BioC 3.2: CHECK report for metagenomeSeq on perceval

Package: metagenomeSeq

Version: 1.12.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings metagenomeSeq_1.12.0.tar.gz

StartedAt: 2015-11-10 06:47:26 -0800 (Tue, 10 Nov 2015)

EndedAt: 2015-11-10 06:50:06 -0800 (Tue, 10 Nov 2015)

EllapsedTime: 159.9 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_1.12.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/metagenomeSeq.Rcheck’
* using R version 3.2.2 Patched (2015-10-08 r69496)
* 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 ‘1.12.0’
* 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 ... [9s/9s] 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 ... [39s/50s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’ [16s/16s]
 [17s/17s] 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-3.2-bioc/meat/metagenomeSeq.Rcheck/00check.log’
for details.

* 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	2.121	0.129	2.251
MRcounts	0.354	0.024	0.378
MRexperiment-class	0.001	0.000	0.001
MRfulltable	1.453	0.053	1.506
MRtable	1.457	0.034	1.491
aggregateBySample	0.225	0.017	0.242
aggregateByTaxonomy	0.213	0.022	0.236
biom2MRexperiment	0.000	0.000	0.001
calcNormFactors	1.001	0.139	1.140
correctIndices	0.163	0.018	0.181
correlationTest	0.337	0.037	0.375
cumNorm	0.816	0.083	0.900
cumNormMat	0.880	0.088	0.969
cumNormStat	1.579	0.072	1.650
cumNormStatFast	0.484	0.014	0.499
expSummary	0.154	0.015	0.169
exportMat	0.001	0.000	0.001
exportStats	0.000	0.000	0.001
filterData	0.274	0.034	0.308
fitDO	0.772	0.084	4.606
fitFeatureModel	1.609	0.104	1.714
fitPA	0.696	0.024	4.297
fitSSTimeSeries	2.016	0.112	2.142
fitTimeSeries	1.823	0.092	1.916
fitZig	3.760	0.437	4.197
libSize	0.361	0.024	0.386
load_biom	0.000	0.000	0.001
load_meta	0.037	0.000	0.038
load_metaQ	0.001	0.000	0.001
load_phenoData	0.001	0.000	0.001
newMRexperiment	0.053	0.000	0.053
normFactors	0.365	0.011	0.377
plotBubble	0.823	0.116	4.431
plotClassTimeSeries	1.811	0.119	1.930
plotCorr	0.656	0.061	0.717
plotFeature	0.225	0.036	0.268
plotGenus	0.197	0.039	0.237
plotMRheatmap	3.298	0.081	3.384
plotOTU	0.192	0.020	0.214
plotOrd	0.525	0.043	0.568
plotRare	0.177	0.018	0.194
plotTimeSeries	1.556	0.043	1.600
posteriorProbs	0.000	0.000	0.001
returnAppropriateObj	0.365	0.024	0.390
ssFit	0.001	0.000	0.000
ssIntervalCandidate	0.001	0.000	0.000
ssPerm	0	0	0
ssPermAnalysis	0	0	0
trapz	0.002	0.000	0.002
uniqueFeatures	0.187	0.017	0.204
zigControl	0.001	0.000	0.001