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CHECK report for bioDist on machv2

This page was generated on 2020-10-17 11:58:07 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE bioDist PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 171/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
bioDist 1.60.0
Bioconductor Package Maintainer
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/bioDist
Branch: RELEASE_3_11
Last Commit: 32d5806
Last Changed Date: 2020-04-27 14:10:44 -0400 (Mon, 27 Apr 2020)
malbec2 Linux (Ubuntu 18.04.4 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
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: bioDist
Version: 1.60.0
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_1.60.0.tar.gz
StartedAt: 2020-10-16 23:06:38 -0400 (Fri, 16 Oct 2020)
EndedAt: 2020-10-16 23:07:21 -0400 (Fri, 16 Oct 2020)
EllapsedTime: 43.4 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_1.60.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/bioDist.Rcheck’
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘bioDist/DESCRIPTION’ ... OK
* this is package ‘bioDist’ version ‘1.60.0’
* 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
* 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-3.11-bioc/meat/bioDist.Rcheck/00check.log’
for details.



Installation output

bioDist.Rcheck/00install.out

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL bioDist
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’
* installing *source* package ‘bioDist’ ...
** using staged installation
** 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 from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (bioDist)

Tests output


Example timings

bioDist.Rcheck/bioDist-Ex.timings

nameusersystemelapsed
KLD.matrix0.2140.0280.271
KLdist.matrix0.0660.0030.068
closest.top2.1590.0332.202
cor.dist0.0010.0000.002
euc0.0010.0010.001
man0.0010.0000.001
mutualInfo0.0080.0000.009
spearman.dist0.0010.0000.002
tau.dist0.0020.0010.003