Back to Mac ARM64 build report for BioC 3.20 |
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This page was generated on 2024-05-13 11:32:02 -0400 (Mon, 13 May 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4378 |
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 494/2230 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
dar 1.1.0 (landing page) Francesc Catala-Moll
| kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | ||||||||
To the developers/maintainers of the dar package: - 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: 1.1.0 |
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_1.1.0.tar.gz |
StartedAt: 2024-05-12 10:50:54 -0400 (Sun, 12 May 2024) |
EndedAt: 2024-05-12 11:04:53 -0400 (Sun, 12 May 2024) |
EllapsedTime: 838.7 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_1.1.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc-mac-arm64/meat/dar.Rcheck’ * using R version 4.4.0 Patched (2024-04-24 r86482) * using platform: aarch64-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 Ventura 13.6.6 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘dar/DESCRIPTION’ ... OK * this is package ‘dar’ version ‘1.1.0’ * 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_aldex 20.067 2.162 22.507 step_ancom 17.366 0.690 18.076 step_deseq 7.434 0.097 7.562 step_metagenomeseq 3.814 0.117 11.103 prep 2.152 0.069 41.503 export_steps 1.858 0.151 14.614 import_steps 1.450 0.079 40.181 recipe 0.823 0.027 19.948 * 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-arm64/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 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: aarch64-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-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 255.850 17.929 443.123
dar.Rcheck/dar-Ex.timings
name | user | system | elapsed | |
abundance_plt | 2.398 | 0.096 | 2.509 | |
add_tax | 0.892 | 0.010 | 0.904 | |
add_var | 0.183 | 0.007 | 0.192 | |
bake | 0.530 | 0.011 | 0.542 | |
contains_rarefaction | 0.312 | 0.015 | 0.328 | |
cool | 0.333 | 0.008 | 0.341 | |
corr_heatmap | 4.285 | 0.091 | 4.397 | |
exclusion_plt | 0.949 | 0.014 | 0.966 | |
export_steps | 1.858 | 0.151 | 14.614 | |
find_intersections | 0.203 | 0.005 | 0.219 | |
get_comparisons | 0.035 | 0.002 | 0.037 | |
get_phy | 0.028 | 0.002 | 0.029 | |
get_tax | 0.034 | 0.001 | 0.035 | |
get_var | 0.035 | 0.002 | 0.038 | |
import_steps | 1.450 | 0.079 | 40.181 | |
intersection_df | 0.191 | 0.007 | 0.199 | |
intersection_plt | 1.659 | 0.019 | 1.684 | |
mutual_plt | 2.120 | 0.028 | 2.157 | |
otu_table | 0.413 | 0.004 | 0.418 | |
overlap_df | 0.304 | 0.011 | 0.316 | |
phy_qc | 1.227 | 0.019 | 1.249 | |
prep | 2.152 | 0.069 | 41.503 | |
rand_id | 0 | 0 | 0 | |
read_data | 1.512 | 0.121 | 1.604 | |
recipe | 0.823 | 0.027 | 19.948 | |
required_deps | 0.068 | 0.009 | 0.077 | |
sample_data | 0.041 | 0.002 | 0.044 | |
step_aldex | 20.067 | 2.162 | 22.507 | |
step_ancom | 17.366 | 0.690 | 18.076 | |
step_corncob | 2.980 | 0.150 | 3.142 | |
step_deseq | 7.434 | 0.097 | 7.562 | |
step_filter_by_abundance | 0.053 | 0.008 | 0.060 | |
step_filter_by_prevalence | 0.053 | 0.004 | 0.057 | |
step_filter_by_rarity | 0.048 | 0.004 | 0.052 | |
step_filter_by_variance | 0.049 | 0.004 | 0.053 | |
step_filter_taxa | 0.049 | 0.012 | 0.061 | |
step_lefse | 0.076 | 0.012 | 0.089 | |
step_maaslin | 3.517 | 0.186 | 3.719 | |
step_metagenomeseq | 3.814 | 0.117 | 11.103 | |
step_rarefaction | 0.062 | 0.010 | 0.072 | |
step_subset_taxa | 0.053 | 0.009 | 0.062 | |
step_wilcox | 1.892 | 0.030 | 1.927 | |
steps_ids | 0.027 | 0.007 | 0.033 | |
tax_table | 0.062 | 0.007 | 0.070 | |
tidyeval | 0.018 | 0.002 | 0.019 | |
to_tibble | 0.492 | 0.011 | 0.503 | |
use_rarefy | 0.023 | 0.008 | 0.031 | |
zero_otu | 0.414 | 0.009 | 0.424 | |