Back to Multiple platform build/check report for BioC 3.19: simplified long |
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This page was generated on 2024-07-24 09:04 -0400 (Wed, 24 Jul 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" | 4747 |
palomino7 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4489 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4518 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4467 |
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 | ERROR | |||||||||
palomino7 | Windows Server 2022 Datacenter / x64 | OK | 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: E:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:dar.install-out.txt --library=E:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings dar_1.0.0.tar.gz |
StartedAt: 2024-07-22 01:09:26 -0400 (Mon, 22 Jul 2024) |
EndedAt: 2024-07-22 01:24:02 -0400 (Mon, 22 Jul 2024) |
EllapsedTime: 876.6 seconds |
RetCode: 0 |
Status: OK |
CheckDir: dar.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### E:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:dar.install-out.txt --library=E:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings dar_1.0.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'E:/biocbuild/bbs-3.19-bioc/meat/dar.Rcheck' * using R version 4.4.1 (2024-06-14 ucrt) * using platform: x86_64-w64-mingw32 * R was compiled by gcc.exe (GCC) 13.2.0 GNU Fortran (GCC) 13.2.0 * running under: Windows Server 2022 x64 (build 20348) * 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 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_aldex 21.64 4.35 85.19 step_ancom 18.50 1.55 20.11 step_deseq 8.36 0.16 8.52 step_metagenomeseq 4.98 0.18 12.33 step_maaslin 4.70 0.29 5.01 corr_heatmap 4.14 0.15 6.32 prep 2.36 0.12 45.78 import_steps 1.48 0.14 42.11 export_steps 1.50 0.10 16.30 recipe 0.80 0.13 20.34 * 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: ### ### E:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD INSTALL dar ### ############################################################################## ############################################################################## * installing to library 'E:/biocbuild/bbs-3.19-bioc/R/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 ucrt) -- "Race for Your Life" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 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-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' [ FAIL 0 | WARN 0 | SKIP 10 | PASS 82 ] > > proc.time() user system elapsed 8.79 1.07 389.98
dar.Rcheck/dar-Ex.timings
name | user | system | elapsed | |
abundance_plt | 3.39 | 0.17 | 3.74 | |
add_tax | 0.28 | 0.05 | 0.33 | |
add_var | 0.22 | 0.09 | 0.32 | |
bake | 0.56 | 0.16 | 0.71 | |
contains_rarefaction | 0.37 | 0.00 | 0.40 | |
cool | 0.40 | 0.14 | 0.53 | |
corr_heatmap | 4.14 | 0.15 | 6.32 | |
exclusion_plt | 1.23 | 0.11 | 1.35 | |
export_steps | 1.5 | 0.1 | 16.3 | |
find_intersections | 0.28 | 0.03 | 0.31 | |
get_comparisons | 0.05 | 0.03 | 0.08 | |
get_phy | 0.01 | 0.05 | 0.06 | |
get_tax | 0.05 | 0.02 | 0.07 | |
get_var | 0.02 | 0.04 | 0.06 | |
import_steps | 1.48 | 0.14 | 42.11 | |
intersection_df | 0.16 | 0.07 | 0.22 | |
intersection_plt | 2.01 | 0.07 | 2.10 | |
mutual_plt | 2.16 | 0.15 | 2.31 | |
otu_table | 0.53 | 0.08 | 0.61 | |
overlap_df | 0.42 | 0.08 | 0.50 | |
phy_qc | 1.44 | 0.03 | 1.47 | |
prep | 2.36 | 0.12 | 45.78 | |
rand_id | 0 | 0 | 0 | |
read_data | 3.12 | 0.80 | 3.31 | |
recipe | 0.80 | 0.13 | 20.34 | |
required_deps | 0.09 | 0.07 | 0.18 | |
sample_data | 0.07 | 0.04 | 0.09 | |
step_aldex | 21.64 | 4.35 | 85.19 | |
step_ancom | 18.50 | 1.55 | 20.11 | |
step_corncob | 3.54 | 0.22 | 4.06 | |
step_deseq | 8.36 | 0.16 | 8.52 | |
step_filter_by_abundance | 0.05 | 0.04 | 0.09 | |
step_filter_by_prevalence | 0.03 | 0.05 | 0.08 | |
step_filter_by_rarity | 0.06 | 0.00 | 0.06 | |
step_filter_by_variance | 0.05 | 0.03 | 0.08 | |
step_filter_taxa | 0.05 | 0.02 | 0.06 | |
step_lefse | 0.08 | 0.04 | 0.13 | |
step_maaslin | 4.70 | 0.29 | 5.01 | |
step_metagenomeseq | 4.98 | 0.18 | 12.33 | |
step_rarefaction | 0.07 | 0.02 | 0.08 | |
step_subset_taxa | 0.03 | 0.05 | 0.08 | |
step_wilcox | 2.20 | 0.10 | 2.31 | |
steps_ids | 0.00 | 0.05 | 0.04 | |
tax_table | 0.06 | 0.03 | 0.10 | |
tidyeval | 0.03 | 0.00 | 0.03 | |
to_tibble | 0.80 | 0.03 | 0.83 | |
use_rarefy | 0.02 | 0.04 | 0.04 | |
zero_otu | 0.61 | 0.04 | 0.66 | |