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BioC 3.5: CHECK report for kimod on toluca2

This page was generated on 2017-04-23 14:41:03 -0400 (Sun, 23 Apr 2017).

Package 704/1377HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
kimod 1.3.0
M L Zingaretti
Snapshot Date: 2017-04-22 17:18:01 -0400 (Sat, 22 Apr 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/kimod
Last Changed Rev: 122712 / Revision: 129046
Last Changed Date: 2016-10-17 15:10:43 -0400 (Mon, 17 Oct 2016)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
toluca2 Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK [ OK ] OK 
veracruz2 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: kimod
Version: 1.3.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings kimod_1.3.0.tar.gz
StartedAt: 2017-04-23 05:49:29 -0400 (Sun, 23 Apr 2017)
EndedAt: 2017-04-23 05:50:42 -0400 (Sun, 23 Apr 2017)
EllapsedTime: 73.2 seconds
RetCode: 0
Status:  OK 
CheckDir: kimod.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings kimod_1.3.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/kimod.Rcheck’
* using R Under development (unstable) (2017-02-15 r72187)
* using platform: x86_64-apple-darwin13.4.0 (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 ‘1.3.0’
* 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 loading without being on the library search path ... 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
DiStatis-Bootstrap 5.719  0.059   5.818
* 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-3.5-bioc/meat/kimod.Rcheck/00check.log’
for details.


kimod.Rcheck/00install.out:

* installing *source* package ‘kimod’ ...
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (kimod)

kimod.Rcheck/kimod-Ex.timings:

nameusersystemelapsed
BootPlot2.1590.0442.217
Bootstrap-Class0.0020.0000.002
Bootstrap-print.Boot2.5880.0242.616
Bootstrap-summary1.7880.0211.812
DiStatis-Bootstrap5.7190.0595.818
DiStatis-Class0.0010.0000.001
DiStatis-CompPlot0.0010.0000.000
DiStatis-DiStatis0.1330.0040.136
DiStatis-PanelPlot0.1290.0060.138
DiStatis-RVPlot0.0790.0040.083
DiStatis-SelectVar4.4070.0164.432
DiStatis-TrajPlot0.1310.0050.136
DiStatis-print0.1190.0080.127
DiStatis-summary0.9940.2071.204
GroupProj-Class000
GroupProj-print2.1990.0152.216
GroupProj-summary2.3560.0152.374
GroupProj2.4520.0122.467
NCI60Selec0.0020.0010.002
NCI60Selec_ESet0.0020.0010.002
SelectVar-Biplot2.7770.0142.800
SelectVar-Class0.0010.0000.001
SelectVar-print2.3140.0162.339
SelectVar-summary1.9720.0111.984
winesassesors0.0020.0010.001