BioC 3.2: CHECK report for metagenomeSeq on oaxaca

Package: metagenomeSeq

Version: 1.11.10

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings metagenomeSeq_1.11.10.tar.gz

StartedAt: 2015-08-24 01:33:57 -0700 (Mon, 24 Aug 2015)

EndedAt: 2015-08-24 01:36:45 -0700 (Mon, 24 Aug 2015)

EllapsedTime: 168.0 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_1.11.10.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 ‘1.11.10’
* 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/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 ... [37s/51s] OK
Examples with CPU or elapsed time > 5s
           user system elapsed
plotBubble  0.8  0.097   5.459
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’ [15s/15s]
 [15s/16s] 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	2.114	0.100	2.369
MRcounts	0.391	0.020	0.419
MRexperiment-class	0.000	0.000	0.001
MRfulltable	1.526	0.060	1.599
MRtable	1.479	0.025	1.606
aggregateBySample	0.225	0.013	0.237
aggregateByTaxonomy	0.208	0.015	0.224
biom2MRexperiment	0.001	0.000	0.001
calcNormFactors	0.919	0.127	1.054
correctIndices	0.171	0.015	0.190
correlationTest	0.359	0.029	0.393
cumNorm	0.773	0.090	0.884
cumNormMat	0.866	0.099	0.983
cumNormStat	1.579	0.077	1.746
cumNormStatFast	0.530	0.033	0.565
expSummary	0.159	0.014	0.178
exportMat	0	0	0
exportStats	0.000	0.000	0.001
filterData	0.227	0.026	0.252
fitDO	0.776	0.061	4.825
fitFeatureModel	1.616	0.078	1.704
fitPA	0.689	0.025	4.399
fitSSTimeSeries	1.679	0.101	1.866
fitTimeSeries	1.510	0.096	1.622
fitZig	3.339	0.356	3.786
libSize	0.387	0.021	0.409
load_biom	0.001	0.001	0.001
load_meta	0.065	0.001	0.065
load_metaQ	0.001	0.000	0.000
load_phenoData	0.001	0.000	0.000
newMRexperiment	0.058	0.001	0.058
normFactors	0.394	0.008	0.403
plotBubble	0.800	0.097	5.459
plotClassTimeSeries	1.519	0.113	1.642
plotCorr	0.694	0.061	0.843
plotFeature	0.210	0.023	0.240
plotGenus	0.210	0.022	0.234
plotMRheatmap	3.068	0.080	3.253
plotOTU	0.207	0.015	0.225
plotOrd	0.503	0.036	0.541
plotRare	0.173	0.010	0.199
plotTimeSeries	1.311	0.071	1.428
posteriorProbs	0	0	0
returnAppropriateObj	0.401	0.021	0.465
ssFit	0.000	0.000	0.001
ssIntervalCandidate	0.000	0.001	0.001
ssPerm	0.001	0.000	0.000
ssPermAnalysis	0.001	0.000	0.000
trapz	0.002	0.000	0.001
uniqueFeatures	0.199	0.019	0.220
zigControl	0.000	0.000	0.001