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CHECK report for kimod on merida2

This page was generated on 2018-10-17 08:55:46 -0400 (Wed, 17 Oct 2018).

Package 777/1561HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
kimod 1.8.0
M L Zingaretti
Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018)
URL: https://git.bioconductor.org/packages/kimod
Branch: RELEASE_3_7
Last Commit: 573ca12
Last Changed Date: 2018-04-30 10:35:39 -0400 (Mon, 30 Apr 2018)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: kimod
Version: 1.8.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:kimod.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings kimod_1.8.0.tar.gz
StartedAt: 2018-10-16 22:14:07 -0400 (Tue, 16 Oct 2018)
EndedAt: 2018-10-16 22:15:21 -0400 (Tue, 16 Oct 2018)
EllapsedTime: 73.7 seconds
RetCode: 0
Status:  OK 
CheckDir: kimod.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:kimod.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings kimod_1.8.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.7-bioc/meat/kimod.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘kimod/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘kimod’ version ‘1.8.0’
* 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 ‘kimod’ can be installed ... 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 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 ... NOTE
Continous: no visible global function definition for ‘lm’
Continous: no visible global function definition for ‘pf’
Continous: no visible global function definition for ‘AIC’
Continous: no visible global function definition for ‘BIC’
DiStatis: no visible global function definition for ‘as.dist’
compbin: no visible global function definition for ‘na.omit’
confelli: no visible global function definition for ‘qf’
confelli: no visible global function definition for ‘runif’
dist.binary: no visible global function definition for ‘as.dist’
distan: no visible global function definition for ‘dist’
distan: no visible global function definition for ‘cor’
maha: no visible global function definition for ‘cov’
Biplot,SelectVar: no visible global function definition for ‘cutree’
BootPlot,Bootstrap: no visible global function definition for ‘cov’
BootPlot,Bootstrap: no visible global function definition for ‘rgb’
Bootstrap,DiStatis: no visible binding for global variable ‘sd’
Bootstrap,DiStatis: no visible global function definition for ‘qt’
GroupProj,SelectVar: no visible global function definition for ‘cutree’
SelectVar,DiStatis: no visible global function definition for
  ‘p.adjust’
TrajPlot,DiStatis: no visible global function definition for ‘rgb’
print,Bootstrap: no visible global function definition for ‘head’
print,DiStatis: no visible global function definition for ‘head’
print,GroupProj: no visible global function definition for ‘head’
print,SelectVar: no visible global function definition for ‘head’
Undefined global functions or variables:
  AIC BIC as.dist cor cov cutree dist head lm na.omit p.adjust pf qf qt
  rgb runif sd
Consider adding
  importFrom("grDevices", "rgb")
  importFrom("stats", "AIC", "BIC", "as.dist", "cor", "cov", "cutree",
             "dist", "lm", "na.omit", "p.adjust", "pf", "qf", "qt",
             "runif", "sd")
  importFrom("utils", "head")
to your NAMESPACE file.
* 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
DiStatis-Bootstrap 6.677  0.153   6.863
* 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: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.7-bioc/meat/kimod.Rcheck/00check.log’
for details.



Installation output

kimod.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL kimod
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘kimod’ ...
** R
** data
*** moving datasets to lazyload DB
** 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 (kimod)

Tests output


Example timings

kimod.Rcheck/kimod-Ex.timings

nameusersystemelapsed
BootPlot2.3140.1062.431
Bootstrap-Class0.0020.0000.002
Bootstrap-print.Boot2.2520.0732.336
Bootstrap-summary2.2590.0422.311
DiStatis-Bootstrap6.6770.1536.863
DiStatis-Class0.0020.0000.002
DiStatis-CompPlot0.0020.0000.002
DiStatis-DiStatis0.1280.0090.137
DiStatis-PanelPlot0.1180.0060.127
DiStatis-RVPlot0.0860.0060.092
DiStatis-SelectVar3.4520.0213.487
DiStatis-TrajPlot0.0990.0050.105
DiStatis-print0.0830.0080.091
DiStatis-summary0.9200.2601.186
GroupProj-Class0.0010.0000.002
GroupProj-print2.0160.0192.049
GroupProj-summary2.0930.0132.122
GroupProj2.0800.0122.102
NCI60Selec0.0030.0020.003
NCI60Selec_ESet0.0030.0010.004
SelectVar-Biplot2.5470.0142.590
SelectVar-Class0.0030.0000.003
SelectVar-print2.0480.0242.088
SelectVar-summary2.0430.0202.075
winesassesors0.0020.0010.002