Back to Multiple platform build/check report for BioC 3.19: simplified long |
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This page was generated on 2024-03-04 11:39:04 -0500 (Mon, 04 Mar 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences" | 4676 |
palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-01-14 r85805 ucrt) -- "Unsuffered Consequences" | 4414 |
merida1 | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences" | 4441 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-01-16 r85812) -- "Unsuffered Consequences" | 4417 |
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 503/2251 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
dar 0.99.9 (landing page) Francesc Catala-Moll
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | ![]() | ||||||||
merida1 | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / 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: 0.99.9 |
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_0.99.9.tar.gz |
StartedAt: 2024-03-02 02:38:42 -0500 (Sat, 02 Mar 2024) |
EndedAt: 2024-03-02 03:05:43 -0500 (Sat, 02 Mar 2024) |
EllapsedTime: 1621.8 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_0.99.9.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/dar.Rcheck’ * using R Under development (unstable) (2024-01-16 r85808) * 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 12.7.1 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘dar/DESCRIPTION’ ... OK * this is package ‘dar’ version ‘0.99.9’ * 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 R 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_aldex 34.045 4.056 48.910 step_ancom 36.284 1.754 48.711 step_deseq 15.472 0.270 19.859 step_metagenomeseq 8.472 0.181 26.312 step_maaslin 7.213 0.263 9.568 corr_heatmap 5.799 0.315 29.934 prep 5.870 0.177 101.326 abundance_plt 5.805 0.225 7.154 mutual_plt 4.318 0.060 5.058 import_steps 4.191 0.173 83.326 export_steps 3.100 0.319 32.475 recipe 2.053 0.056 46.866 * 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 Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences" 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 80 ] ══ 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 80 ] > > proc.time() user system elapsed 409.847 19.584 744.593
dar.Rcheck/dar-Ex.timings
name | user | system | elapsed | |
abundance_plt | 5.805 | 0.225 | 7.154 | |
add_tax | 0.386 | 0.014 | 0.467 | |
add_var | 0.353 | 0.011 | 0.424 | |
bake | 1.090 | 0.022 | 1.322 | |
contains_rarefaction | 0.458 | 0.026 | 0.555 | |
cool | 0.558 | 0.018 | 0.583 | |
corr_heatmap | 5.799 | 0.315 | 29.934 | |
exclusion_plt | 1.752 | 0.036 | 2.954 | |
export_steps | 3.100 | 0.319 | 32.475 | |
find_intersections | 0.384 | 0.011 | 0.429 | |
get_comparisons | 0.047 | 0.005 | 0.060 | |
get_phy | 0.038 | 0.005 | 0.058 | |
get_tax | 0.045 | 0.004 | 0.061 | |
get_var | 0.046 | 0.004 | 0.061 | |
import_steps | 4.191 | 0.173 | 83.326 | |
intersection_df | 0.377 | 0.014 | 0.467 | |
intersection_plt | 3.526 | 0.049 | 4.115 | |
mutual_plt | 4.318 | 0.060 | 5.058 | |
otu_table | 0.965 | 0.013 | 1.162 | |
overlap_df | 0.606 | 0.015 | 0.733 | |
phy_qc | 2.657 | 0.041 | 3.135 | |
prep | 5.870 | 0.177 | 101.326 | |
rand_id | 0.000 | 0.001 | 0.001 | |
read_data | 3.399 | 0.409 | 4.490 | |
recipe | 2.053 | 0.056 | 46.866 | |
required_deps | 0.093 | 0.015 | 0.121 | |
sample_data | 0.062 | 0.004 | 0.083 | |
step_aldex | 34.045 | 4.056 | 48.910 | |
step_ancom | 36.284 | 1.754 | 48.711 | |
step_deseq | 15.472 | 0.270 | 19.859 | |
step_filter_by_abundance | 0.080 | 0.011 | 0.113 | |
step_filter_by_prevalence | 0.080 | 0.008 | 0.119 | |
step_filter_by_rarity | 0.082 | 0.009 | 0.113 | |
step_filter_by_variance | 0.078 | 0.008 | 0.108 | |
step_filter_taxa | 0.081 | 0.008 | 0.110 | |
step_lefse | 0.134 | 0.010 | 0.182 | |
step_maaslin | 7.213 | 0.263 | 9.568 | |
step_metagenomeseq | 8.472 | 0.181 | 26.312 | |
step_rarefaction | 0.098 | 0.007 | 0.118 | |
step_subset_taxa | 0.079 | 0.007 | 0.095 | |
step_wilcox | 3.925 | 0.066 | 4.893 | |
steps_ids | 0.031 | 0.007 | 0.047 | |
tax_table | 0.097 | 0.008 | 0.126 | |
tidyeval | 0.039 | 0.004 | 0.051 | |
to_tibble | 1.036 | 0.012 | 1.289 | |
use_rarefy | 0.027 | 0.006 | 0.042 | |
zero_otu | 1.120 | 0.031 | 1.504 | |