Back to Multiple platform build/check report for BioC 3.19: simplified long |
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This page was generated on 2024-10-15 21:54 -0400 (Tue, 15 Oct 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4763 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4529 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4479 |
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 510/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
dar 1.0.0 (landing page) Francesc Catala-Moll
| nebbiolo1 | Linux (Ubuntu 22.04.3 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 | |||||||||
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: 1.0.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:dar.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings dar_1.0.0.tar.gz |
StartedAt: 2024-10-14 03:32:14 -0400 (Mon, 14 Oct 2024) |
EndedAt: 2024-10-14 04:01:46 -0400 (Mon, 14 Oct 2024) |
EllapsedTime: 1771.7 seconds |
RetCode: 0 |
Status: OK |
CheckDir: dar.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:dar.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings dar_1.0.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/dar.Rcheck’ * using R version 4.4.1 (2024-06-14) * using platform: x86_64-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 Monterey 12.7.6 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘dar/DESCRIPTION’ ... OK * this is package ‘dar’ version ‘1.0.0’ * 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 ‘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 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_ancom 39.156 1.760 53.860 step_aldex 36.015 4.508 52.916 step_deseq 16.075 0.247 20.945 step_maaslin 9.215 0.320 12.371 step_metagenomeseq 8.903 0.193 29.292 prep 6.540 0.168 105.380 step_corncob 6.370 0.237 8.697 abundance_plt 6.314 0.272 8.471 corr_heatmap 5.818 0.239 7.973 import_steps 4.784 0.180 97.658 mutual_plt 4.709 0.062 6.070 step_wilcox 4.197 0.080 5.285 export_steps 3.286 0.310 35.322 recipe 2.163 0.054 48.015 * 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 running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: OK
dar.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL dar ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’ * installing *source* package ‘dar’ ... ** 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 4.4.1 (2024-06-14) -- "Race for Your Life" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin20 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 82 ] ══ Skipped tests (10) ══════════════════════════════════════════════════════════ • On CRAN (10): 'test-roxytest-tests-bake.R:18:3', 'test-roxytest-tests-ancom.R:14:3', 'test-roxytest-tests-lefse.R:15:3', 'test-roxytest-tests-misc.R:73:3', 'test-roxytest-tests-misc.R:101:3', 'test-roxytest-tests-misc.R:108:3', 'test-roxytest-tests-pkg_check.R:6:3', 'test-roxytest-tests-maaslin2.R:16:3', 'test-roxytest-tests-read_data.R:24:3', 'test-roxytest-tests-steps_and_checks.R:7:3' [ FAIL 0 | WARN 0 | SKIP 10 | PASS 82 ] > > proc.time() user system elapsed 444.882 18.707 824.505
dar.Rcheck/dar-Ex.timings
name | user | system | elapsed | |
abundance_plt | 6.314 | 0.272 | 8.471 | |
add_tax | 0.398 | 0.014 | 0.520 | |
add_var | 0.372 | 0.013 | 0.572 | |
bake | 1.114 | 0.023 | 1.434 | |
contains_rarefaction | 0.477 | 0.026 | 0.659 | |
cool | 0.701 | 0.015 | 0.908 | |
corr_heatmap | 5.818 | 0.239 | 7.973 | |
exclusion_plt | 2.196 | 0.031 | 2.883 | |
export_steps | 3.286 | 0.310 | 35.322 | |
find_intersections | 0.398 | 0.010 | 0.471 | |
get_comparisons | 0.048 | 0.004 | 0.066 | |
get_phy | 0.040 | 0.004 | 0.052 | |
get_tax | 0.047 | 0.005 | 0.059 | |
get_var | 0.048 | 0.005 | 0.080 | |
import_steps | 4.784 | 0.180 | 97.658 | |
intersection_df | 0.411 | 0.012 | 0.505 | |
intersection_plt | 3.872 | 0.041 | 4.817 | |
mutual_plt | 4.709 | 0.062 | 6.070 | |
otu_table | 1.044 | 0.012 | 1.354 | |
overlap_df | 0.651 | 0.015 | 0.825 | |
phy_qc | 3.013 | 0.034 | 3.910 | |
prep | 6.540 | 0.168 | 105.380 | |
rand_id | 0.000 | 0.000 | 0.001 | |
read_data | 3.644 | 0.411 | 4.934 | |
recipe | 2.163 | 0.054 | 48.015 | |
required_deps | 0.096 | 0.013 | 0.121 | |
sample_data | 0.066 | 0.004 | 0.082 | |
step_aldex | 36.015 | 4.508 | 52.916 | |
step_ancom | 39.156 | 1.760 | 53.860 | |
step_corncob | 6.370 | 0.237 | 8.697 | |
step_deseq | 16.075 | 0.247 | 20.945 | |
step_filter_by_abundance | 0.081 | 0.009 | 0.108 | |
step_filter_by_prevalence | 0.085 | 0.011 | 0.147 | |
step_filter_by_rarity | 0.082 | 0.009 | 0.129 | |
step_filter_by_variance | 0.083 | 0.011 | 0.119 | |
step_filter_taxa | 0.081 | 0.010 | 0.114 | |
step_lefse | 0.143 | 0.013 | 0.200 | |
step_maaslin | 9.215 | 0.320 | 12.371 | |
step_metagenomeseq | 8.903 | 0.193 | 29.292 | |
step_rarefaction | 0.098 | 0.012 | 0.128 | |
step_subset_taxa | 0.081 | 0.009 | 0.107 | |
step_wilcox | 4.197 | 0.080 | 5.285 | |
steps_ids | 0.029 | 0.009 | 0.053 | |
tax_table | 0.105 | 0.006 | 0.136 | |
tidyeval | 0.043 | 0.006 | 0.066 | |
to_tibble | 1.181 | 0.031 | 1.572 | |
use_rarefy | 0.028 | 0.013 | 0.067 | |
zero_otu | 1.111 | 0.020 | 1.483 | |