Multiple platform build/check report for BioC 3.20 - CHECK results for RedeR on kjohnson3

Hostname	OS	Arch (*)	R version	Installed pkgs
teran2	Linux (Ubuntu 24.04.1 LTS)	x86_64	4.4.1 (2024-06-14) -- "Race for Your Life"	4501
nebbiolo2	Linux (Ubuntu 24.04.1 LTS)	x86_64	4.4.1 (2024-06-14) -- "Race for Your Life"	4761
palomino8	Windows Server 2022 Datacenter	x64	4.4.1 (2024-06-14 ucrt) -- "Race for Your Life"	4504
lconway	macOS 12.7.1 Monterey	x86_64	4.4.1 (2024-06-14) -- "Race for Your Life"	4535
kjohnson3	macOS 13.6.5 Ventura	arm64	4.4.1 (2024-06-14) -- "Race for Your Life"	4483
kunpeng2	Linux (openEuler 22.03 LTS-SP1)	aarch64	4.4.1 (2024-06-14) -- "Race for Your Life"	4491
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 RedeR on kjohnson3

To the developers/maintainers of the RedeR package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/RedeR.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: RedeR

Version: 3.1.0

Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:RedeR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings RedeR_3.1.0.tar.gz

StartedAt: 2024-10-27 23:58:29 -0400 (Sun, 27 Oct 2024)

EndedAt: 2024-10-28 00:02:28 -0400 (Mon, 28 Oct 2024)

EllapsedTime: 238.4 seconds

RetCode: 0

Status: OK

CheckDir: RedeR.Rcheck

Warnings: 0

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:RedeR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings RedeR_3.1.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/RedeR.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.6.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘RedeR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘RedeR’ version ‘3.1.0’
* package encoding: UTF-8
* 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 ‘RedeR’ 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 whether startup messages can be suppressed ... 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 ... OK
* checking Rd files ... NOTE
checkRd: (-1) nestNodes-methods.Rd:47: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nestNodes-methods.Rd:48: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nestNodes-methods.Rd:49: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nestNodes-methods.Rd:50: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nestNodes-methods.Rd:51: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nestNodes-methods.Rd:52: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nestNodes-methods.Rd:53-54: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nestNodes-methods.Rd:55: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nestNodes-methods.Rd:56: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nestNodes-methods.Rd:57: Lost braces in \itemize; meant \describe ?
checkRd: (-1) startRedeR.Rd:24: Lost braces in \itemize; meant \describe ?
checkRd: (-1) startRedeR.Rd:25: Lost braces in \itemize; meant \describe ?
checkRd: (-1) startRedeR.Rd:26: Lost braces in \itemize; meant \describe ?
checkRd: (-1) startRedeR.Rd:27: Lost braces in \itemize; meant \describe ?
checkRd: (-1) startRedeR.Rd:28: Lost braces in \itemize; meant \describe ?
checkRd: (-1) startRedeR.Rd:29: Lost braces in \itemize; meant \describe ?
checkRd: (-1) startRedeR.Rd:30: Lost braces in \itemize; meant \describe ?
checkRd: (-1) startRedeR.Rd:31: Lost braces in \itemize; meant \describe ?
checkRd: (-1) startRedeR.Rd:32: Lost braces in \itemize; meant \describe ?
checkRd: (-1) startRedeR.Rd:33: Lost braces in \itemize; meant \describe ?
checkRd: (-1) startRedeR.Rd:34: Lost braces in \itemize; meant \describe ?
checkRd: (-1) startRedeR.Rd:35: Lost braces in \itemize; meant \describe ?
checkRd: (-1) startRedeR.Rd:36: Lost braces in \itemize; meant \describe ?
checkRd: (-1) startRedeR.Rd:37: Lost braces in \itemize; meant \describe ?
checkRd: (-1) startRedeR.Rd:38: 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.20-bioc/meat/RedeR.Rcheck/00check.log’
for details.

Installation output

RedeR.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL RedeR
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library’
* installing *source* package ‘RedeR’ ...
** using staged installation
** R
** data
** inst
** 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 (RedeR)

Tests output

Example timings

RedeR.Rcheck/RedeR-Ex.timings

name	user	system	elapsed
Deprecated	0	0	0
RedPort	0.001	0.000	0.001
RedeR-data1	0.022	0.002	0.023
RedeR-data2	0.009	0.001	0.009
addEdges-methods	0.004	0.000	0.004
addGraph-methods	0.031	0.003	0.033
addGraphToRedeR	0.004	0.000	0.004
addLegendToRedeR	0	0	0
addNodes-methods	0.002	0.000	0.003
calld-methods	0.001	0.000	0.001
deleteEdges-methods	0.002	0.001	0.003
deleteNodes-methods	0.002	0.000	0.003
exitRedeR	0	0	0
exitd-methods	0.001	0.000	0.000
getGraph-methods	0.003	0.001	0.004
getGraphFromRedeR	0.003	0.000	0.003
mergeOutEdges-methods	0.006	0.001	0.007
nestNodes-methods	0.010	0.001	0.010
ping-methods	0	0	0
pingRedeR	0	0	0
relax-methods	0.003	0.000	0.004
relaxRedeR	0.003	0.001	0.003
resetRedeR	0	0	0
resetd-methods	0	0	0
selectEdges-methods	0.003	0.000	0.003
selectNodes-methods	0.003	0.001	0.003
startRedeR	0	0	0
subg	0	0	0
transform.attributes	0.007	0.000	0.007
updateLayoutFromRedeR	0.003	0.001	0.004
version-methods	0.001	0.000	0.001