BioC 3.3: CHECK report for metagenomeSeq on morelia

Package: metagenomeSeq

Version: 1.13.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings metagenomeSeq_1.13.0.tar.gz

StartedAt: 2015-10-22 08:09:39 -0400 (Thu, 22 Oct 2015)

EndedAt: 2015-10-22 08:11:32 -0400 (Thu, 22 Oct 2015)

EllapsedTime: 112.7 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_1.13.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.3-bioc/meat/metagenomeSeq.Rcheck’
* using R Under development (unstable) (2015-10-08 r69496)
* 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 ‘1.13.0’
* 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 ... [6s/7s] 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 ... [25s/33s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’ [10s/10s]
 [10s/10s] 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-3.3-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	1.416	0.070	1.509
MRcounts	0.298	0.013	0.312
MRexperiment-class	0	0	0
MRfulltable	0.998	0.041	1.040
MRtable	1.173	0.024	1.198
aggregateBySample	0.152	0.011	0.163
aggregateByTaxonomy	0.143	0.018	0.161
biom2MRexperiment	0.000	0.000	0.001
calcNormFactors	0.556	0.095	0.650
correctIndices	0.109	0.012	0.120
correlationTest	0.218	0.022	0.241
cumNorm	0.492	0.086	0.578
cumNormMat	0.728	0.094	0.822
cumNormStat	0.922	0.053	0.974
cumNormStatFast	0.385	0.016	0.402
expSummary	0.102	0.010	0.113
exportMat	0	0	0
exportStats	0.000	0.001	0.000
filterData	0.283	0.025	0.309
fitDO	0.572	0.056	3.429
fitFeatureModel	1.253	0.069	1.323
fitPA	0.513	0.020	3.141
fitSSTimeSeries	1.119	0.088	1.231
fitTimeSeries	1.178	0.082	1.261
fitZig	2.038	0.250	2.289
libSize	0.325	0.017	0.343
load_biom	0.001	0.001	0.000
load_meta	0.036	0.000	0.037
load_metaQ	0	0	0
load_phenoData	0.001	0.000	0.001
newMRexperiment	0.031	0.000	0.031
normFactors	0.375	0.007	0.383
plotBubble	0.448	0.071	2.865
plotClassTimeSeries	0.792	0.082	0.874
plotCorr	0.479	0.041	0.520
plotFeature	0.135	0.012	0.155
plotGenus	0.137	0.023	0.288
plotMRheatmap	2.086	0.091	2.183
plotOTU	0.129	0.010	0.142
plotOrd	0.208	0.016	0.230
plotRare	0.111	0.009	0.120
plotTimeSeries	0.803	0.033	0.836
posteriorProbs	0.000	0.000	0.001
returnAppropriateObj	0.335	0.018	0.353
ssFit	0.000	0.000	0.001
ssIntervalCandidate	0	0	0
ssPerm	0.001	0.000	0.000
ssPermAnalysis	0.001	0.000	0.000
trapz	0.001	0.000	0.001
uniqueFeatures	0.159	0.018	0.177
zigControl	0.001	0.000	0.001