BioC 3.2: CHECK report for metagenomeSeq on zin1

Package: metagenomeSeq

Version: 1.12.1

Command: /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings metagenomeSeq_1.12.1.tar.gz

StartedAt: 2016-04-23 02:41:08 -0700 (Sat, 23 Apr 2016)

EndedAt: 2016-04-23 02:43:00 -0700 (Sat, 23 Apr 2016)

EllapsedTime: 111.5 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_1.12.1.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/metagenomeSeq.Rcheck’
* using R version 3.2.4 Revised (2016-03-16 r70336)
* 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 ‘1.12.1’
* 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 ... [6s/6s] 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 ... [28s/36s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’ [11s/11s]
 [11s/11s] 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	1.753	0.056	1.808
MRcounts	0.340	0.012	0.352
MRexperiment-class	0.000	0.000	0.001
MRfulltable	1.156	0.028	1.186
MRtable	1.248	0.000	1.255
aggregateBySample	0.176	0.004	0.180
aggregateByTaxonomy	0.147	0.004	0.151
biom2MRexperiment	0.001	0.000	0.000
calcNormFactors	0.714	0.008	0.722
correctIndices	0.130	0.004	0.133
correlationTest	0.281	0.000	0.282
cumNorm	0.588	0.004	0.591
cumNormMat	0.631	0.004	0.635
cumNormStat	1.033	0.008	1.043
cumNormStatFast	0.394	0.008	0.419
expSummary	0.111	0.003	0.114
exportMat	0.001	0.000	0.000
exportStats	0	0	0
filterData	0.314	0.000	0.314
fitDO	0.540	0.017	3.283
fitFeatureModel	1.293	0.044	1.336
fitPA	0.445	0.025	3.037
fitSSTimeSeries	1.472	0.040	1.510
fitTimeSeries	1.205	0.008	1.212
fitZig	2.729	0.044	2.772
libSize	0.339	0.016	0.351
load_biom	0.000	0.000	0.001
load_meta	0.028	0.000	0.029
load_metaQ	0.001	0.000	0.000
load_phenoData	0.000	0.000	0.001
newMRexperiment	0.042	0.000	0.042
normFactors	0.348	0.008	0.361
plotBubble	0.716	0.033	3.236
plotClassTimeSeries	1.200	0.008	1.207
plotCorr	0.664	0.000	0.663
plotFeature	0.186	0.004	0.189
plotGenus	0.178	0.000	0.178
plotMRheatmap	2.334	0.004	2.339
plotOTU	0.161	0.004	0.166
plotOrd	0.386	0.000	0.385
plotRare	0.149	0.000	0.149
plotTimeSeries	1.213	0.000	1.214
posteriorProbs	0.000	0.000	0.001
returnAppropriateObj	0.347	0.008	0.356
ssFit	0.000	0.000	0.001
ssIntervalCandidate	0	0	0
ssPerm	0.000	0.000	0.001
ssPermAnalysis	0	0	0
trapz	0.002	0.000	0.001
uniqueFeatures	0.14	0.00	0.14
zigControl	0	0	0