BioC 2.12: CHECK report for LMGene on petty

Package: LMGene

Version: 2.16.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch LMGene_2.16.0.tar.gz

StartedAt: 2013-10-08 22:56:13 -0700 (Tue, 08 Oct 2013)

EndedAt: 2013-10-08 22:59:41 -0700 (Tue, 08 Oct 2013)

EllapsedTime: 208.3 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: LMGene.Rcheck

Warnings: 1

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/LMGene.Rcheck'
* using R version 3.0.1 (2013-05-16)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: ASCII
* 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 ... [7s/7s] 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 sizes of PDF files under 'inst/doc' ... OK
* checking installed files from 'inst/doc' ... OK
* checking examples ... [135s/137s] OK
Examples with CPU or elapsed time > 5s
                        user system elapsed
tranestAffyProbeLevel 90.974 12.295 104.901
tranest               14.562  1.225  15.889
* 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
  '/Users/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	3.800	0.211	4.019
genediff	3.411	0.225	3.643
glog	0.020	0.004	0.023
lnorm	0.185	0.006	0.191
lnormeS	0.103	0.004	0.107
neweS	0.110	0.003	0.113
norm	0.106	0.003	0.109
plotMeanSD	0.177	0.005	0.183
psmeans	0.283	0.005	0.288
rowaov	3.201	0.219	3.424
sample.eS	0.110	0.003	0.113
sample.ind	0.188	0.006	0.194
sample.mat	0.106	0.005	0.111
tranest	14.562	1.225	15.889
tranestAffyProbeLevel	90.974	12.295	104.901
transeS	0.012	0.009	0.020
vlist	0.008	0.006	0.014