Multiple platform build/check report for BioC 3.20 - CHECK results for bioDist on nebbiolo2

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 24.04.1 LTS)	x86_64	4.4.2 (2024-10-31) -- "Pile of Leaves"	4744
palomino8	Windows Server 2022 Datacenter	x64	4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves"	4487
merida1	macOS 12.7.5 Monterey	x86_64	4.4.2 (2024-10-31) -- "Pile of Leaves"	4515
kjohnson1	macOS 13.6.6 Ventura	arm64	4.4.2 (2024-10-31) -- "Pile of Leaves"	4467
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*

CHECK results for bioDist on nebbiolo2

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: 1.78.0

Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:bioDist.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings bioDist_1.78.0.tar.gz

StartedAt: 2024-12-19 20:39:01 -0500 (Thu, 19 Dec 2024)

EndedAt: 2024-12-19 20:43:17 -0500 (Thu, 19 Dec 2024)

EllapsedTime: 255.3 seconds

RetCode: 0

Status: OK

CheckDir: bioDist.Rcheck

Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:bioDist.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings bioDist_1.78.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/bioDist.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
    GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* checking for file ‘bioDist/DESCRIPTION’ ... OK
* this is package ‘bioDist’ version ‘1.78.0’
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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 code 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'.

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 ... NOTE
checkRd: (-1) KLD.matrix.Rd:19-20: Lost braces in \itemize; meant \describe ?
checkRd: (-1) KLD.matrix.Rd:21-23: Lost braces in \itemize; meant \describe ?
checkRd: (-1) KLD.matrix.Rd:24: Lost braces in \itemize; meant \describe ?
checkRd: (-1) KLD.matrix.Rd:25-26: Lost braces in \itemize; meant \describe ?
checkRd: (-1) KLD.matrix.Rd:27-28: Lost braces in \itemize; meant \describe ?
checkRd: (-1) KLD.matrix.Rd:29-30: Lost braces in \itemize; meant \describe ?
checkRd: (-1) cor.dist.Rd:18: Lost braces in \itemize; meant \describe ?
checkRd: (-1) cor.dist.Rd:19-20: Lost braces in \itemize; meant \describe ?
checkRd: (-1) cor.dist.Rd:21-22: Lost braces in \itemize; meant \describe ?
checkRd: (-1) cor.dist.Rd:23-25: Lost braces in \itemize; meant \describe ?
checkRd: (-1) euc.Rd:20-21: Lost braces in \itemize; meant \describe ?
checkRd: (-1) euc.Rd:22-23: Lost braces in \itemize; meant \describe ?
checkRd: (-1) euc.Rd:24-26: Lost braces in \itemize; meant \describe ?
checkRd: (-1) man.Rd:16-17: Lost braces in \itemize; meant \describe ?
checkRd: (-1) man.Rd:18-19: Lost braces in \itemize; meant \describe ?
checkRd: (-1) mutualInfo.Rd:20-21: Lost braces in \itemize; meant \describe ?
checkRd: (-1) mutualInfo.Rd:22-23: Lost braces in \itemize; meant \describe ?
checkRd: (-1) mutualInfo.Rd:24-25: Lost braces in \itemize; meant \describe ?
checkRd: (-1) mutualInfo.Rd:26-27: Lost braces in \itemize; meant \describe ?
checkRd: (-1) spearman.dist.Rd:17: Lost braces in \itemize; meant \describe ?
checkRd: (-1) spearman.dist.Rd:18-19: Lost braces in \itemize; meant \describe ?
checkRd: (-1) spearman.dist.Rd:20-21: Lost braces in \itemize; meant \describe ?
checkRd: (-1) spearman.dist.Rd:22-23: Lost braces in \itemize; meant \describe ?
checkRd: (-1) tau.dist.Rd:19: Lost braces in \itemize; meant \describe ?
checkRd: (-1) tau.dist.Rd:20-21: Lost braces in \itemize; meant \describe ?
checkRd: (-1) tau.dist.Rd:22-23: Lost braces in \itemize; meant \describe ?
checkRd: (-1) tau.dist.Rd:24-25: Lost braces in \itemize; meant \describe ?
* 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: 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.20-bioc/meat/bioDist.Rcheck/00check.log’
for details.

Installation output

bioDist.Rcheck/00install.out

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### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL bioDist
###
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* installing to library ‘/home/biocbuild/bbs-3.20-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

name	user	system	elapsed
KLD.matrix	0.132	0.004	0.136
KLdist.matrix	0.027	0.006	0.034
closest.top	0.848	0.014	0.861
cor.dist	0.001	0.000	0.001
euc	0.001	0.000	0.000
man	0.001	0.001	0.000
mutualInfo	0.003	0.000	0.004
spearman.dist	0.000	0.000	0.001
tau.dist	0.000	0.000	0.001