Martha Luka
| Snapshot Date: 2025-10-24 13:45 -0400 (Fri, 24 Oct 2025) |
| git_url: https://git.bioconductor.org/packages/rhinotypeR |
| git_branch: devel |
| git_last_commit: cd2e13f |
| git_last_commit_date: 2025-10-21 12:08:48 -0400 (Tue, 21 Oct 2025) |
| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-10-25 12:04 -0400 (Sat, 25 Oct 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" | 4901 |
| lconway | macOS 12.7.6 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4691 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4637 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4658 |
| 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 1792/2361 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| rhinotypeR 1.3.1 (landing page) Martha Luka
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.6 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | NA | NA | ||||||||||
|
To the developers/maintainers of the rhinotypeR package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/rhinotypeR.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: rhinotypeR |
| Version: 1.3.1 |
| Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:rhinotypeR.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings rhinotypeR_1.3.1.tar.gz |
| StartedAt: 2025-10-25 03:22:13 -0400 (Sat, 25 Oct 2025) |
| EndedAt: 2025-10-25 03:29:34 -0400 (Sat, 25 Oct 2025) |
| EllapsedTime: 440.5 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: rhinotypeR.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:rhinotypeR.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings rhinotypeR_1.3.1.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/rhinotypeR.Rcheck’
* using R version 4.5.1 Patched (2025-08-23 r88802)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘rhinotypeR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘rhinotypeR’ version ‘1.3.1’
* package encoding: UTF-8
* 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 ‘rhinotypeR’ 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
assignTypes: no visible binding for global variable ‘prototypes’
Undefined global functions or variables:
prototypes
* 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 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
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
alignToRefs 78.561 0.085 78.651
overallMeanDistance 5.621 0.057 5.676
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
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: 1 NOTE
See
‘/home/biocbuild/bbs-3.22-bioc/meat/rhinotypeR.Rcheck/00check.log’
for details.
rhinotypeR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL rhinotypeR ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’ * installing *source* package ‘rhinotypeR’ ... ** this is package ‘rhinotypeR’ version ‘1.3.1’ ** 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 (rhinotypeR)
rhinotypeR.Rcheck/tests/testthat.Rout
R version 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
> # * https://testthat.r-lib.org/articles/special-files.html
>
> library(testthat)
> library(rhinotypeR)
>
> test_check("rhinotypeR")
use default substitution matrix
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[ FAIL 0 | WARN 0 | SKIP 0 | PASS 140 ]
>
> proc.time()
user system elapsed
237.836 0.869 238.690
rhinotypeR.Rcheck/rhinotypeR-Ex.timings
| name | user | system | elapsed | |
| SNPeek-internal | 0.000 | 0.000 | 0.001 | |
| SNPeek | 0.535 | 0.011 | 0.545 | |
| alignToRefs | 78.561 | 0.085 | 78.651 | |
| assignTypes | 0 | 0 | 0 | |
| countSNPs | 0.000 | 0.000 | 0.001 | |
| getPrototypeSeqs | 0.001 | 0.000 | 0.000 | |
| overallMeanDistance | 5.621 | 0.057 | 5.676 | |
| pairwiseDistances | 0.000 | 0.000 | 0.001 | |
| plotAA | 0.061 | 0.001 | 0.061 | |
| plotDistances | 3.880 | 0.038 | 3.918 | |
| plotFrequency | 3.384 | 0.005 | 3.389 | |
| plotTree | 3.260 | 0.001 | 3.261 | |
| rhinovirusPrototypesVP4 | 0.033 | 0.002 | 0.035 | |
| rhinovirusVP4 | 0.021 | 0.001 | 0.021 | |