BioC 3.1: 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 metagenomeSeq_1.10.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.1-bioc/meat/metagenomeSeq.Rcheck’
* using R version 3.2.2 Patched (2015-08-14 r69078)
* 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 ‘1.10.0’
* 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 ... [7s/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 dependencies in R code ... NOTE
'library' or 'require' call to ‘biom’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
* 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 ... [44s/59s] OK
Examples with CPU or elapsed time > 5s
             user system elapsed
MRfulltable 1.417  0.144   5.333
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’ [18s/18s]
 [18s/19s] 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: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.1-bioc/meat/metagenomeSeq.Rcheck/00check.log’
for details.

* 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	1.564	0.153	1.829
MRcounts	0.483	0.036	0.533
MRexperiment-class	0	0	0
MRfulltable	1.417	0.144	5.333
MRtable	1.375	0.091	1.486
aggregateBySample	0.339	0.036	0.375
aggregateByTaxonomy	0.336	0.018	0.367
biom2MRexperiment	0.001	0.000	0.001
calcNormFactors	1.149	0.186	1.335
correctIndices	0.199	0.035	0.242
correlationTest	0.483	0.047	0.539
cumNorm	1.244	0.146	1.416
cumNormMat	1.340	0.158	1.522
cumNormStat	2.322	0.157	2.542
cumNormStatFast	0.699	0.064	0.763
expSummary	0.234	0.016	0.254
exportMat	0.000	0.001	0.001
exportStats	0.001	0.000	0.000
filterData	0.365	0.031	0.396
fitDO	0.879	0.095	4.092
fitPA	0.824	0.081	3.745
fitSSTimeSeries	2.631	0.165	2.812
fitTimeSeries	2.525	0.162	2.687
fitZig	4.259	0.600	4.863
libSize	0.443	0.031	0.474
load_biom	0.001	0.001	0.001
load_meta	0.062	0.001	0.133
load_metaQ	0.000	0.000	0.001
load_phenoData	0.001	0.000	0.001
newMRexperiment	0.082	0.002	0.083
normFactors	0.503	0.014	0.519
plotBubble	0.840	0.133	3.772
plotClassTimeSeries	2.036	0.134	2.181
plotCorr	1.099	0.138	1.394
plotFeature	0.322	0.031	0.405
plotGenus	0.297	0.046	0.343
plotMRheatmap	3.960	0.183	4.724
plotOTU	0.296	0.024	0.322
plotOrd	0.503	0.036	0.546
plotRare	0.242	0.018	0.315
plotTimeSeries	2.015	0.126	2.143
posteriorProbs	0.001	0.000	0.001
returnAppropriateObj	0.501	0.049	0.551
ssFit	0.000	0.001	0.001
ssIntervalCandidate	0.001	0.000	0.001
ssPerm	0.001	0.000	0.001
ssPermAnalysis	0.001	0.000	0.001
trapz	0.002	0.000	0.003
uniqueFeatures	0.295	0.011	0.307
zigControl	0.001	0.000	0.001

BioC 3.1: CHECK report for metagenomeSeq on petty

Summary

Command output