| Back to Multiple platform build/check report for BioC 3.23: simplified long |
|
This page was generated on 2026-04-29 10:14 -0400 (Wed, 29 Apr 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.4 LTS) | x86_64 | 4.6.0 RC (2026-04-17 r89917) -- "Because it was There" | 4988 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.6.0 Patched (2026-04-24 r89963) -- "Because it was There" | 4694 |
| 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 218/2415 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| bioDist 1.84.0 (landing page) Bioconductor Package Maintainer
| nebbiolo1 | Linux (Ubuntu 24.04.4 LTS) / x86_64 | OK | OK | OK |  | ||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| See other builds for bioDist in R Universe. | ||||||||||||||
|
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. |
| Package: bioDist |
| Version: 1.84.0 |
| Command: /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:bioDist.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings bioDist_1.84.0.tar.gz |
| StartedAt: 2026-04-28 22:10:37 -0400 (Tue, 28 Apr 2026) |
| EndedAt: 2026-04-28 22:11:14 -0400 (Tue, 28 Apr 2026) |
| EllapsedTime: 36.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: bioDist.Rcheck |
| Warnings: 0 |
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### Running command:
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### /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:bioDist.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings bioDist_1.84.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.23-bioc/meat/bioDist.Rcheck’
* using R version 4.6.0 RC (2026-04-17 r89917)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0
GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0
* running under: Ubuntu 24.04.4 LTS
* using session charset: UTF-8
* current time: 2026-04-29 02:10:38 UTC
* checking for file ‘bioDist/DESCRIPTION’ ... OK
* this is package ‘bioDist’ version ‘1.84.0’
* 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 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 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
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 sizes of PDF files under ‘inst/doc’ ...* 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-3.23-bioc/meat/bioDist.Rcheck/00check.log’
for details.
bioDist.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD INSTALL bioDist ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.23-bioc/R/site-library’ * installing *source* package ‘bioDist’ ... ** this is package ‘bioDist’ version ‘1.84.0’ ** 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)
bioDist.Rcheck/bioDist-Ex.timings
| name | user | system | elapsed | |
| KLD.matrix | 0.168 | 0.005 | 0.174 | |
| KLdist.matrix | 0.035 | 0.005 | 0.039 | |
| closest.top | 0.930 | 0.010 | 0.939 | |
| cor.dist | 0.000 | 0.001 | 0.001 | |
| euc | 0.001 | 0.001 | 0.001 | |
| man | 0.000 | 0.000 | 0.001 | |
| mutualInfo | 0.003 | 0.002 | 0.004 | |
| spearman.dist | 0.000 | 0.000 | 0.001 | |
| tau.dist | 0.001 | 0.000 | 0.001 | |