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This page was generated on 2024-07-18 11:40 -0400 (Thu, 18 Jul 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.4.1 (2024-06-14) -- "Race for Your Life" 4683
palomino8Windows Server 2022 Datacenterx644.4.1 (2024-06-14 ucrt) -- "Race for Your Life" 4379
lconwaymacOS 12.7.1 Montereyx86_644.4.1 (2024-06-14) -- "Race for Your Life" 4450
kjohnson3macOS 13.6.5 Venturaarm644.4.1 (2024-06-14) -- "Race for Your Life" 4399
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 499/2248HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
dar 1.1.0  (landing page)
Francesc Catala-Moll
Snapshot Date: 2024-07-17 14:00 -0400 (Wed, 17 Jul 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    ERROR  
palomino8Windows Server 2022 Datacenter / x64  OK    OK    ERROR    OK  
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    ERROR    OK  
kjohnson3macOS 13.6.5 Ventura / arm64  OK    OK    ERROR    OK  


CHECK results for dar on lconway

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: 2024-07-17 20:39:22 -0400 (Wed, 17 Jul 2024)
EndedAt: 2024-07-17 20:53:13 -0400 (Wed, 17 Jul 2024)
EllapsedTime: 831.5 seconds
RetCode: 1
Status:   ERROR  
CheckDir: dar.Rcheck
Warnings: NA

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 4.4.1 (2024-06-14)
* 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 12.7.1
* 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         19.993  2.858  23.110
step_ancom         20.956  1.184  22.517
step_deseq          8.888  0.148   9.094
step_metagenomeseq  4.590  0.104  12.655
prep                2.604  0.069  46.177
export_steps        1.900  0.249  16.380
import_steps        1.662  0.083  43.139
recipe              0.923  0.028  21.714
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  i In index: 1.
  i With name: RiskGroup2.
  Caused by error in `map()`:
  i In index: 1.
  Caused by error in `dplyr::rename()`:
  ! Can't rename columns that don't exist.
  x Column `Names` doesn't exist.
  Backtrace:
      ▆
   1. └─testthat::expect_snapshot(...) at test-roxytest-tests-lefse.R:15:3
   2.   └─rlang::cnd_signal(state$error)
  
  [ FAIL 1 | WARN 2 | SKIP 9 | PASS 81 ]
  Error: Test failures
  Execution halted
* 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: 1 ERROR
See
  ‘/Users/biocbuild/bbs-3.20-bioc/meat/dar.Rcheck/00check.log’
for details.


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.fail


R version 4.4.1 (2024-06-14) -- "Race for Your Life"
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 1 | WARN 2 | SKIP 9 | PASS 81 ]

══ Skipped tests (9) ═══════════════════════════════════════════════════════════
• On CRAN (9): 'test-roxytest-tests-bake.R:18:3',
  'test-roxytest-tests-ancom.R:14:3', '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'

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-roxytest-tests-lefse.R:15:3'): [unknown alias] @ L82 ───────────
<purrr_error_indexed/rlang_error/error/condition>
Error in `(function (.x, .f, ..., .progress = FALSE) 
{
    map_("list", .x, .f, ..., .progress = .progress)
})(.x = "rec %>% run_lefse(kruskal.threshold = 0.05, wilcox.threshold = 0.05, lda.threshold = 2, blockCol = NULL, assay = 1, trim.names = FALSE, rarefy = TRUE)", 
    .f = function (...) 
    {
        {
            ...furrr_chunk_seeds_i <- ...furrr_chunk_seeds_env[["i"]]
            ...furrr_chunk_seeds_env[["i"]] <- ...furrr_chunk_seeds_i + 
                1L
            assign(x = ".Random.seed", value = ...furrr_chunk_seeds[[...furrr_chunk_seeds_i]], 
                envir = globalenv(), inherits = FALSE)
        }
        NULL
        ...furrr_out <- ...furrr_fn(...)
        ...furrr_out
    })`: i In index: 1.
Caused by error in `purrr::map()`:
i In index: 1.
i With name: RiskGroup2.
Caused by error in `map()`:
i In index: 1.
Caused by error in `dplyr::rename()`:
! Can't rename columns that don't exist.
x Column `Names` doesn't exist.
Backtrace:
    ▆
 1. └─testthat::expect_snapshot(...) at test-roxytest-tests-lefse.R:15:3
 2.   └─rlang::cnd_signal(state$error)

[ FAIL 1 | WARN 2 | SKIP 9 | PASS 81 ]
Error: Test failures
Execution halted

Example timings

dar.Rcheck/dar-Ex.timings

nameusersystemelapsed
abundance_plt3.4250.1333.587
add_tax0.2070.0080.218
add_var0.1940.0070.203
bake0.6380.0150.658
contains_rarefaction0.3080.0180.332
cool0.3710.0080.380
corr_heatmap4.0720.1384.242
exclusion_plt1.1620.0181.189
export_steps 1.900 0.24916.380
find_intersections0.2360.0040.242
get_comparisons0.0340.0030.036
get_phy0.0270.0030.030
get_tax0.0300.0030.032
get_var0.0300.0020.033
import_steps 1.662 0.08343.139
intersection_df0.1960.0070.203
intersection_plt2.0010.0212.029
mutual_plt2.5520.0292.594
otu_table0.4870.0050.497
overlap_df0.3610.0100.372
phy_qc1.4650.0251.494
prep 2.604 0.06946.177
rand_id0.0000.0000.001
read_data1.9320.4022.078
recipe 0.923 0.02821.714
required_deps0.0660.0090.076
sample_data0.0420.0040.045
step_aldex19.993 2.85823.110
step_ancom20.956 1.18422.517
step_corncob3.1680.1433.344
step_deseq8.8880.1489.094
step_filter_by_abundance0.0500.0070.057
step_filter_by_prevalence0.0540.0050.060
step_filter_by_rarity0.0520.0070.060
step_filter_by_variance0.0550.0050.061
step_filter_taxa0.0500.0050.055
step_lefse0.0870.0080.097
step_maaslin3.9790.1894.256
step_metagenomeseq 4.590 0.10412.655
step_rarefaction0.0640.0070.071
step_subset_taxa0.0510.0110.067
step_wilcox2.2720.0532.350
steps_ids0.0180.0040.022
tax_table0.0670.0030.070
tidyeval0.0170.0020.019
to_tibble0.5720.0080.582
use_rarefy0.0210.0050.026
zero_otu0.5720.0090.582