BioC 3.5: CHECK report for metagenomeSeq on toluca2

Package: metagenomeSeq

Version: 1.17.3

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings metagenomeSeq_1.17.3.tar.gz

StartedAt: 2017-04-23 06:26:46 -0400 (Sun, 23 Apr 2017)

EndedAt: 2017-04-23 06:29:49 -0400 (Sun, 23 Apr 2017)

EllapsedTime: 183.7 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_1.17.3.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/metagenomeSeq.Rcheck’
* using R Under development (unstable) (2017-02-15 r72187)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘metagenomeSeq/DESCRIPTION’ ... OK
* this is package ‘metagenomeSeq’ version ‘1.17.3’
* 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
Examples with CPU or elapsed time > 5s
               user system elapsed
plotMRheatmap 5.445  0.099   5.629
* 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	3.263	0.105	3.390
MRcounts	0.347	0.022	0.370
MRexperiment-class	0.001	0.000	0.001
MRfulltable	2.251	0.044	2.310
MRtable	1.480	0.029	1.514
aggregateBySample	0.261	0.013	0.275
aggregateByTaxonomy	0.319	0.013	0.333
biom2MRexperiment	0.627	0.007	0.637
calcNormFactors	0.687	0.097	0.785
correctIndices	0.173	0.020	0.195
correlationTest	0.373	0.034	0.408
cumNorm	0.624	0.071	0.696
cumNormMat	0.599	0.068	0.670
cumNormStat	0.600	0.064	0.665
cumNormStatFast	0.371	0.028	0.401
expSummary	0.126	0.011	0.137
exportMat	1.655	1.320	2.978
exportStats	0.573	0.057	0.633
extractMR	2.726	0.656	3.387
filterData	0.220	0.026	0.247
fitDO	0.545	0.046	4.076
fitFeatureModel	1.511	0.075	1.607
fitLogNormal	2.169	0.280	2.469
fitMultipleTimeSeries	4.648	0.180	4.886
fitPA	0.510	0.026	3.876
fitSSTimeSeries	1.225	0.111	1.349
fitTimeSeries	1.201	0.080	1.300
fitZig	2.580	0.355	2.966
libSize-set	0.389	0.022	0.427
libSize	0.361	0.008	0.371
loadBiom	0.288	0.001	0.301
loadMeta	0.058	0.001	0.062
loadMetaQ	0	0	0
loadPhenoData	0.038	0.007	0.045
makeLabels	0.001	0.000	0.001
mergeMRexperiments	2.469	0.439	2.970
newMRexperiment	0.044	0.000	0.045
normFactors-set	0.391	0.020	0.416
normFactors	0.355	0.019	0.379
plotBubble	0.800	0.181	4.199
plotClassTimeSeries	1.019	0.093	1.113
plotCorr	0.648	0.087	0.739
plotFeature	0.179	0.017	0.197
plotGenus	0.191	0.022	0.215
plotMRheatmap	5.445	0.099	5.629
plotOTU	0.188	0.019	0.211
plotOrd	0.295	0.045	0.343
plotRare	0.150	0.020	0.173
plotTimeSeries	1.026	0.093	1.129
posteriorProbs	2.130	0.379	2.524
returnAppropriateObj	0.371	0.026	0.399
ssFit	0.000	0.000	0.001
ssIntervalCandidate	0.001	0.000	0.001
ssPerm	0.001	0.000	0.001
ssPermAnalysis	0.000	0.000	0.001
trapz	0.001	0.000	0.002
ts2MRexperiment	2.340	0.286	2.635
uniqueFeatures	0.147	0.021	0.169
zigControl	0.000	0.000	0.001