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This page was generated on 2024-06-11 15:41 -0400 (Tue, 11 Jun 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" 4679
palomino4Windows Server 2022 Datacenterx644.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup" 4414
merida1macOS 12.7.4 Montereyx86_644.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" 4441
kjohnson1macOS 13.6.6 Venturaarm644.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" 4394
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 495/2239HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
dar 1.1.0  (landing page)
Francesc Catala-Moll
Snapshot Date: 2024-06-09 14:00 -0400 (Sun, 09 Jun 2024)
git_url: https://git.bioconductor.org/packages/dar
git_branch: devel
git_last_commit: b69c1d0
git_last_commit_date: 2024-04-30 11:53:50 -0400 (Tue, 30 Apr 2024)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino4Windows 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: 1.1.0
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: 2024-06-10 02:17:52 -0400 (Mon, 10 Jun 2024)
EndedAt: 2024-06-10 02:44:18 -0400 (Mon, 10 Jun 2024)
EllapsedTime: 1586.0 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_1.1.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/dar.Rcheck’
* using R version 4.4.0 Patched (2024-04-24 r86482)
* 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 ‘1.1.0’
* 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         36.188  3.939  50.497
step_ancom         38.263  1.824  49.076
step_deseq         15.992  0.299  19.902
step_metagenomeseq  8.775  0.131  26.503
step_maaslin        7.658  0.260   9.819
step_corncob        6.244  0.285   8.440
prep                6.243  0.149  92.565
corr_heatmap        5.706  0.222   6.699
abundance_plt       5.625  0.230   6.395
import_steps        4.430  0.164  86.487
mutual_plt          4.538  0.040   5.049
export_steps        3.182  0.290  30.653
recipe              2.428  0.074  51.084
* 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 Patched (2024-04-24 r86482) -- "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 
429.970  16.975 737.513 

Example timings

dar.Rcheck/dar-Ex.timings

nameusersystemelapsed
abundance_plt5.6250.2306.395
add_tax0.9240.0201.016
add_var0.3560.0100.403
bake1.0740.0171.179
contains_rarefaction0.4650.0260.530
cool0.6990.0150.780
corr_heatmap5.7060.2226.699
exclusion_plt2.1770.0272.484
export_steps 3.182 0.29030.653
find_intersections0.3930.0060.423
get_comparisons0.0490.0040.060
get_phy0.0380.0040.046
get_tax0.0490.0040.057
get_var0.0460.0030.052
import_steps 4.430 0.16486.487
intersection_df0.3980.0110.454
intersection_plt3.8700.0344.395
mutual_plt4.5380.0405.049
otu_table1.0380.0081.163
overlap_df0.6270.0120.698
phy_qc2.8430.0303.190
prep 6.243 0.14992.565
rand_id0.0010.0010.000
read_data3.6110.3894.370
recipe 2.428 0.07451.084
required_deps0.0950.0110.118
sample_data0.0630.0050.082
step_aldex36.188 3.93950.497
step_ancom38.263 1.82449.076
step_corncob6.2440.2858.440
step_deseq15.992 0.29919.902
step_filter_by_abundance0.0830.0080.106
step_filter_by_prevalence0.0800.0090.108
step_filter_by_rarity0.0800.0080.110
step_filter_by_variance0.0800.0080.106
step_filter_taxa0.0770.0080.092
step_lefse0.2790.0140.350
step_maaslin7.6580.2609.819
step_metagenomeseq 8.775 0.13126.503
step_rarefaction0.1010.0100.120
step_subset_taxa0.0830.0080.101
step_wilcox4.1310.0494.938
steps_ids0.0290.0070.041
tax_table0.1030.0060.131
tidyeval0.0370.0040.049
to_tibble1.0830.0101.313
use_rarefy0.0280.0070.041
zero_otu1.0720.0131.289