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: 2017-10-18 05:52:55 -0400 (Wed, 18 Oct 2017)

EndedAt: 2017-10-18 05:55:47 -0400 (Wed, 18 Oct 2017)

EllapsedTime: 171.9 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 3.4.2 (2017-09-28)
* 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	2.842	0.125	3.164
MRcounts	0.405	0.023	0.432
MRexperiment-class	0	0	0
MRfulltable	2.207	0.052	2.330
MRtable	1.267	0.040	1.338
aggregateBySample	0.239	0.017	0.266
aggregateByTaxonomy	0.289	0.020	0.316
biom2MRexperiment	0.515	0.009	0.553
calcNormFactors	0.556	0.093	0.666
correctIndices	0.161	0.019	0.193
correlationTest	0.375	0.040	0.428
cumNorm	0.578	0.065	0.663
cumNormMat	0.751	0.074	0.866
cumNormStat	0.489	0.054	0.553
cumNormStatFast	0.339	0.019	0.364
expSummary	0.132	0.011	0.145
exportMat	1.335	1.476	2.920
exportStats	0.701	0.053	0.774
extractMR	2.369	0.650	3.107
filterData	0.188	0.033	0.223
fitDO	0.554	0.047	3.653
fitFeatureModel	1.295	0.087	1.402
fitLogNormal	1.973	0.266	2.294
fitMultipleTimeSeries	3.834	0.132	4.091
fitPA	0.550	0.044	3.662
fitSSTimeSeries	1.072	0.063	1.162
fitTimeSeries	1.105	0.091	1.236
fitZig	2.213	0.302	2.592
libSize-set	0.443	0.022	0.480
libSize	0.408	0.015	0.432
loadBiom	0.224	0.001	0.239
loadMeta	0.040	0.001	0.041
loadMetaQ	0	0	0
loadPhenoData	0.032	0.001	0.033
makeLabels	0.001	0.000	0.001
mergeMRexperiments	2.498	0.474	3.069
newMRexperiment	0.035	0.000	0.037
normFactors-set	0.420	0.018	0.448
normFactors	0.391	0.018	0.415
plotBubble	0.547	0.089	3.774
plotClassTimeSeries	0.999	0.085	1.114
plotCorr	0.572	0.059	0.646
plotFeature	0.183	0.019	0.208
plotGenus	0.177	0.036	0.220
plotMRheatmap	4.372	0.161	4.666
plotOTU	0.130	0.041	0.183
plotOrd	0.232	0.065	0.316
plotRare	0.142	0.044	0.199
plotTimeSeries	0.914	0.129	1.073
posteriorProbs	1.786	0.325	2.195
returnAppropriateObj	0.411	0.024	0.449
ssFit	0.001	0.000	0.001
ssIntervalCandidate	0.000	0.000	0.001
ssPerm	0	0	0
ssPermAnalysis	0	0	0
trapz	0.001	0.001	0.002
ts2MRexperiment	2.056	0.134	2.268
uniqueFeatures	0.163	0.015	0.180
zigControl	0.001	0.001	0.000