Back to Multiple platform build/check report for BioC 3.20:   simplified   long
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This page was generated on 2024-07-16 11:40 -0400 (Tue, 16 Jul 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.4.1 (2024-06-14) -- "Race for Your Life" 4677
palomino6Windows Server 2022 Datacenterx644.4.1 (2024-06-14 ucrt) -- "Race for Your Life" 4416
lconwaymacOS 12.7.1 Montereyx86_644.4.1 (2024-06-14) -- "Race for Your Life" 4444
kjohnson3macOS 13.6.5 Venturaarm644.4.1 (2024-06-14) -- "Race for Your Life" 4393
palomino8Windows Server 2022 Datacenterx644.4.1 (2024-06-14 ucrt) -- "Race for Your Life" 4373
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 496/2243HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
dar 1.1.0  (landing page)
Francesc Catala-Moll
Snapshot Date: 2024-07-15 14:00 -0400 (Mon, 15 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  
palomino6Windows 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  
palomino8Windows Server 2022 Datacenter / x64  OK    OK    ERROR    OK  


CHECK results for dar on palomino6

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: C:\Users\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:dar.install-out.txt --library=C:\Users\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings dar_1.1.0.tar.gz
StartedAt: 2024-07-15 23:15:04 -0400 (Mon, 15 Jul 2024)
EndedAt: 2024-07-15 23:25:11 -0400 (Mon, 15 Jul 2024)
EllapsedTime: 606.5 seconds
RetCode: 1
Status:   ERROR  
CheckDir: dar.Rcheck
Warnings: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:dar.install-out.txt --library=C:\Users\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings dar_1.1.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.20-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 '1.1.0'
* 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 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         16.59   3.02   19.75
step_ancom         14.60   0.98   15.66
read_data           3.97   2.83    5.21
step_deseq          5.61   0.15    5.74
step_metagenomeseq  3.38   0.11    8.34
recipe              1.80   0.06   19.52
prep                1.59   0.11   38.35
import_steps        1.11   0.31   32.47
export_steps        1.21   0.13   12.78
* 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
  'C:/Users/biocbuild/bbs-3.20-bioc/meat/dar.Rcheck/00check.log'
for details.


Installation output

dar.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL dar
###
##############################################################################
##############################################################################


* installing to library 'C:/Users/biocbuild/bbs-3.20-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)

Tests output

dar.Rcheck/tests/testthat.Rout.fail


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 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_plt2.390.142.53
add_tax0.110.040.18
add_var0.130.030.15
bake0.400.070.47
contains_rarefaction0.190.000.19
cool0.270.060.33
corr_heatmap3.510.664.17
exclusion_plt0.810.010.83
export_steps 1.21 0.1312.78
find_intersections0.150.010.17
get_comparisons0.020.030.05
get_phy0.020.020.04
get_tax0.030.010.05
get_var0.010.020.03
import_steps 1.11 0.3132.47
intersection_df0.160.030.19
intersection_plt1.230.081.33
mutual_plt1.670.101.79
otu_table0.330.030.38
overlap_df0.250.030.28
phy_qc2.020.062.41
prep 1.59 0.1138.35
rand_id000
read_data3.972.835.21
recipe 1.80 0.0619.52
required_deps0.040.050.09
sample_data0.020.030.05
step_aldex16.59 3.0219.75
step_ancom14.60 0.9815.66
step_corncob2.310.192.50
step_deseq5.610.155.74
step_filter_by_abundance0.030.040.06
step_filter_by_prevalence0.030.010.05
step_filter_by_rarity0.030.030.06
step_filter_by_variance0.050.020.06
step_filter_taxa0.030.030.06
step_lefse0.140.010.16
step_maaslin3.140.253.45
step_metagenomeseq3.380.118.34
step_rarefaction0.040.030.08
step_subset_taxa0.040.020.05
step_wilcox1.640.041.70
steps_ids0.030.000.03
tax_table0.040.020.07
tidyeval0.020.000.01
to_tibble0.340.030.38
use_rarefy0.020.020.03
zero_otu0.440.030.47