Back to Multiple platform build/check report for BioC 3.19: simplified long |
|
This page was generated on 2024-05-31 17:02:54 -0400 (Fri, 31 May 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4753 |
kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4464 |
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 | |||||||||
kjohnson3 | macOS 13.6.5 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: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:dar.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings dar_1.0.0.tar.gz |
StartedAt: 2024-05-31 02:52:45 -0400 (Fri, 31 May 2024) |
EndedAt: 2024-05-31 03:05:29 -0400 (Fri, 31 May 2024) |
EllapsedTime: 763.7 seconds |
RetCode: 0 |
Status: OK |
CheckDir: dar.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:dar.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings dar_1.0.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/dar.Rcheck’ * using R version 4.4.0 (2024-04-24) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 * running under: Ubuntu 22.04.4 LTS * using session charset: UTF-8 * 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 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 14.402 0.960 15.363 step_ancom 14.504 0.660 15.164 step_deseq 6.416 0.144 6.560 step_metagenomeseq 3.300 0.101 9.322 prep 2.503 0.221 34.262 import_steps 1.799 0.191 31.773 export_steps 1.665 0.183 11.737 recipe 0.959 0.061 15.907 * 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-3.19-bioc/R/bin/R CMD INSTALL dar ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/site-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 4.4.0 (2024-04-24) -- "Puppy Cup" Copyright (C) 2024 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 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-maaslin2.R:16:3', '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-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 211.329 10.319 313.225
dar.Rcheck/dar-Ex.timings
name | user | system | elapsed | |
abundance_plt | 2.082 | 0.113 | 2.197 | |
add_tax | 0.146 | 0.001 | 0.145 | |
add_var | 0.134 | 0.004 | 0.138 | |
bake | 0.425 | 0.000 | 0.424 | |
contains_rarefaction | 0.235 | 0.011 | 0.246 | |
cool | 0.267 | 0.000 | 0.267 | |
corr_heatmap | 3.349 | 0.120 | 3.469 | |
exclusion_plt | 0.827 | 0.004 | 0.830 | |
export_steps | 1.665 | 0.183 | 11.737 | |
find_intersections | 0.181 | 0.008 | 0.189 | |
get_comparisons | 0.027 | 0.000 | 0.027 | |
get_phy | 0.022 | 0.000 | 0.022 | |
get_tax | 0.025 | 0.000 | 0.026 | |
get_var | 0.026 | 0.000 | 0.025 | |
import_steps | 1.799 | 0.191 | 31.773 | |
intersection_df | 0.170 | 0.012 | 0.181 | |
intersection_plt | 1.441 | 0.064 | 1.505 | |
mutual_plt | 1.754 | 0.052 | 1.807 | |
otu_table | 0.370 | 0.000 | 0.369 | |
overlap_df | 0.262 | 0.012 | 0.273 | |
phy_qc | 1.065 | 0.056 | 1.121 | |
prep | 2.503 | 0.221 | 34.262 | |
rand_id | 0.001 | 0.000 | 0.000 | |
read_data | 1.458 | 0.529 | 1.805 | |
recipe | 0.959 | 0.061 | 15.907 | |
required_deps | 0.051 | 0.004 | 0.055 | |
sample_data | 0.032 | 0.000 | 0.033 | |
step_aldex | 14.402 | 0.960 | 15.363 | |
step_ancom | 14.504 | 0.660 | 15.164 | |
step_corncob | 2.607 | 0.108 | 2.715 | |
step_deseq | 6.416 | 0.144 | 6.560 | |
step_filter_by_abundance | 0.045 | 0.000 | 0.045 | |
step_filter_by_prevalence | 0.044 | 0.000 | 0.044 | |
step_filter_by_rarity | 0.038 | 0.004 | 0.042 | |
step_filter_by_variance | 0.146 | 0.004 | 0.150 | |
step_filter_taxa | 0.04 | 0.00 | 0.04 | |
step_lefse | 0.058 | 0.008 | 0.066 | |
step_maaslin | 4.280 | 0.136 | 4.416 | |
step_metagenomeseq | 3.300 | 0.101 | 9.322 | |
step_rarefaction | 0.040 | 0.011 | 0.052 | |
step_subset_taxa | 0.078 | 0.028 | 0.106 | |
step_wilcox | 1.756 | 0.128 | 1.883 | |
steps_ids | 0.015 | 0.004 | 0.018 | |
tax_table | 0.056 | 0.000 | 0.056 | |
tidyeval | 0.020 | 0.000 | 0.021 | |
to_tibble | 0.473 | 0.060 | 0.533 | |
use_rarefy | 0.016 | 0.000 | 0.015 | |
zero_otu | 0.377 | 0.048 | 0.425 | |