Back to Multiple platform build/check report for BioC 3.22: simplified long |
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This page was generated on 2025-08-30 12:04 -0400 (Sat, 30 Aug 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4824 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4615 |
kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4562 |
taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4541 |
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 513/2320 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
dar 1.5.0 (landing page) Francesc Catala-Moll
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
lconway | macOS 12.7.1 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 | OK | OK | ||||||||||
To the developers/maintainers of the dar package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/dar.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: dar |
Version: 1.5.0 |
Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:dar.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings dar_1.5.0.tar.gz |
StartedAt: 2025-08-29 21:51:51 -0400 (Fri, 29 Aug 2025) |
EndedAt: 2025-08-29 22:05:34 -0400 (Fri, 29 Aug 2025) |
EllapsedTime: 823.8 seconds |
RetCode: 0 |
Status: OK |
CheckDir: dar.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:dar.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings dar_1.5.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/dar.Rcheck’ * using R version 4.5.1 (2025-06-13) * 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 ‘dar/DESCRIPTION’ ... OK * this is package ‘dar’ version ‘1.5.0’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... INFO Imports includes 21 non-default packages. Importing from so many packages makes the package vulnerable to any of them becoming unavailable. Move as many as possible to Suggests and use conditionally. * 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 ‘dar’ 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 ... OK * 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 R/sysdata.rda ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed step_aldex 16.056 0.457 16.513 prep 5.946 0.402 39.325 step_deseq 5.723 0.041 5.764 import_steps 3.815 0.347 32.785 step_metagenomeseq 3.111 0.113 9.023 export_steps 2.640 0.218 12.766 recipe 2.207 0.211 16.583 * 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: OK
dar.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL dar ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’ * installing *source* package ‘dar’ ... ** this is package ‘dar’ version ‘1.5.0’ ** using staged installation ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** 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 (dar)
dar.Rcheck/tests/testthat.Rout
R version 4.5.1 (2025-06-13) -- "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. > library(testthat) > library(dar) > > test_check("dar") Starting 2 test processes [ FAIL 0 | WARN 0 | SKIP 10 | PASS 81 ] ══ Skipped tests (10) ══════════════════════════════════════════════════════════ • On CRAN (9): 'test-roxytest-tests-bake.R:18:3', 'test-roxytest-tests-lefse.R:15:3', 'test-roxytest-tests-maaslin2.R:16:3', 'test-roxytest-tests-pkg_check.R:6:3', 'test-roxytest-tests-misc.R:73:3', 'test-roxytest-tests-misc.R:101:3', 'test-roxytest-tests-misc.R:108:3', 'test-roxytest-tests-read_data.R:24:3', 'test-roxytest-tests-steps_and_checks.R:7:3' • Temporary disabling due to problems with the ANCOM package (1): 'test-roxytest-tests-ancom.R:6:3' [ FAIL 0 | WARN 0 | SKIP 10 | PASS 81 ] > > proc.time() user system elapsed 200.413 11.396 243.664
dar.Rcheck/dar-Ex.timings
name | user | system | elapsed | |
abundance_plt | 2.450 | 0.052 | 2.503 | |
add_tax | 0.169 | 0.002 | 0.171 | |
add_var | 0.148 | 0.001 | 0.149 | |
bake | 0.446 | 0.029 | 0.475 | |
contains_rarefaction | 0.275 | 0.015 | 0.290 | |
cool | 0.274 | 0.000 | 0.274 | |
corr_heatmap | 3.340 | 0.103 | 3.443 | |
exclusion_plt | 0.847 | 0.016 | 0.863 | |
export_steps | 2.640 | 0.218 | 12.766 | |
find_intersections | 0.167 | 0.000 | 0.167 | |
get_comparisons | 0.026 | 0.000 | 0.026 | |
get_phy | 0.019 | 0.001 | 0.020 | |
get_tax | 0.025 | 0.000 | 0.025 | |
get_var | 0.025 | 0.000 | 0.025 | |
import_steps | 3.815 | 0.347 | 32.785 | |
intersection_df | 0.166 | 0.012 | 0.178 | |
intersection_plt | 1.497 | 0.073 | 1.569 | |
mutual_plt | 1.826 | 0.056 | 1.882 | |
otu_table | 0.399 | 0.028 | 0.427 | |
overlap_df | 0.254 | 0.012 | 0.265 | |
phy_qc | 1.114 | 0.055 | 1.168 | |
prep | 5.946 | 0.402 | 39.325 | |
rand_id | 0 | 0 | 0 | |
read_data | 1.125 | 0.554 | 1.694 | |
recipe | 2.207 | 0.211 | 16.583 | |
required_deps | 0.050 | 0.001 | 0.051 | |
sample_data | 0.031 | 0.000 | 0.031 | |
step_aldex | 16.056 | 0.457 | 16.513 | |
step_ancom | 0.000 | 0.000 | 0.001 | |
step_corncob | 1.825 | 0.037 | 1.863 | |
step_deseq | 5.723 | 0.041 | 5.764 | |
step_filter_by_abundance | 0.035 | 0.004 | 0.039 | |
step_filter_by_prevalence | 0.037 | 0.001 | 0.038 | |
step_filter_by_rarity | 0.036 | 0.001 | 0.037 | |
step_filter_by_variance | 0.037 | 0.004 | 0.040 | |
step_filter_taxa | 0.035 | 0.002 | 0.037 | |
step_lefse | 0.059 | 0.003 | 0.062 | |
step_maaslin | 2.919 | 0.089 | 3.010 | |
step_metagenomeseq | 3.111 | 0.113 | 9.023 | |
step_rarefaction | 0.046 | 0.003 | 0.049 | |
step_subset_taxa | 0.171 | 0.007 | 0.178 | |
step_wilcox | 1.611 | 0.027 | 1.639 | |
steps_ids | 0.016 | 0.000 | 0.017 | |
tax_table | 0.047 | 0.000 | 0.048 | |
tidyeval | 0.013 | 0.000 | 0.014 | |
to_tibble | 0.367 | 0.003 | 0.370 | |
use_rarefy | 0.015 | 0.000 | 0.015 | |
zero_otu | 0.406 | 0.001 | 0.408 | |