Back to Multiple platform build/check report for BioC 3.21:   simplified   long
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This page was generated on 2025-01-21 11:41 -0500 (Tue, 21 Jan 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.1 LTS)x86_64R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" 4777
palomino7Windows Server 2022 Datacenterx64R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" 4502
lconwaymacOS 12.7.1 Montereyx86_64R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" 4467
kjohnson3macOS 13.7.1 Venturaarm64R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" 4422
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch64R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" 4406
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 500/2286HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
dar 1.3.0  (landing page)
Francesc Catala-Moll
Snapshot Date: 2025-01-20 13:40 -0500 (Mon, 20 Jan 2025)
git_url: https://git.bioconductor.org/packages/dar
git_branch: devel
git_last_commit: fceb04a
git_last_commit_date: 2024-10-29 11:26:58 -0500 (Tue, 29 Oct 2024)
nebbiolo1Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  NO, package depends on 'phyloseq' which is not available
palomino7Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.7.1 Ventura / arm64  OK    OK    OK    OK  NO, package depends on 'phyloseq' which is not available
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    OK  


CHECK results for dar on palomino7

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: 1.3.0
Command: E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:dar.install-out.txt --library=E:\biocbuild\bbs-3.21-bioc\R\library --no-vignettes --timings dar_1.3.0.tar.gz
StartedAt: 2025-01-21 00:22:09 -0500 (Tue, 21 Jan 2025)
EndedAt: 2025-01-21 00:37:14 -0500 (Tue, 21 Jan 2025)
EllapsedTime: 905.0 seconds
RetCode: 0
Status:   OK  
CheckDir: dar.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:dar.install-out.txt --library=E:\biocbuild\bbs-3.21-bioc\R\library --no-vignettes --timings dar_1.3.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'E:/biocbuild/bbs-3.21-bioc/meat/dar.Rcheck'
* using R Under development (unstable) (2024-10-26 r87273 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 '1.3.0'
* 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         22.82   4.42   99.22
step_ancom         15.86   1.50   20.17
step_deseq          8.78   0.19    8.98
step_metagenomeseq  4.52   0.11   11.49
corr_heatmap        4.44   0.12    6.69
step_corncob        3.20   0.11    6.63
prep                2.52   0.13   45.39
import_steps        1.56   0.22   43.34
export_steps        1.52   0.19   16.91
recipe              0.82   0.13   20.24
* 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:
###
###   E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD INSTALL dar
###
##############################################################################
##############################################################################


* installing to library 'E:/biocbuild/bbs-3.21-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

R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences"
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 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 
   8.85    0.82  385.45 

Example timings

dar.Rcheck/dar-Ex.timings

nameusersystemelapsed
abundance_plt3.250.183.57
add_tax0.240.040.28
add_var0.210.100.30
bake0.610.120.75
contains_rarefaction0.280.020.31
cool0.420.110.53
corr_heatmap4.440.126.69
exclusion_plt1.170.061.23
export_steps 1.52 0.1916.91
find_intersections0.210.030.25
get_comparisons0.040.030.06
get_phy0.000.070.06
get_tax0.040.030.08
get_var0.050.030.08
import_steps 1.56 0.2243.34
intersection_df0.270.030.30
intersection_plt1.810.091.92
mutual_plt2.580.102.67
otu_table0.580.060.64
overlap_df0.310.060.38
phy_qc1.450.061.51
prep 2.52 0.1345.39
rand_id000
read_data2.860.783.22
recipe 0.82 0.1320.24
required_deps0.050.040.10
sample_data0.030.050.08
step_aldex22.82 4.4299.22
step_ancom15.86 1.5020.17
step_corncob3.200.116.63
step_deseq8.780.198.98
step_filter_by_abundance0.060.030.09
step_filter_by_prevalence0.080.030.11
step_filter_by_rarity0.060.020.08
step_filter_by_variance0.060.030.09
step_filter_taxa0.050.010.06
step_lefse0.080.030.11
step_maaslin4.820.145.00
step_metagenomeseq 4.52 0.1111.49
step_rarefaction0.090.020.11
step_subset_taxa0.070.030.09
step_wilcox2.370.132.50
steps_ids0.030.030.06
tax_table0.080.030.11
tidyeval000
to_tibble0.580.050.63
use_rarefy0.030.030.06
zero_otu0.560.030.59