BioC 3.4: CHECK report for metagenomeSeq on zin1

Package: metagenomeSeq

Version: 1.15.4

Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings metagenomeSeq_1.15.4.tar.gz

StartedAt: 2016-09-20 09:06:37 -0700 (Tue, 20 Sep 2016)

EndedAt: 2016-09-20 09:08:19 -0700 (Tue, 20 Sep 2016)

EllapsedTime: 101.4 seconds

RetCode: 0

Status:  OK

CheckDir: metagenomeSeq.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings metagenomeSeq_1.15.4.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/metagenomeSeq.Rcheck’
* using R version 3.3.1 (2016-06-21)
* 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 ‘1.15.4’
* 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 ... 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 ... OK
* 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 ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 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: OK

* 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	1.348	0.064	1.412
MRcounts	0.300	0.004	0.306
MRexperiment-class	0.000	0.004	0.001
MRfulltable	0.996	0.012	1.010
MRtable	1.028	0.008	1.037
aggregateBySample	0.156	0.000	0.155
aggregateByTaxonomy	0.144	0.000	0.142
biom2MRexperiment	0	0	0
calcNormFactors	0.488	0.004	0.493
correctIndices	0.116	0.000	0.115
correlationTest	0.240	0.000	0.242
cumNorm	0.584	0.004	0.587
cumNormMat	0.504	0.004	0.504
cumNormStat	0.972	0.004	0.979
cumNormStatFast	0.344	0.000	0.345
expSummary	0.108	0.000	0.108
exportMat	0.000	0.004	0.001
exportStats	0.000	0.000	0.001
filterData	0.168	0.004	0.170
fitDO	0.580	0.020	2.706
fitFeatureModel	1.040	0.012	1.052
fitPA	0.412	0.016	2.371
fitSSTimeSeries	1.160	0.024	1.187
fitTimeSeries	1.040	0.000	1.042
fitZig	2.212	0.008	2.219
libSize	0.296	0.004	0.302
load_biom	0	0	0
load_meta	0.028	0.000	0.027
load_metaQ	0.004	0.000	0.000
load_phenoData	0	0	0
mergeMRexperiments	1.632	0.112	1.745
newMRexperiment	0.032	0.000	0.032
normFactors	0.308	0.000	0.309
plotBubble	0.396	0.024	2.353
plotClassTimeSeries	0.972	0.020	0.992
plotCorr	0.532	0.016	0.544
plotFeature	0.172	0.000	0.172
plotGenus	0.152	0.008	0.158
plotMRheatmap	2.208	0.016	2.225
plotOTU	0.144	0.004	0.147
plotOrd	0.212	0.012	0.225
plotRare	0.116	0.000	0.118
plotTimeSeries	0.908	0.000	0.910
posteriorProbs	0	0	0
returnAppropriateObj	0.276	0.016	0.290
ssFit	0	0	0
ssIntervalCandidate	0.000	0.000	0.001
ssPerm	0.000	0.000	0.001
ssPermAnalysis	0	0	0
trapz	0.004	0.000	0.001
uniqueFeatures	0.128	0.000	0.129
zigControl	0.004	0.000	0.000