BioC 2.12: CHECK report for metagenomeSeq on george2

Package: metagenomeSeq

Version: 1.0.6

Command: /home/biocbuild/bbs-2.12-bioc/R/bin/R CMD check --no-vignettes --timings metagenomeSeq_1.0.6.tar.gz

StartedAt: 2013-10-09 03:08:58 -0700 (Wed, 09 Oct 2013)

EndedAt: 2013-10-09 03:11:27 -0700 (Wed, 09 Oct 2013)

EllapsedTime: 149.7 seconds

RetCode: 0

Status:  OK

CheckDir: metagenomeSeq.Rcheck

Warnings: 0

* using log directory ‘/home/biocbuild/bbs-2.12-bioc/meat/metagenomeSeq.Rcheck’
* using R version 3.0.1 (2013-05-16)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘metagenomeSeq/DESCRIPTION’ ... OK
* this is package ‘metagenomeSeq’ version ‘1.0.6’
* 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 ... [10s/10s] OK
* checking installed package size ... OK
* checking package 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 for unstated 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 installed files from ‘inst/doc’ ... OK
* checking examples ... [50s/50s] OK
Examples with CPU or elapsed time > 5s
         user system elapsed
fitZig 12.901  0.232  13.171
* 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 vignettes ... SKIPPED
* checking PDF version of manual ... 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	2.460	0.240	2.791
MRcounts	0.496	0.072	0.577
MRexperiment-class	0.208	0.020	0.227
MRfisher	1.972	0.148	2.121
MRfulltable	4.488	0.024	4.515
MRtable	1.956	0.044	2.000
cumNorm	4.145	0.016	4.160
cumNormMat	4.044	0.028	4.076
cumNormStat	2.024	0.016	2.043
expSummary	0.160	0.016	0.178
exportMat	0.008	0.000	0.005
exportStats	0.004	0.000	0.005
fitZig	12.901	0.232	13.171
libSize	0.456	0.032	0.488
load_meta	0.104	0.000	0.105
load_metaQ	0.004	0.000	0.006
load_phenoData	0.008	0.000	0.005
newMRexperiment	0.128	0.000	0.129
normFactors	0.448	0.020	0.471
plotCorr	4.288	0.088	4.376
plotGenus	0.304	0.020	0.323
plotMRheatmap	4.481	0.004	4.487
plotOTU	0.256	0.016	0.273
posterior.probs	0.004	0.000	0.005
zigControl	0.008	0.000	0.006