BioC 3.0: CHECK report for LMGene on oaxaca

Package: LMGene

Version: 2.22.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch LMGene_2.22.0.tar.gz

StartedAt: 2015-04-10 00:51:34 -0700 (Fri, 10 Apr 2015)

EndedAt: 2015-04-10 00:53:20 -0700 (Fri, 10 Apr 2015)

EllapsedTime: 106.2 seconds

RetCode: 0

Status:  OK

CheckDir: LMGene.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch LMGene_2.22.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.0-bioc/meat/LMGene.Rcheck’
* using R version 3.1.3 (2015-03-09)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘LMGene/DESCRIPTION’ ... OK
* this is package ‘LMGene’ version ‘2.22.0’
* 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 ... [4s/4s] 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 loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
'library' or 'require' call to ‘multtest’ which was already attached by Depends.
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘Biobase’ ‘affy’ ‘multtest’ ‘survival’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
GetLMObj: no visible global function definition for ‘exprs’
GetLMObj: no visible global function definition for ‘varLabels’
GetLMObj: no visible global function definition for ‘pData’
LMGene: no visible global function definition for ‘exprs’
arrayGlogSDStability: no visible global function definition for ‘exprs’
arrayGlogSDStability: no visible global function definition for ‘pData’
genediff: no visible global function definition for ‘exprs’
genediff: no visible global function definition for ‘varLabels’
genediff : owaov: no visible global function definition for ‘pData’
lnormeS: no visible global function definition for ‘exprs’
lnormeS: no visible global function definition for ‘exprs<-’
msecalc: no visible global function definition for ‘exprs’
msecalcmult: no visible global function definition for ‘exprs’
neweS: no visible global function definition for ‘pData<-’
neweS: no visible global function definition for ‘varLabels<-’
plotMeanSD: no visible global function definition for ‘exprs’
psmeans: no visible global function definition for ‘exprs’
psmeans: no visible global function definition for ‘pData’
pvadjust: no visible global function definition for ‘mt.rawp2adjp’
rowaov: no visible global function definition for ‘exprs’
rowaov: no visible global function definition for ‘varLabels’
rowaov: no visible global function definition for ‘pData’
tranest: no visible global function definition for ‘exprs’
tranest: no visible global function definition for ‘phenoData’
tranest2: no visible global function definition for ‘exprs’
tranestAffyProbeLevel: no visible global function definition for
  ‘featureNames’
tranestAffyProbeLevel: no visible global function definition for ‘pm’
tranestAffyProbeLevel: no visible global function definition for
  ‘exprs<-’
tranestAffyProbeLevel: no visible global function definition for
  ‘exprs’
tranestmult: no visible global function definition for ‘exprs’
transeS: no visible global function definition for ‘exprs’
transeS: no visible global function definition for ‘exprs<-’
* 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 ... [59s/61s] OK
Examples with CPU or elapsed time > 5s
                        user system elapsed
tranestAffyProbeLevel 38.749  3.739  43.929
tranest                7.547  0.565   8.638
* 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
* DONE

NOTE: There were 2 notes.
See
  ‘/Users/biocbuild/bbs-3.0-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	1.615	0.011	1.672
genediff	1.453	0.007	1.464
glog	0.005	0.001	0.006
lnorm	0.099	0.002	0.102
lnormeS	0.108	0.002	0.110
neweS	0.056	0.002	0.058
norm	0.062	0.003	0.064
plotMeanSD	0.088	0.003	0.103
psmeans	0.088	0.002	0.091
pvadjust	1.299	0.003	1.310
rowaov	1.317	0.006	1.338
sample.eS	0.058	0.004	0.062
sample.ind	0.100	0.002	0.104
sample.mat	0.061	0.002	0.063
tranest	7.547	0.565	8.638
tranestAffyProbeLevel	38.749	3.739	43.929
transeS	0.006	0.001	0.006
vlist	0.004	0.000	0.004