BioC 3.2: CHECK report for metagenomeSeq on oaxaca

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: 2015-10-27 05:26:21 -0400 (Tue, 27 Oct 2015)

EndedAt: 2015-10-27 05:28:49 -0400 (Tue, 27 Oct 2015)

EllapsedTime: 148.2 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 (2015-08-14)
* 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 ‘1.12.0’
* 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 ... [8s/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 ... [35s/45s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’ [14s/14s]
 [14s/14s] 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	2.014	0.101	2.150
MRcounts	0.388	0.021	0.410
MRexperiment-class	0.000	0.000	0.001
MRfulltable	1.511	0.050	1.563
MRtable	1.524	0.042	1.566
aggregateBySample	0.244	0.014	0.258
aggregateByTaxonomy	0.208	0.016	0.225
biom2MRexperiment	0	0	0
calcNormFactors	0.873	0.127	1.001
correctIndices	0.159	0.019	0.178
correlationTest	0.335	0.032	0.367
cumNorm	0.793	0.093	0.886
cumNormMat	0.869	0.120	0.990
cumNormStat	1.470	0.083	1.553
cumNormStatFast	0.496	0.019	0.516
expSummary	0.154	0.010	0.164
exportMat	0	0	0
exportStats	0.000	0.000	0.001
filterData	0.401	0.029	0.431
fitDO	0.627	0.039	4.247
fitFeatureModel	1.609	0.099	1.710
fitPA	0.535	0.030	3.930
fitSSTimeSeries	1.530	0.096	1.654
fitTimeSeries	1.394	0.076	1.471
fitZig	2.975	0.357	3.336
libSize	0.378	0.028	0.405
load_biom	0.001	0.000	0.001
load_meta	0.063	0.001	0.064
load_metaQ	0.001	0.000	0.000
load_phenoData	0.001	0.001	0.000
newMRexperiment	0.053	0.000	0.054
normFactors	0.361	0.007	0.368
plotBubble	0.736	0.101	4.245
plotClassTimeSeries	1.277	0.097	1.374
plotCorr	0.583	0.050	0.647
plotFeature	0.192	0.045	0.244
plotGenus	0.183	0.025	0.209
plotMRheatmap	2.709	0.099	2.817
plotOTU	0.180	0.013	0.194
plotOrd	0.328	0.031	0.359
plotRare	0.164	0.011	0.176
plotTimeSeries	1.228	0.055	1.285
posteriorProbs	0	0	0
returnAppropriateObj	0.406	0.025	0.431
ssFit	0.000	0.000	0.001
ssIntervalCandidate	0	0	0
ssPerm	0.000	0.000	0.001
ssPermAnalysis	0.000	0.000	0.001
trapz	0.002	0.000	0.002
uniqueFeatures	0.180	0.016	0.197
zigControl	0.000	0.001	0.001