BioC 3.2: CHECK report for metagenomeSeq on linux1.bioconductor.org

Package: metagenomeSeq

Version: 1.12.0

Command: /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings metagenomeSeq_1.12.0.tar.gz

StartedAt: 2015-10-27 05:29:36 -0400 (Tue, 27 Oct 2015)

EndedAt: 2015-10-27 05:31:35 -0400 (Tue, 27 Oct 2015)

EllapsedTime: 119.2 seconds

RetCode: 0

Status:  OK

CheckDir: metagenomeSeq.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings metagenomeSeq_1.12.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/metagenomeSeq.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-pc-linux-gnu (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/8s] 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [31s/40s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’ [13s/13s]
 [13s/13s] 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
  ‘/home/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	1.496	0.064	1.560
MRcounts	0.253	0.004	0.257
MRexperiment-class	0.000	0.000	0.001
MRfulltable	1.016	0.036	1.051
MRtable	1.005	0.016	1.022
aggregateBySample	0.151	0.000	0.151
aggregateByTaxonomy	0.136	0.004	0.140
biom2MRexperiment	0	0	0
calcNormFactors	0.697	0.020	0.718
correctIndices	0.173	0.004	0.177
correlationTest	0.386	0.003	0.392
cumNorm	0.854	0.005	0.861
cumNormMat	0.886	0.007	0.899
cumNormStat	1.351	0.000	1.351
cumNormStatFast	0.583	0.004	0.587
expSummary	0.169	0.008	0.177
exportMat	0.000	0.000	0.001
exportStats	0.001	0.000	0.001
filterData	0.301	0.000	0.300
fitDO	0.613	0.012	3.466
fitFeatureModel	1.606	0.048	1.655
fitPA	0.668	0.051	3.698
fitSSTimeSeries	1.876	0.031	1.908
fitTimeSeries	1.719	0.008	1.727
fitZig	2.885	0.016	2.903
libSize	0.323	0.004	0.328
load_biom	0.001	0.000	0.000
load_meta	0.043	0.000	0.043
load_metaQ	0.000	0.000	0.001
load_phenoData	0.000	0.000	0.001
newMRexperiment	0.053	0.000	0.053
normFactors	0.358	0.004	0.363
plotBubble	0.674	0.054	3.989
plotClassTimeSeries	1.329	0.004	1.333
plotCorr	0.578	0.016	0.595
plotFeature	0.232	0.004	0.237
plotGenus	0.240	0.012	0.252
plotMRheatmap	3.465	0.000	3.473
plotOTU	0.136	0.008	0.144
plotOrd	0.452	0.004	0.456
plotRare	0.115	0.000	0.115
plotTimeSeries	0.975	0.004	0.980
posteriorProbs	0.000	0.000	0.001
returnAppropriateObj	0.227	0.020	0.246
ssFit	0	0	0
ssIntervalCandidate	0	0	0
ssPerm	0	0	0
ssPermAnalysis	0	0	0
trapz	0.001	0.000	0.001
uniqueFeatures	0.109	0.004	0.112
zigControl	0.001	0.000	0.000