BioC 3.4: CHECK report for metagenomeSeq on malbec1

Package: metagenomeSeq

Version: 1.16.0

Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings metagenomeSeq_1.16.0.tar.gz

StartedAt: 2017-04-14 23:44:09 -0400 (Fri, 14 Apr 2017)

EndedAt: 2017-04-14 23:46:13 -0400 (Fri, 14 Apr 2017)

EllapsedTime: 124.9 seconds

RetCode: 0

Status:  OK

CheckDir: metagenomeSeq.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings metagenomeSeq_1.16.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/metagenomeSeq.Rcheck’
* using R version 3.3.3 (2017-03-06)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘metagenomeSeq/DESCRIPTION’ ... OK
* this is package ‘metagenomeSeq’ version ‘1.16.0’
* 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 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	1.548	0.052	1.603
MRcounts	0.568	0.016	0.589
MRexperiment-class	0.000	0.000	0.001
MRfulltable	1.216	0.020	1.235
MRtable	1.080	0.008	1.089
aggregateBySample	0.148	0.004	0.151
aggregateByTaxonomy	0.140	0.004	0.144
biom2MRexperiment	0.256	0.004	0.266
calcNormFactors	0.620	0.008	0.630
correctIndices	0.104	0.004	0.108
correlationTest	0.292	0.008	0.301
cumNorm	0.516	0.000	0.514
cumNormMat	0.476	0.004	0.480
cumNormStat	0.932	0.004	0.936
cumNormStatFast	0.396	0.000	0.394
expSummary	0.100	0.004	0.106
exportMat	0.980	0.604	1.584
exportStats	0.456	0.012	0.468
extractMR	0.916	0.252	1.170
filterData	0.176	0.000	0.177
fitDO	0.604	0.024	2.839
fitFeatureModel	1.032	0.028	1.060
fitLogNormal	2.492	0.024	2.518
fitMultipleTimeSeries	1.768	0.008	1.778
fitPA	0.436	0.024	2.899
fitSSTimeSeries	1.256	0.036	1.292
fitTimeSeries	1.168	0.000	1.175
fitZig	2.376	0.012	2.392
libSize-set	0.332	0.000	0.328
libSize	0.308	0.004	0.314
loadBiom	0.048	0.000	0.044
loadMeta	0.040	0.000	0.039
loadMetaQ	0	0	0
loadPhenoData	0.032	0.000	0.030
makeLabels	0.004	0.000	0.000
mergeMRexperiments	2.312	0.048	2.364
newMRexperiment	0.032	0.000	0.032
normFactors-set	0.340	0.008	0.348
normFactors	0.328	0.000	0.327
plotBubble	0.436	0.024	2.701
plotClassTimeSeries	0.904	0.012	0.915
plotCorr	0.492	0.004	0.494
plotFeature	0.156	0.012	0.168
plotGenus	0.152	0.004	0.153
plotMRheatmap	2.124	0.028	2.154
plotOTU	0.136	0.000	0.135
plotOrd	0.204	0.000	0.206
plotRare	0.112	0.000	0.112
plotTimeSeries	0.812	0.004	0.817
posteriorProbs	1.868	0.012	1.880
returnAppropriateObj	0.320	0.008	0.328
ssFit	0	0	0
ssIntervalCandidate	0.004	0.000	0.000
ssPerm	0	0	0
ssPermAnalysis	0	0	0
trapz	0.004	0.000	0.000
ts2MRexperiment	1.976	0.012	1.993
uniqueFeatures	0.132	0.004	0.136
zigControl	0	0	0