregateByTaxonomy	0.267	0.018	0.289
biom2MRexperiment	0.517	0.016	0.548
calcNormFactors	0.491	0.086	0.591
correctIndices	0.147	0.017	0.167
correlationTest	0.349	0.030	0.390
cumNorm	0.571	0.055	0.638
cumNormMat	0.659	0.073	0.750
cumNormStat	0.433	0.046	0.506
cumNormStatFast	0.298	0.019	0.325
expSummary	0.109	0.012	0.123
exportMat	1.258	1.226	2.554
exportStats	0.756	0.054	0.832
extractMR	2.131	0.550	2.769
filterData	0.217	0.032	0.252
fitDO	0.566	0.045	3.673
fitFeatureModel	1.370	0.091	1.518
fitLogNormal	2.020	0.266	2.362
fitMultipleTimeSeries	3.889	0.133	4.138
fitPA	0.532	0.030	3.458
fitSSTimeSeries	1.063	0.090	1.167
fitTimeSeries	1.089	0.055	1.184
fitZig	2.247	0.317	2.638
libSize-set	0.434	0.028	0.477
libSize	0.415	0.018	0.453
loadBiom	0.217	0.002	0.222
loadMeta	0.039	0.001	0.039
loadMetaQ	0.001	0.000	0.001
loadPhenoData	0.034	0.005	0.043
makeLabels	0.001	0.000	0.001
mergeMRexperiments	2.527	0.434	3.082
newMRexperiment	0.038	0.000	0.038
normFactors-set	0.431	0.016	0.456
normFactors	0.385	0.016	0.413
plotBubble	0.531	0.090	3.319
plotClassTimeSeries	0.928	0.083	1.043
plotCorr	0.536	0.050	0.603
plotFeature	0.165	0.017	0.186
plotGenus	0.170	0.034	0.218
plotMRheatmap	4.260	0.138	4.515
plotOTU	0.159	0.037	0.196
plotOrd	0.266	0.070	0.347
plotRare	0.137	0.050	0.190
plotTimeSeries	0.921	0.140	1.094
posteriorProbs	1.891	0.330	2.286
returnAppropriateObj	0.398	0.023	0.434
ssFit	0.001	0.000	0.000
ssIntervalCandidate	0	0	0
ssPerm	0	0	0
ssPermAnalysis	0.001	0.000	0.000
trapz	0.001	0.000	0.001
ts2MRexperiment	1.995	0.123	2.178
uniqueFeatures	0.157	0.017	0.175
zigControl	0	0	0