BioC 3.2: CHECK report for metagenomeSeq on perceval

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 02:32:21 -0700 (Mon, 24 Aug 2015)

EndedAt: 2015-08-24 02:35:21 -0700 (Mon, 24 Aug 2015)

EllapsedTime: 180.0 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 Patched (2015-08-14 r69078)
* 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 ‘1.11.10’
* 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 ... [11s/11s] 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 ... [42s/54s] OK
Examples with CPU or elapsed time > 5s
            user system elapsed
plotBubble 0.854  0.163   5.136
fitDO      0.891  0.123   5.236
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’ [18s/18s]
 [19s/19s] 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	2.498	0.197	2.696
MRcounts	0.318	0.036	0.354
MRexperiment-class	0.001	0.000	0.001
MRfulltable	1.650	0.080	1.731
MRtable	1.656	0.046	1.705
aggregateBySample	0.239	0.032	0.271
aggregateByTaxonomy	0.198	0.029	0.228
biom2MRexperiment	0	0	0
calcNormFactors	0.993	0.190	1.183
correctIndices	0.154	0.022	0.177
correlationTest	0.333	0.055	0.387
cumNorm	0.762	0.119	0.882
cumNormMat	0.901	0.137	1.038
cumNormStat	1.635	0.103	1.739
cumNormStatFast	0.474	0.024	0.498
expSummary	0.163	0.027	0.190
exportMat	0.001	0.000	0.000
exportStats	0	0	0
filterData	0.294	0.048	0.342
fitDO	0.891	0.123	5.236
fitFeatureModel	1.687	0.148	1.839
fitPA	0.846	0.031	4.877
fitSSTimeSeries	2.080	0.155	2.246
fitTimeSeries	1.778	0.125	1.903
fitZig	4.108	0.670	4.779
libSize	0.334	0.039	0.372
load_biom	0.001	0.000	0.001
load_meta	0.040	0.001	0.041
load_metaQ	0.000	0.000	0.001
load_phenoData	0.001	0.000	0.000
newMRexperiment	0.051	0.000	0.051
normFactors	0.382	0.018	0.399
plotBubble	0.854	0.163	5.136
plotClassTimeSeries	1.882	0.177	2.059
plotCorr	0.653	0.107	0.760
plotFeature	0.205	0.038	0.247
plotGenus	0.200	0.039	0.240
plotMRheatmap	3.018	0.108	3.130
plotOTU	0.191	0.025	0.218
plotOrd	0.654	0.056	0.711
plotRare	0.163	0.019	0.181
plotTimeSeries	1.556	0.064	1.622
posteriorProbs	0.001	0.001	0.001
returnAppropriateObj	0.308	0.030	0.339
ssFit	0.000	0.000	0.001
ssIntervalCandidate	0.001	0.000	0.000
ssPerm	0.001	0.000	0.000
ssPermAnalysis	0	0	0
trapz	0.002	0.000	0.002
uniqueFeatures	0.181	0.036	0.217
zigControl	0.001	0.000	0.000