BioC 2.14: CHECK report for metagenomeSeq on zin2

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### Running command:
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###   /home/biocbuild/bbs-2.14-bioc/R/bin/R CMD check --no-vignettes --timings metagenomeSeq_1.6.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-2.14-bioc/meat/metagenomeSeq.Rcheck’
* using R version 3.1.1 (2014-07-10)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘metagenomeSeq/DESCRIPTION’ ... OK
* this is package ‘metagenomeSeq’ version ‘1.6.0’
* 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 ... [5s/5s] 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [22s/22s] 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

* 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	1.140	0.060	1.201
MRcounts	0.300	0.036	0.335
MRexperiment-class	0	0	0
MRfulltable	2.248	0.044	2.300
MRtable	0.964	0.020	0.985
aggregateByTaxonomy	0.000	0.000	0.001
biom2MRexperiment	0	0	0
correctIndices	0.204	0.008	0.212
correlationTest	0.156	0.008	0.163
cumNorm	0.764	0.024	0.790
cumNormMat	0.856	0.000	0.858
cumNormStat	1.224	0.008	1.232
cumNormStatFast	0.444	0.000	0.443
expSummary	0.140	0.008	0.151
exportMat	0.000	0.000	0.001
exportStats	0	0	0
filterData	0.236	0.008	0.246
fitDO	1.136	0.052	1.192
fitPA	0.860	0.012	0.871
fitZig	3.368	0.068	3.451
libSize	0.308	0.004	0.313
load_biom	0.000	0.000	0.001
load_meta	0.028	0.004	0.033
load_metaQ	0.000	0.000	0.001
load_phenoData	0	0	0
newMRexperiment	0.060	0.000	0.061
normFactors	0.329	0.008	0.336
plotCorr	1.372	0.000	1.376
plotFeature	0.192	0.004	0.196
plotGenus	0.200	0.008	0.206
plotMRheatmap	1.468	0.032	1.502
plotOTU	0.212	0.008	0.221
plotOrd	0.968	0.004	0.977
plotRare	0.148	0.004	0.155
posterior.probs	0	0	0
uniqueFeatures	0.148	0.012	0.163
zigControl	0	0	0

BioC 2.14: CHECK report for metagenomeSeq on zin2

Summary

Command output