Back to Multiple platform build/check report for BioC 3.19:   simplified   long
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This page was generated on 2024-06-25 17:41 -0400 (Tue, 25 Jun 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 (2024-04-24) -- "Puppy Cup" 4760
palomino3Windows Server 2022 Datacenterx644.4.0 (2024-04-24 ucrt) -- "Puppy Cup" 4494
merida1macOS 12.7.4 Montereyx86_644.4.0 (2024-04-24) -- "Puppy Cup" 4508
kjohnson1macOS 13.6.6 Venturaarm644.4.0 (2024-04-24) -- "Puppy Cup" 4466
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 510/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
dar 1.0.0  (landing page)
Francesc Catala-Moll
Snapshot Date: 2024-06-23 14:00 -0400 (Sun, 23 Jun 2024)
git_url: https://git.bioconductor.org/packages/dar
git_branch: RELEASE_3_19
git_last_commit: 1d07d5f
git_last_commit_date: 2024-04-30 11:53:50 -0400 (Tue, 30 Apr 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.4 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published


CHECK results for dar on merida1

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.

raw results


Summary

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: 2024-06-24 03:02:15 -0400 (Mon, 24 Jun 2024)
EndedAt: 2024-06-24 03:31:07 -0400 (Mon, 24 Jun 2024)
EllapsedTime: 1731.8 seconds
RetCode: 0
Status:   OK  
CheckDir: dar.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### 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 4.4.0 (2024-04-24)
* 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 12.7.4
* 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         38.923  1.809  52.128
step_aldex         36.193  4.366  47.965
step_deseq         16.188  0.245  19.754
step_metagenomeseq  9.155  0.166  27.472
step_maaslin        7.856  0.262   9.958
prep                7.507  0.226 135.169
step_corncob        6.112  0.224   8.316
corr_heatmap        5.912  0.222   7.700
abundance_plt       5.749  0.239   7.421
mutual_plt          4.721  0.050   6.190
import_steps        4.606  0.163  94.409
step_wilcox         4.314  0.068   5.338
intersection_plt    4.017  0.040   5.096
export_steps        3.277  0.304  34.259
recipe              2.151  0.052  46.634
* 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


Installation output

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)

Tests output

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-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 
437.266  18.301 794.280 

Example timings

dar.Rcheck/dar-Ex.timings

nameusersystemelapsed
abundance_plt5.7490.2397.421
add_tax0.9340.0201.137
add_var0.3780.0140.494
bake1.1000.0191.360
contains_rarefaction0.4710.0230.609
cool0.7090.0140.865
corr_heatmap5.9120.2227.700
exclusion_plt2.1190.0252.649
export_steps 3.277 0.30434.259
find_intersections0.4070.0080.456
get_comparisons0.0490.0060.064
get_phy0.0410.0040.057
get_tax0.0480.0040.056
get_var0.0500.0040.069
import_steps 4.606 0.16394.409
intersection_df0.4140.0120.542
intersection_plt4.0170.0405.096
mutual_plt4.7210.0506.190
otu_table1.0820.0091.353
overlap_df0.6580.0140.838
phy_qc2.9520.0383.770
prep 7.507 0.226135.169
rand_id0.0000.0010.001
read_data3.7200.4004.875
recipe 2.151 0.05246.634
required_deps0.1000.0120.125
sample_data0.0660.0040.082
step_aldex36.193 4.36647.965
step_ancom38.923 1.80952.128
step_corncob6.1120.2248.316
step_deseq16.188 0.24519.754
step_filter_by_abundance0.0820.0080.104
step_filter_by_prevalence0.0810.0080.103
step_filter_by_rarity0.0810.0080.103
step_filter_by_variance0.0830.0100.107
step_filter_taxa0.0830.0080.102
step_lefse0.1390.0090.170
step_maaslin7.8560.2629.958
step_metagenomeseq 9.155 0.16627.472
step_rarefaction0.0990.0090.115
step_subset_taxa0.0810.0110.103
step_wilcox4.3140.0685.338
steps_ids0.0300.0060.044
tax_table0.1070.0090.143
tidyeval0.0400.0050.064
to_tibble1.1020.0161.385
use_rarefy0.0270.0100.055
zero_otu1.1100.0171.463