BioC 3.5: CHECK report for metagenomeSeq on malbec2

Package: metagenomeSeq

Version: 1.18.0

Command: /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings metagenomeSeq_1.18.0.tar.gz

StartedAt: 2017-10-18 00:40:19 -0400 (Wed, 18 Oct 2017)

EndedAt: 2017-10-18 00:42:32 -0400 (Wed, 18 Oct 2017)

EllapsedTime: 133.1 seconds

RetCode: 0

Status:  OK

CheckDir: metagenomeSeq.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings metagenomeSeq_1.18.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.5-bioc/meat/metagenomeSeq.Rcheck’
* using R version 3.4.2 (2017-09-28)
* 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 ‘1.18.0’
* 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 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	2.240	0.156	2.398
MRcounts	0.304	0.064	0.371
MRexperiment-class	0	0	0
MRfulltable	1.572	0.144	1.717
MRtable	1.128	0.144	1.275
aggregateBySample	0.188	0.036	0.221
aggregateByTaxonomy	0.208	0.028	0.235
biom2MRexperiment	0.400	0.004	0.415
calcNormFactors	0.452	0.080	0.531
correctIndices	0.124	0.020	0.144
correlationTest	0.304	0.052	0.355
cumNorm	0.636	0.068	0.705
cumNormMat	0.448	0.028	0.474
cumNormStat	0.452	0.032	0.483
cumNormStatFast	0.304	0.028	0.332
expSummary	0.104	0.032	0.138
exportMat	0.972	0.664	1.639
exportStats	0.480	0.000	0.482
extractMR	0.908	0.296	1.204
filterData	0.344	0.036	0.380
fitDO	0.496	0.060	2.981
fitFeatureModel	1.116	0.076	1.195
fitLogNormal	2.232	0.068	2.304
fitMultipleTimeSeries	2.996	0.088	3.085
fitPA	0.428	0.024	2.845
fitSSTimeSeries	1.004	0.048	1.051
fitTimeSeries	0.916	0.032	0.949
fitZig	2.160	0.080	2.242
libSize-set	0.316	0.020	0.337
libSize	0.300	0.012	0.313
loadBiom	0.16	0.00	0.16
loadMeta	0.028	0.000	0.026
loadMetaQ	0	0	0
loadPhenoData	0.024	0.000	0.022
makeLabels	0	0	0
mergeMRexperiments	1.772	1.488	3.262
newMRexperiment	0.028	0.000	0.028
normFactors-set	0.336	0.004	0.339
normFactors	0.300	0.012	0.313
plotBubble	0.712	0.096	3.124
plotClassTimeSeries	0.808	0.052	0.863
plotCorr	0.456	0.000	0.455
plotFeature	0.140	0.036	0.175
plotGenus	0.128	0.036	0.163
plotMRheatmap	3.216	0.044	3.262
plotOTU	0.132	0.028	0.161
plotOrd	0.204	0.032	0.237
plotRare	0.104	0.036	0.143
plotTimeSeries	0.756	0.088	0.848
posteriorProbs	1.864	0.160	2.027
returnAppropriateObj	0.304	0.008	0.314
ssFit	0.000	0.000	0.001
ssIntervalCandidate	0.000	0.000	0.001
ssPerm	0.000	0.000	0.001
ssPermAnalysis	0.000	0.000	0.001
trapz	0.000	0.000	0.001
ts2MRexperiment	1.620	0.032	1.654
uniqueFeatures	0.112	0.032	0.144
zigControl	0	0	0