Package: metaR

Version: 0.99.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch metaR_0.99.0.tar.gz

StartedAt: 2013-03-29 23:54:28 -0700 (Fri, 29 Mar 2013)

EndedAt: 2013-03-29 23:56:51 -0700 (Fri, 29 Mar 2013)

EllapsedTime: 143.5 seconds

RetCode: 0

Status:  OK

CheckDir: metaR.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.13-bioc/meat/metaR.Rcheck'
* using R version 3.0.0 RC (2013-03-27 r62426)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'metaR/DESCRIPTION' ... OK
* this is package 'metaR' version '0.99.0'
* 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 'metaR' can be installed ... [8s/8s] 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 ... NOTE
  '.path.package' is deprecated.
  Use 'path.package' instead.
  See help("Deprecated")
* checking data for ASCII and uncompressed saves ... OK
* checking installed files from 'inst/doc' ... OK
* checking examples ... [54s/55s] OK
Examples with CPU or elapsed time > 5s
             user system elapsed
fitZig      9.794  1.943  11.869
normFactors 7.684  2.299  10.139
* 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

NOTE: There was 1 note.
See
  '/Users/biocbuild/bbs-2.13-bioc/meat/metaR.Rcheck/00check.log'
for details.

* installing *source* package 'metaR' ...
** R
** data
** inst
** preparing package for lazy loading
'.path.package' is deprecated.
Use 'path.package' instead.
See help("Deprecated")
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
'.path.package' is deprecated.
Use 'path.package' instead.
See help("Deprecated")
* DONE (metaR)

name	user	system	elapsed
MRcoefs	2.154	0.307	2.555
MRcounts	0.002	0.005	0.007
MRexperiment-class	0.010	0.009	0.019
MRfisher	1.301	0.160	1.467
MRfulltable	3.371	0.228	3.752
MRtable	1.486	0.252	1.748
cumNorm	2.914	0.405	3.434
cumNormMat	2.374	0.343	2.733
cumNormStat	3.702	0.414	4.183
expSummary	0.006	0.022	0.029
exportMat	0.002	0.004	0.006
exportStats	0.003	0.004	0.007
fitZig	9.794	1.943	11.869
libSize	0.417	0.053	0.485
load_meta	0.019	0.035	0.055
load_metaQ	0.002	0.004	0.007
load_phenoData	0.002	0.004	0.005
newMRexperiment	0.074	0.005	0.079
normFactors	7.684	2.299	10.139
plotCorr	3.242	0.665	3.992
plotGenus	0.249	0.032	0.288
plotMRheatmap	3.430	0.600	4.086
plotOTU	0.205	0.019	0.240
posterior.probs	0.002	0.004	0.008
zigControl	0.002	0.004	0.006