Back to Multiple platform build/check report for BioC 3.21: simplified long |
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This page was generated on 2025-10-13 11:37 -0400 (Mon, 13 Oct 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4833 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.5.1 RC (2025-06-05 r88288) -- "Great Square Root" | 4614 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4555 |
kunpeng2 | Linux (openEuler 24.03 LTS) | aarch64 | R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" | 4586 |
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 516/2341 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
dar 1.4.0 (landing page) Francesc Catala-Moll
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | ![]() | ||||||||
kunpeng2 | Linux (openEuler 24.03 LTS) / aarch64 | OK | ERROR | skipped | ||||||||||
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: 1.4.0 |
Command: /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:dar.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings dar_1.4.0.tar.gz |
StartedAt: 2025-10-12 22:23:42 -0400 (Sun, 12 Oct 2025) |
EndedAt: 2025-10-12 22:38:55 -0400 (Sun, 12 Oct 2025) |
EllapsedTime: 913.1 seconds |
RetCode: 0 |
Status: OK |
CheckDir: dar.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:dar.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings dar_1.4.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.21-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 ‘1.4.0’ * 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 16.213 0.719 16.933 prep 6.835 0.684 44.600 step_deseq 6.032 0.061 6.093 import_steps 4.220 0.460 37.826 step_metagenomeseq 3.394 0.022 9.542 recipe 2.805 0.307 18.828 export_steps 2.759 0.239 13.508 * 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-3.21-bioc/R/bin/R CMD INSTALL dar ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-library’ * installing *source* package ‘dar’ ... ** this is package ‘dar’ version ‘1.4.0’ ** 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 3 | 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 3 | SKIP 10 | PASS 81 ] > > proc.time() user system elapsed 217.621 11.134 259.961
dar.Rcheck/dar-Ex.timings
name | user | system | elapsed | |
abundance_plt | 2.771 | 0.084 | 2.863 | |
add_tax | 0.167 | 0.001 | 0.169 | |
add_var | 0.162 | 0.003 | 0.164 | |
bake | 0.448 | 0.003 | 0.451 | |
contains_rarefaction | 0.743 | 0.022 | 0.767 | |
cool | 0.274 | 0.014 | 0.287 | |
corr_heatmap | 4.761 | 0.140 | 4.902 | |
exclusion_plt | 1.056 | 0.001 | 1.058 | |
export_steps | 2.759 | 0.239 | 13.508 | |
find_intersections | 0.169 | 0.000 | 0.170 | |
get_comparisons | 0.026 | 0.007 | 0.033 | |
get_phy | 0.019 | 0.003 | 0.022 | |
get_tax | 0.026 | 0.001 | 0.027 | |
get_var | 0.024 | 0.002 | 0.026 | |
import_steps | 4.220 | 0.460 | 37.826 | |
intersection_df | 0.166 | 0.003 | 0.170 | |
intersection_plt | 2.169 | 0.069 | 2.238 | |
mutual_plt | 2.436 | 0.051 | 2.487 | |
otu_table | 0.423 | 0.030 | 0.452 | |
overlap_df | 0.295 | 0.019 | 0.315 | |
phy_qc | 1.205 | 0.034 | 1.238 | |
prep | 6.835 | 0.684 | 44.600 | |
rand_id | 0 | 0 | 0 | |
read_data | 1.285 | 0.599 | 1.897 | |
recipe | 2.805 | 0.307 | 18.828 | |
required_deps | 0.050 | 0.003 | 0.053 | |
sample_data | 0.034 | 0.000 | 0.034 | |
step_aldex | 16.213 | 0.719 | 16.933 | |
step_ancom | 0 | 0 | 0 | |
step_corncob | 1.988 | 0.016 | 2.004 | |
step_deseq | 6.032 | 0.061 | 6.093 | |
step_filter_by_abundance | 0.038 | 0.002 | 0.041 | |
step_filter_by_prevalence | 0.039 | 0.000 | 0.039 | |
step_filter_by_rarity | 0.039 | 0.000 | 0.039 | |
step_filter_by_variance | 0.042 | 0.000 | 0.043 | |
step_filter_taxa | 0.039 | 0.002 | 0.042 | |
step_lefse | 0.066 | 0.003 | 0.069 | |
step_maaslin | 3.089 | 0.059 | 3.148 | |
step_metagenomeseq | 3.394 | 0.022 | 9.542 | |
step_rarefaction | 0.047 | 0.003 | 0.050 | |
step_subset_taxa | 0.036 | 0.002 | 0.038 | |
step_wilcox | 1.825 | 0.008 | 1.834 | |
steps_ids | 0.015 | 0.002 | 0.016 | |
tax_table | 0.046 | 0.001 | 0.047 | |
tidyeval | 0.014 | 0.000 | 0.014 | |
to_tibble | 0.442 | 0.000 | 0.442 | |
use_rarefy | 0.016 | 0.000 | 0.016 | |
zero_otu | 0.389 | 0.001 | 0.390 | |