BioC 2.12: CHECK report for LMGene on george2

Package: LMGene

Version: 2.16.0

Command: /home/biocbuild/bbs-2.12-bioc/R/bin/R CMD check --no-vignettes --timings LMGene_2.16.0.tar.gz

StartedAt: 2013-10-09 02:55:50 -0700 (Wed, 09 Oct 2013)

EndedAt: 2013-10-09 03:00:11 -0700 (Wed, 09 Oct 2013)

EllapsedTime: 261.3 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: LMGene.Rcheck

Warnings: 1

* using log directory ‘/home/biocbuild/bbs-2.12-bioc/meat/LMGene.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 ‘LMGene/DESCRIPTION’ ... OK
* this is package ‘LMGene’ version ‘2.16.0’
* 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 ‘LMGene’ can be installed ... [6s/6s] 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 ... WARNING
Undocumented code objects:
  ‘pvadjust’
All user-level objects in a package should have documentation entries.
See the chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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 ... [190s/194s] OK
Examples with CPU or elapsed time > 5s
                         user system elapsed
tranestAffyProbeLevel 154.257  0.680 156.345
tranest                18.918  0.012  20.713
* 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

WARNING: There was 1 warning.
See
  ‘/home/biocbuild/bbs-2.12-bioc/meat/LMGene.Rcheck/00check.log’
for details.

* installing *source* package ‘LMGene’ ...
** 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 (LMGene)

name	user	system	elapsed
LMGene	3.996	0.016	4.294
genediff	3.268	0.008	3.585
glog	0.020	0.000	0.021
lnorm	0.144	0.000	0.145
lnormeS	0.096	0.000	0.093
neweS	0.072	0.008	0.083
norm	0.084	0.000	0.087
plotMeanSD	0.144	0.000	0.154
psmeans	0.216	0.000	0.226
rowaov	4.492	0.000	4.752
sample.eS	0.088	0.000	0.091
sample.ind	0.156	0.004	0.173
sample.mat	0.084	0.000	0.086
tranest	18.918	0.012	20.713
tranestAffyProbeLevel	154.257	0.680	156.345
transeS	0.012	0.004	0.017
vlist	0.012	0.000	0.012