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CHECK report for bioDist on merida1

This page was generated on 2019-04-16 11:54:13 -0400 (Tue, 16 Apr 2019).

Package 149/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
bioDist 1.54.0
Bioconductor Package Maintainer
Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019)
URL: https://git.bioconductor.org/packages/bioDist
Branch: RELEASE_3_8
Last Commit: a0f74b8
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: bioDist
Version: 1.54.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:bioDist.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings bioDist_1.54.0.tar.gz
StartedAt: 2019-04-15 22:36:46 -0400 (Mon, 15 Apr 2019)
EndedAt: 2019-04-15 22:37:24 -0400 (Mon, 15 Apr 2019)
EllapsedTime: 37.7 seconds
RetCode: 0
Status:  OK 
CheckDir: bioDist.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:bioDist.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings bioDist_1.54.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/bioDist.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 ‘bioDist/DESCRIPTION’ ... OK
* this is package ‘bioDist’ version ‘1.54.0’
* 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 ‘bioDist’ 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 ... NOTE
'library' or 'require' call to ‘methods’ which was already attached by Depends.
  Please remove these calls from your code.
'library' or 'require' call to ‘locfit’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Package in Depends field not imported from: ‘KernSmooth’
  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
File ‘bioDist/R/zzz.R’:
  .onLoad calls:
    require("methods")

Package startup functions should not change the search path.
See section ‘Good practice’ in '?.onAttach'.

KLD: no visible global function definition for ‘integrate’
dens2func: no visible global function definition for ‘density’
dens2func : f: no visible global function definition for ‘approx’
locf2func: no visible global function definition for ‘locfit’
locf2func: no visible global function definition for ‘preplot’
locf2func : f: no visible global function definition for ‘approx’
KLdist.matrix,list : interpfunc : f: no visible global function
  definition for ‘approx’
KLdist.matrix,list: no visible global function definition for ‘dpih’
KLdist.matrix,matrix : interpfunc : f: no visible global function
  definition for ‘approx’
KLdist.matrix,matrix: no visible global function definition for ‘dpih’
cor.dist,matrix: no visible global function definition for ‘cor’
euc,eSet: no visible binding for global variable ‘X’
euc,matrix: no visible global function definition for ‘dist’
man,matrix: no visible global function definition for ‘dist’
spearman.dist,matrix: no visible global function definition for ‘cor’
tau.dist,matrix: no visible global function definition for ‘cor’
Undefined global functions or variables:
  X approx cor density dist dpih integrate locfit preplot
Consider adding
  importFrom("stats", "approx", "cor", "density", "dist", "integrate",
             "preplot")
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 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
closest.top 4.924  0.047    5.02
* 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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.8-bioc/meat/bioDist.Rcheck/00check.log’
for details.



Installation output

bioDist.Rcheck/00install.out

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL bioDist
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘bioDist’ ...
** R
** 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 (bioDist)

Tests output


Example timings

bioDist.Rcheck/bioDist-Ex.timings

nameusersystemelapsed
KLD.matrix0.4180.0180.439
KLdist.matrix0.0580.0020.059
closest.top4.9240.0475.020
cor.dist0.0010.0000.001
euc0.0010.0000.001
man0.0000.0000.001
mutualInfo0.0050.0000.006
spearman.dist0.0010.0000.001
tau.dist0.0010.0010.001