BioC 3.2: CHECK report for LMGene on zin1

Package: LMGene

Version: 2.26.0

Command: /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings LMGene_2.26.0.tar.gz

StartedAt: 2016-04-23 02:19:56 -0700 (Sat, 23 Apr 2016)

EndedAt: 2016-04-23 02:21:46 -0700 (Sat, 23 Apr 2016)

EllapsedTime: 109.5 seconds

RetCode: 0

Status:  OK

CheckDir: LMGene.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings LMGene_2.26.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/LMGene.Rcheck’
* using R version 3.2.4 Revised (2016-03-16 r70336)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘LMGene/DESCRIPTION’ ... OK
* this is package ‘LMGene’ version ‘2.26.0’
* 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 ... [5s/5s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* 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 ... [62s/62s] OK
Examples with CPU or elapsed time > 5s
                        user system elapsed
tranestAffyProbeLevel 47.414  0.296  47.844
tranest                6.966  0.008   6.980
* 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

Status: 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.2-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	1.312	0.008	1.323
genediff	1.015	0.004	1.021
glog	0.005	0.000	0.004
lnorm	0.072	0.000	0.072
lnormeS	0.045	0.000	0.044
neweS	0.037	0.000	0.038
norm	0.038	0.004	0.039
plotMeanSD	0.076	0.000	0.077
psmeans	0.078	0.000	0.079
pvadjust	1.139	0.000	1.140
rowaov	1.146	0.016	1.163
sample.eS	0.039	0.000	0.039
sample.ind	0.077	0.000	0.077
sample.mat	0.039	0.000	0.039
tranest	6.966	0.008	6.980
tranestAffyProbeLevel	47.414	0.296	47.844
transeS	0.006	0.000	0.006
vlist	0.003	0.000	0.003