BioC 2.14: CHECK report for metagenomeSeq on petty

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch metagenomeSeq_1.6.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-2.14-bioc/meat/metagenomeSeq.Rcheck’
* using R version 3.1.1 (2014-07-10)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘metagenomeSeq/DESCRIPTION’ ... OK
* this is package ‘metagenomeSeq’ version ‘1.6.0’
* 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 ... [10s/10s] 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 loading without being on the library search path ... 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 ... [46s/48s] OK
Examples with CPU or elapsed time > 5s
       user system elapsed
fitZig 6.56  0.726   7.347
* 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

* installing *source* package ‘metagenomeSeq’ ...
** R
** data
** inst
** preparing package for lazy loading
Creating a generic function for ‘colSums’ from package ‘base’ in package ‘metagenomeSeq’
Creating a generic function for ‘rowSums’ from package ‘base’ in package ‘metagenomeSeq’
Creating a generic function for ‘rowMeans’ from package ‘base’ in package ‘metagenomeSeq’
Creating a generic function for ‘colMeans’ from package ‘base’ in package ‘metagenomeSeq’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (metagenomeSeq)

name	user	system	elapsed
MRcoefs	2.302	0.198	2.515
MRcounts	0.534	0.040	0.580
MRexperiment-class	0.001	0.000	0.001
MRfulltable	4.414	0.120	4.559
MRtable	1.777	0.134	1.963
aggregateByTaxonomy	0.001	0.001	0.002
biom2MRexperiment	0.001	0.000	0.001
correctIndices	0.371	0.062	0.473
correlationTest	0.281	0.014	0.305
cumNorm	1.719	0.196	2.036
cumNormMat	1.907	0.178	2.186
cumNormStat	3.237	0.150	3.710
cumNormStatFast	0.874	0.038	0.974
expSummary	0.247	0.008	0.271
exportMat	0.001	0.000	0.001
exportStats	0.001	0.000	0.000
filterData	0.443	0.035	0.511
fitDO	2.276	0.161	2.609
fitPA	1.665	0.073	1.846
fitZig	6.560	0.726	7.347
libSize	0.539	0.041	0.584
load_biom	0.001	0.000	0.001
load_meta	0.073	0.019	0.091
load_metaQ	0.001	0.000	0.001
load_phenoData	0.001	0.000	0.001
newMRexperiment	0.133	0.001	0.135
normFactors	0.523	0.006	0.533
plotCorr	2.679	0.390	3.077
plotFeature	0.328	0.011	0.348
plotGenus	0.318	0.014	0.334
plotMRheatmap	3.014	0.252	3.285
plotOTU	0.341	0.010	0.359
plotOrd	1.985	0.267	2.334
plotRare	0.274	0.011	0.309
posterior.probs	0.001	0.000	0.000
uniqueFeatures	0.288	0.003	0.302
zigControl	0.001	0.000	0.001

BioC 2.14: CHECK report for metagenomeSeq on petty

Summary

Command output