BioC 3.1: CHECK report for metagenomeSeq on morelia

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings metagenomeSeq_1.10.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.1-bioc/meat/metagenomeSeq.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘metagenomeSeq/DESCRIPTION’ ... OK
* this is package ‘metagenomeSeq’ version ‘1.10.0’
* 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 ... [5s/5s] 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 ... [27s/34s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’ [10s/10s]
 [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
  ‘/Users/biocbuild/bbs-3.1-bioc/meat/metagenomeSeq.Rcheck/00check.log’
for details.

* installing *source* package ‘metagenomeSeq’ ...
** R
** data
** inst
** preparing package for lazy loading
Creating a generic function for ‘colSums’ from package ‘base’ in package ‘metagenomeSeq’
Creating a generic function for ‘rowSums’ from package ‘base’ in package ‘metagenomeSeq’
Creating a generic function for ‘rowMeans’ from package ‘base’ in package ‘metagenomeSeq’
Creating a generic function for ‘colMeans’ from package ‘base’ in package ‘metagenomeSeq’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (metagenomeSeq)

name	user	system	elapsed
MRcoefs	1.162	0.153	1.315
MRcounts	0.351	0.020	0.371
MRexperiment-class	0.001	0.000	0.001
MRfulltable	0.960	0.062	3.676
MRtable	0.970	0.107	1.078
aggregateBySample	0.214	0.022	0.236
aggregateByTaxonomy	0.182	0.017	0.199
biom2MRexperiment	0.001	0.000	0.001
calcNormFactors	0.744	0.107	0.855
correctIndices	0.161	0.019	0.181
correlationTest	0.303	0.043	0.346
cumNorm	0.719	0.080	0.802
cumNormMat	0.724	0.098	0.824
cumNormStat	1.285	0.105	1.390
cumNormStatFast	0.411	0.054	0.464
expSummary	0.153	0.010	0.163
exportMat	0	0	0
exportStats	0.001	0.000	0.000
filterData	0.259	0.023	0.283
fitDO	0.613	0.068	2.406
fitPA	0.479	0.038	1.725
fitSSTimeSeries	1.107	0.086	1.212
fitTimeSeries	1.258	0.110	1.367
fitZig	2.356	0.422	2.780
libSize	0.372	0.041	0.413
load_biom	0.001	0.000	0.001
load_meta	0.062	0.001	0.062
load_metaQ	0.001	0.000	0.000
load_phenoData	0.001	0.000	0.001
newMRexperiment	0.049	0.007	0.055
normFactors	0.361	0.006	0.367
plotBubble	0.642	0.158	3.060
plotClassTimeSeries	1.031	0.066	1.097
plotCorr	0.593	0.057	0.663
plotFeature	0.179	0.010	0.197
plotGenus	0.205	0.025	0.230
plotMRheatmap	2.607	0.147	2.760
plotOTU	0.223	0.024	0.248
plotOrd	0.310	0.028	0.338
plotRare	0.115	0.009	0.124
plotTimeSeries	1.097	0.195	1.293
posteriorProbs	0	0	0
returnAppropriateObj	0.368	0.027	0.394
ssFit	0.001	0.000	0.000
ssIntervalCandidate	0.001	0.000	0.000
ssPerm	0	0	0
ssPermAnalysis	0	0	0
trapz	0.002	0.000	0.001
uniqueFeatures	0.167	0.008	0.174
zigControl	0	0	0

BioC 3.1: CHECK report for metagenomeSeq on morelia

Summary

Command output