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: 2015-10-27 09:43:46 -0400 (Tue, 27 Oct 2015)

EndedAt: 2015-10-27 09:46:30 -0400 (Tue, 27 Oct 2015)

EllapsedTime: 163.4 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/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 ... [41s/51s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’ [17s/17s]
 [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	2.219	0.138	2.356
MRcounts	0.358	0.024	0.382
MRexperiment-class	0.000	0.000	0.001
MRfulltable	1.543	0.056	1.599
MRtable	1.574	0.037	1.611
aggregateBySample	0.241	0.019	0.259
aggregateByTaxonomy	0.217	0.022	0.238
biom2MRexperiment	0.001	0.000	0.001
calcNormFactors	1.010	0.134	1.145
correctIndices	0.168	0.019	0.187
correlationTest	0.345	0.038	0.383
cumNorm	0.822	0.084	0.906
cumNormMat	0.882	0.086	0.968
cumNormStat	1.683	0.081	1.763
cumNormStatFast	0.498	0.018	0.515
expSummary	0.160	0.018	0.178
exportMat	0.001	0.000	0.001
exportStats	0.001	0.000	0.001
filterData	0.284	0.042	0.327
fitDO	0.803	0.084	4.649
fitFeatureModel	1.579	0.101	1.681
fitPA	0.710	0.025	4.221
fitSSTimeSeries	2.085	0.116	2.205
fitTimeSeries	2.070	0.121	2.191
fitZig	4.186	0.511	4.698
libSize	0.379	0.027	0.406
load_biom	0.001	0.000	0.001
load_meta	0.037	0.001	0.038
load_metaQ	0.001	0.000	0.001
load_phenoData	0	0	0
newMRexperiment	0.054	0.000	0.054
normFactors	0.377	0.012	0.390
plotBubble	0.835	0.121	4.441
plotClassTimeSeries	1.832	0.119	1.950
plotCorr	0.664	0.062	0.727
plotFeature	0.224	0.039	0.270
plotGenus	0.203	0.042	0.245
plotMRheatmap	3.360	0.084	3.477
plotOTU	0.193	0.018	0.212
plotOrd	0.519	0.043	0.561
plotRare	0.176	0.016	0.193
plotTimeSeries	1.577	0.044	1.621
posteriorProbs	0	0	0
returnAppropriateObj	0.385	0.026	0.410
ssFit	0.001	0.000	0.001
ssIntervalCandidate	0.000	0.000	0.001
ssPerm	0.000	0.000	0.001
ssPermAnalysis	0.001	0.000	0.001
trapz	0.002	0.001	0.002
uniqueFeatures	0.186	0.018	0.205
zigControl	0.000	0.000	0.001