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BioC 3.6: CHECK report for LMGene on veracruz1

This page was generated on 2017-08-16 13:39:06 -0400 (Wed, 16 Aug 2017).

Package 730/1410HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
LMGene 2.33.0
Blythe Durbin-Johnson
Snapshot Date: 2017-08-15 17:18:21 -0400 (Tue, 15 Aug 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/LMGene
Last Changed Rev: 129129 / Revision: 131943
Last Changed Date: 2017-04-24 15:50:57 -0400 (Mon, 24 Apr 2017)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
veracruz1 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: LMGene
Version: 2.33.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings LMGene_2.33.0.tar.gz
StartedAt: 2017-08-16 04:55:37 -0400 (Wed, 16 Aug 2017)
EndedAt: 2017-08-16 04:57:37 -0400 (Wed, 16 Aug 2017)
EllapsedTime: 119.8 seconds
RetCode: 0
Status:  OK 
CheckDir: LMGene.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings LMGene_2.33.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/LMGene.Rcheck’
* using R version 3.4.1 (2017-06-30)
* 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 ‘2.33.0’
* 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 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 ‘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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                        user system elapsed
tranestAffyProbeLevel 36.792  3.550  41.386
tranest                5.228  0.941   6.348
* 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-3.6-bioc/meat/LMGene.Rcheck/00check.log’
for details.


LMGene.Rcheck/00install.out:

* 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)

LMGene.Rcheck/LMGene-Ex.timings:

nameusersystemelapsed
LMGene1.5440.0301.620
genediff1.4080.0051.458
glog0.0040.0010.005
lnorm0.0710.0040.076
lnormeS0.0650.0040.070
neweS0.0360.0030.039
norm0.0370.0020.041
plotMeanSD0.1480.0030.153
psmeans0.0670.0030.071
pvadjust1.2320.0091.269
rowaov1.0230.0041.057
sample.eS0.0360.0030.039
sample.ind0.1150.0030.128
sample.mat0.0300.0020.033
tranest5.2280.9416.348
tranestAffyProbeLevel36.792 3.55041.386
transeS0.0070.0010.008
vlist0.0030.0010.004