BioC 3.2: CHECK report for metagenomeSeq on oaxaca

Package: metagenomeSeq

Version: 1.12.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings metagenomeSeq_1.12.1.tar.gz

StartedAt: 2016-04-23 01:55:45 -0700 (Sat, 23 Apr 2016)

EndedAt: 2016-04-23 01:58:21 -0700 (Sat, 23 Apr 2016)

EllapsedTime: 155.2 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_1.12.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/metagenomeSeq.Rcheck’
* using R version 3.2.4 (2016-03-10)
* 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 ‘1.12.1’
* 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 ... [35s/47s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’ [14s/15s]
 [15s/15s] 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	2.049	0.105	2.222
MRcounts	0.372	0.020	0.392
MRexperiment-class	0	0	0
MRfulltable	1.507	0.057	1.570
MRtable	1.520	0.037	1.567
aggregateBySample	0.229	0.014	0.243
aggregateByTaxonomy	0.229	0.013	0.246
biom2MRexperiment	0.000	0.001	0.000
calcNormFactors	0.868	0.134	1.003
correctIndices	0.150	0.015	0.166
correlationTest	0.308	0.026	0.334
cumNorm	0.759	0.095	0.856
cumNormMat	0.864	0.107	0.973
cumNormStat	1.318	0.077	1.396
cumNormStatFast	0.486	0.027	0.515
expSummary	0.136	0.010	0.146
exportMat	0	0	0
exportStats	0.001	0.000	0.000
filterData	0.354	0.027	0.380
fitDO	0.622	0.048	4.415
fitFeatureModel	1.629	0.105	1.739
fitPA	0.523	0.029	4.050
fitSSTimeSeries	1.571	0.098	1.698
fitTimeSeries	1.435	0.070	1.521
fitZig	3.038	0.356	3.410
libSize	0.370	0.025	0.395
load_biom	0	0	0
load_meta	0.064	0.001	0.065
load_metaQ	0.000	0.000	0.001
load_phenoData	0.001	0.000	0.000
newMRexperiment	0.058	0.000	0.058
normFactors	0.369	0.009	0.378
plotBubble	0.750	0.106	4.214
plotClassTimeSeries	1.339	0.095	1.457
plotCorr	0.695	0.054	0.785
plotFeature	0.202	0.024	0.251
plotGenus	0.178	0.020	0.199
plotMRheatmap	2.941	0.102	3.185
plotOTU	0.206	0.017	0.233
plotOrd	0.359	0.036	0.395
plotRare	0.158	0.015	0.173
plotTimeSeries	1.215	0.063	2.214
posteriorProbs	0.001	0.000	0.037
returnAppropriateObj	0.375	0.020	0.396
ssFit	0.000	0.001	0.000
ssIntervalCandidate	0	0	0
ssPerm	0.001	0.000	0.000
ssPermAnalysis	0.000	0.000	0.001
trapz	0.001	0.001	0.001
uniqueFeatures	0.194	0.015	0.210
zigControl	0.000	0.000	0.001