BioC 3.6: CHECK report for metagenomeSeq on malbec1

Package: metagenomeSeq

Version: 1.19.0

Command: /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings metagenomeSeq_1.19.0.tar.gz

StartedAt: 2017-08-16 00:35:17 -0400 (Wed, 16 Aug 2017)

EndedAt: 2017-08-16 00:37:26 -0400 (Wed, 16 Aug 2017)

EllapsedTime: 129.4 seconds

RetCode: 0

Status:  OK

CheckDir: metagenomeSeq.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings metagenomeSeq_1.19.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.6-bioc/meat/metagenomeSeq.Rcheck’
* using R version 3.4.1 (2017-06-30)
* 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 ‘1.19.0’
* 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	2.304	0.040	2.345
MRcounts	0.304	0.008	0.312
MRexperiment-class	0.000	0.000	0.001
MRfulltable	1.492	0.012	1.507
MRtable	1.148	0.016	1.162
aggregateBySample	0.192	0.000	0.192
aggregateByTaxonomy	0.216	0.000	0.217
biom2MRexperiment	0.392	0.004	0.416
calcNormFactors	0.484	0.008	0.494
correctIndices	0.120	0.004	0.127
correlationTest	0.284	0.004	0.290
cumNorm	0.648	0.032	0.678
cumNormMat	0.432	0.036	0.470
cumNormStat	0.472	0.024	0.493
cumNormStatFast	0.308	0.020	0.329
expSummary	0.108	0.028	0.134
exportMat	1.004	0.616	1.621
exportStats	0.428	0.012	0.438
extractMR	0.940	0.268	1.211
filterData	0.348	0.052	0.401
fitDO	0.488	0.024	2.973
fitFeatureModel	1.124	0.052	1.176
fitLogNormal	2.288	0.044	2.332
fitMultipleTimeSeries	3.036	0.068	3.108
fitPA	0.444	0.016	2.840
fitSSTimeSeries	1.116	0.048	1.166
fitTimeSeries	0.888	0.000	0.890
fitZig	2.212	0.024	2.241
libSize-set	0.324	0.012	0.336
libSize	0.316	0.008	0.325
loadBiom	0.168	0.000	0.168
loadMeta	0.032	0.000	0.033
loadMetaQ	0	0	0
loadPhenoData	0.020	0.000	0.017
makeLabels	0.000	0.000	0.001
mergeMRexperiments	2.048	0.512	2.558
newMRexperiment	0.024	0.000	0.027
normFactors-set	0.336	0.008	0.346
normFactors	0.296	0.020	0.315
plotBubble	0.460	0.068	2.819
plotClassTimeSeries	1.064	0.036	1.097
plotCorr	0.456	0.000	0.458
plotFeature	0.152	0.004	0.154
plotGenus	0.144	0.000	0.143
plotMRheatmap	3.048	0.012	3.062
plotOTU	0.136	0.000	0.135
plotOrd	0.208	0.004	0.210
plotRare	0.112	0.004	0.116
plotTimeSeries	0.764	0.008	0.772
posteriorProbs	1.696	0.016	1.712
returnAppropriateObj	0.320	0.016	0.333
ssFit	0	0	0
ssIntervalCandidate	0	0	0
ssPerm	0	0	0
ssPermAnalysis	0.000	0.000	0.001
trapz	0.000	0.000	0.001
ts2MRexperiment	1.668	0.032	1.702
uniqueFeatures	0.140	0.024	0.166
zigControl	0	0	0