BioC 3.2: CHECK report for metagenomeSeq on zin1

Package: metagenomeSeq

Version: 1.11.10

Command: /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings metagenomeSeq_1.11.10.tar.gz

StartedAt: 2015-08-24 01:28:43 -0700 (Mon, 24 Aug 2015)

EndedAt: 2015-08-24 01:30:33 -0700 (Mon, 24 Aug 2015)

EllapsedTime: 109.9 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_1.11.10.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 ‘1.11.10’
* 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 ... [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	1.691	0.036	1.728
MRcounts	0.295	0.012	0.307
MRexperiment-class	0.001	0.000	0.000
MRfulltable	1.152	0.032	1.189
MRtable	1.232	0.012	1.268
aggregateBySample	0.182	0.007	0.191
aggregateByTaxonomy	0.170	0.008	0.178
biom2MRexperiment	0.000	0.000	0.001
calcNormFactors	0.772	0.004	0.779
correctIndices	0.118	0.000	0.118
correlationTest	0.239	0.007	0.247
cumNorm	0.583	0.005	0.586
cumNormMat	0.620	0.004	0.624
cumNormStat	0.974	0.004	0.977
cumNormStatFast	0.411	0.004	0.415
expSummary	0.119	0.008	0.127
exportMat	0	0	0
exportStats	0.001	0.000	0.001
filterData	0.212	0.000	0.212
fitDO	0.676	0.023	3.331
fitFeatureModel	1.235	0.024	1.258
fitPA	0.561	0.017	3.165
fitSSTimeSeries	1.517	0.043	1.580
fitTimeSeries	1.339	0.008	1.347
fitZig	2.758	0.009	2.768
libSize	0.289	0.017	0.308
load_biom	0.001	0.000	0.000
load_meta	0.025	0.000	0.026
load_metaQ	0	0	0
load_phenoData	0.000	0.000	0.001
newMRexperiment	0.039	0.000	0.040
normFactors	0.300	0.013	0.314
plotBubble	0.677	0.031	3.238
plotClassTimeSeries	1.264	0.001	1.264
plotCorr	0.638	0.003	0.642
plotFeature	0.170	0.005	0.174
plotGenus	0.172	0.000	0.172
plotMRheatmap	2.300	0.004	2.307
plotOTU	0.165	0.000	0.165
plotOrd	0.496	0.000	0.497
plotRare	0.131	0.000	0.131
plotTimeSeries	1.176	0.000	1.178
posteriorProbs	0.000	0.000	0.001
returnAppropriateObj	0.331	0.012	0.343
ssFit	0.000	0.000	0.001
ssIntervalCandidate	0.001	0.000	0.000
ssPerm	0.000	0.000	0.001
ssPermAnalysis	0.001	0.000	0.000
trapz	0.001	0.000	0.001
uniqueFeatures	0.149	0.004	0.153
zigControl	0.000	0.000	0.001