BioC 2.13: CHECK report for metagenomeSeq on perceval

* using log directory ‘/Users/biocbuild/bbs-2.13-bioc/meat/metagenomeSeq.Rcheck’
* using R version 3.0.3 (2014-03-06)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘metagenomeSeq/DESCRIPTION’ ... OK
* this is package ‘metagenomeSeq’ version ‘1.4.2’
* 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 ... [7s/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
Packages in Depends field not imported from:
  ‘gplots’ ‘limma’ ‘matrixStats’ ‘methods’ ‘RColorBrewer’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
See the information on DESCRIPTION files in the chapter ‘Creating R
packages’ of 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 ... [43s/47s] OK
Examples with CPU or elapsed time > 5s
       user system elapsed
fitZig 8.61  1.735  11.578
* 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

NOTE: There was 1 note.
See
  ‘/Users/biocbuild/bbs-2.13-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	1.896	0.277	2.246
MRcounts	0.515	0.076	0.595
MRexperiment-class	0.002	0.004	0.006
MRfisher	1.089	0.099	1.204
MRfulltable	2.919	0.214	3.450
MRtable	1.568	0.196	1.991
cumNorm	2.679	0.398	3.331
cumNormMat	2.456	0.368	2.924
cumNormStat	1.821	0.224	2.241
expSummary	0.158	0.021	0.213
exportMat	0.002	0.003	0.005
exportStats	0.002	0.003	0.004
fitZig	8.610	1.735	11.578
libSize	0.356	0.041	0.442
load_meta	0.044	0.006	0.057
load_metaQ	0.002	0.005	0.007
load_phenoData	0.011	0.033	0.047
newMRexperiment	0.088	0.004	0.107
normFactors	0.374	0.051	0.478
plotCorr	3.117	0.599	4.197
plotGenus	0.318	0.021	0.372
plotMRheatmap	3.111	0.505	4.135
plotOTU	0.261	0.021	0.307
plotOrd	2.328	0.349	2.989
plotRare	0.200	0.119	0.367
posterior.probs	0.002	0.003	0.005
zigControl	0.002	0.003	0.005

BioC 2.13: CHECK report for metagenomeSeq on perceval

Summary

Command output