Back to Multiple platform build/check report for BioC 3.19:   simplified   long
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This page was generated on 2024-02-28 11:36:17 -0500 (Wed, 28 Feb 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_64R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences" 4671
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2024-01-14 r85805 ucrt) -- "Unsuffered Consequences" 4411
merida1macOS 12.7.1 Montereyx86_64R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences" 4438
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch64R Under development (unstable) (2024-01-16 r85812) -- "Unsuffered Consequences" 4414
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 206/2251HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
bioDist 1.75.0  (landing page)
Bioconductor Package Maintainer
Snapshot Date: 2024-02-26 14:39:26 -0500 (Mon, 26 Feb 2024)
git_url: https://git.bioconductor.org/packages/bioDist
git_branch: devel
git_last_commit: c8c15c5
git_last_commit_date: 2023-10-24 09:34:28 -0500 (Tue, 24 Oct 2023)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    OK  

CHECK results for bioDist on nebbiolo1


To the developers/maintainers of the bioDist package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/bioDist.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: bioDist
Version: 1.75.0
Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:bioDist.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings bioDist_1.75.0.tar.gz
StartedAt: 2024-02-26 20:53:28 -0500 (Mon, 26 Feb 2024)
EndedAt: 2024-02-26 20:54:05 -0500 (Mon, 26 Feb 2024)
EllapsedTime: 37.4 seconds
RetCode: 0
Status:   OK  
CheckDir: bioDist.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:bioDist.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings bioDist_1.75.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/bioDist.Rcheck’
* using R Under development (unstable) (2024-01-16 r85808)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.3 LTS
* using session charset: UTF-8
* checking for file ‘bioDist/DESCRIPTION’ ... OK
* this is package ‘bioDist’ version ‘1.75.0’
* 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 loading without being on the library search path ... OK
* checking whether startup messages can be suppressed ... 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'.

dens2func: no visible global function definition for ‘density’
dens2func : f: no visible global function definition for ‘approx’
KLD: no visible global function definition for ‘integrate’
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’
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’
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’
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:
  approx cor density dist dpih integrate locfit preplot X
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 files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.19-bioc/meat/bioDist.Rcheck/00check.log’
for details.



Installation output

bioDist.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL bioDist
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/site-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.matrix0.1480.0080.156
KLdist.matrix0.0310.0080.039
closest.top0.9200.0080.927
cor.dist0.0020.0000.001
euc0.0010.0000.000
man0.0010.0000.000
mutualInfo0.0040.0000.004
spearman.dist0.0010.0000.001
tau.dist0.0010.0000.001