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CHECK report for LMGene on merida1

This page was generated on 2019-04-16 11:54:19 -0400 (Tue, 16 Apr 2019).

Package 839/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
LMGene 2.38.0
Blythe Durbin-Johnson
Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019)
URL: https://git.bioconductor.org/packages/LMGene
Branch: RELEASE_3_8
Last Commit: f352587
Last Changed Date: 2018-10-30 11:41:42 -0400 (Tue, 30 Oct 2018)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: LMGene
Version: 2.38.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:LMGene.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings LMGene_2.38.0.tar.gz
StartedAt: 2019-04-16 00:53:52 -0400 (Tue, 16 Apr 2019)
EndedAt: 2019-04-16 00:55:32 -0400 (Tue, 16 Apr 2019)
EllapsedTime: 100.4 seconds
RetCode: 0
Status:  OK 
CheckDir: LMGene.Rcheck
Warnings: 0

Command output

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:LMGene.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings LMGene_2.38.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/LMGene.Rcheck’
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘LMGene/DESCRIPTION’ ... OK
* this is package ‘LMGene’ version ‘2.38.0’
* 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 ... 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 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 ‘as.formula’
GetLMObj: no visible global function definition for ‘lm’
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’
arrayGlogSDStability: no visible binding for global variable ‘sd’
arrayGlogSDStability : pooled.sd: no visible global function definition
  for ‘var’
arrayGlogSDStability: no visible global function definition for ‘lm’
arrayGlogSDStability: no visible global function definition for ‘coef’
fitFDist: no visible global function definition for ‘median’
fitScaledF : like: no visible global function definition for ‘df’
fitScaledF: no visible global function definition for ‘optim’
genediff: no visible global function definition for ‘exprs’
genediff: no visible global function definition for ‘varLabels’
genediff : owaov: no visible global function definition for
  ‘as.formula’
genediff : owaov: no visible global function definition for ‘anova’
genediff : owaov: no visible global function definition for ‘lm’
genediff : owaov: no visible global function definition for ‘pData’
genediff: no visible global function definition for ‘median’
genediff: no visible global function definition for ‘var’
genediff: no visible global function definition for ‘pf’
lnorm : lcol: no visible global function definition for ‘lowess’
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 ‘new’
neweS: no visible global function definition for ‘pData<-’
neweS: no visible global function definition for ‘varLabels<-’
plotMeanSD: no visible global function definition for ‘exprs’
plotMeanSD : msd.row: no visible binding for global variable ‘var’
plotMeanSD: no visible global function definition for ‘plot’
plotMeanSD: no visible global function definition for ‘lines’
plotMeanSD: no visible global function definition for ‘lowess’
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’
rowaov: no visible global function definition for ‘as.formula’
rowaov: no visible global function definition for ‘lm’
rowaov: no visible global function definition for ‘anova’
tranest: no visible global function definition for ‘exprs’
tranest: no visible global function definition for ‘new’
tranest: no visible global function definition for ‘phenoData’
tranest2: no visible global function definition for ‘exprs’
tranest2: no visible global function definition for ‘median’
tranest2: no visible global function definition for ‘quantile’
tranest2: no visible global function definition for ‘nlm’
tranest2: no visible global function definition for ‘optim’
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’
tranestmult: no visible global function definition for ‘median’
tranestmult: no visible global function definition for ‘nlm’
tranestmult: no visible global function definition for ‘optim’
transeS: no visible global function definition for ‘exprs’
transeS: no visible global function definition for ‘exprs<-’
Undefined global functions or variables:
  anova as.formula coef df exprs exprs<- featureNames lines lm lowess
  median mt.rawp2adjp new nlm optim pData pData<- pf phenoData plot pm
  quantile sd var varLabels varLabels<-
Consider adding
  importFrom("graphics", "lines", "plot")
  importFrom("methods", "new")
  importFrom("stats", "anova", "as.formula", "coef", "df", "lm",
             "lowess", "median", "nlm", "optim", "pf", "quantile", "sd",
             "var")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                        user system elapsed
tranestAffyProbeLevel 25.273  5.580  31.053
tranest                4.453  1.407   5.901
* 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
  ‘/Users/biocbuild/bbs-3.8-bioc/meat/LMGene.Rcheck/00check.log’
for details.



Installation output

LMGene.Rcheck/00install.out

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL LMGene
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘LMGene’ ...
** R
** data
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (LMGene)

Tests output


Example timings

LMGene.Rcheck/LMGene-Ex.timings

nameusersystemelapsed
LMGene1.4800.0891.578
genediff1.5460.0101.564
glog0.0050.0020.007
lnorm0.0760.0060.084
lnormeS0.0410.0040.046
neweS0.0310.0030.034
norm0.0300.0020.032
plotMeanSD0.2010.0070.212
psmeans0.0880.0030.092
pvadjust1.4540.0111.473
rowaov1.4080.0061.420
sample.eS0.0310.0030.034
sample.ind0.0630.0020.067
sample.mat0.0380.0040.042
tranest4.4531.4075.901
tranestAffyProbeLevel25.273 5.58031.053
transeS0.0060.0010.007
vlist0.0020.0010.004