Back to Multiple platform build/check report for BioC 3.21:   simplified   long
ABC[D]EFGHIJKLMNOPQRSTUVWXYZ

This page was generated on 2024-12-24 11:39 -0500 (Tue, 24 Dec 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.1 LTS)x86_64R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" 4754
palomino7Windows Server 2022 Datacenterx64R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" 4472
lconwaymacOS 12.7.1 Montereyx86_64R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" 4426
kjohnson3macOS 13.7.1 Venturaarm64R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" 4381
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch64R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" 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 498/2274HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
dar 1.3.0  (landing page)
Francesc Catala-Moll
Snapshot Date: 2024-12-23 13:40 -0500 (Mon, 23 Dec 2024)
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 nebbiolo1

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: /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:dar.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings dar_1.3.0.tar.gz
StartedAt: 2024-12-23 21:10:59 -0500 (Mon, 23 Dec 2024)
EndedAt: 2024-12-23 21:23:49 -0500 (Mon, 23 Dec 2024)
EllapsedTime: 769.9 seconds
RetCode: 0
Status:   OK  
CheckDir: dar.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:dar.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings dar_1.3.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/dar.Rcheck’
* using R Under development (unstable) (2024-10-21 r87258)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
    GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* 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 ... INFO
Imports includes 21 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
* 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 loading without being on the library search path ... 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         15.237  0.972  16.236
step_ancom         11.493  0.480  12.055
step_deseq          6.415  0.038   6.456
step_metagenomeseq  3.637  0.014   9.333
prep                2.765  0.220  36.137
import_steps        2.356  0.211  34.386
export_steps        1.693  0.172  13.062
recipe              1.014  0.044  17.961
* 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: OK


Installation output

dar.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL dar
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-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) (2024-10-21 r87258) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

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-maaslin2.R:16:3',
  'test-roxytest-tests-pkg_check.R:6:3',
  '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 
212.846   9.996 311.842 

Example timings

dar.Rcheck/dar-Ex.timings

nameusersystemelapsed
abundance_plt2.7550.2312.986
add_tax0.1550.0010.156
add_var0.1470.0000.147
bake0.4820.0030.486
contains_rarefaction0.2460.0170.265
cool0.2880.0010.289
corr_heatmap3.7330.3854.121
exclusion_plt0.8330.0170.850
export_steps 1.693 0.17213.062
find_intersections0.2170.0330.251
get_comparisons0.0260.0020.028
get_phy0.0220.0000.022
get_tax0.0240.0020.027
get_var0.0240.0030.027
import_steps 2.356 0.21134.386
intersection_df0.1890.0110.200
intersection_plt1.5160.0721.591
mutual_plt1.7960.0451.841
otu_table0.3700.0140.384
overlap_df0.2650.0010.266
phy_qc1.0840.0801.164
prep 2.765 0.22036.137
rand_id0.0010.0000.000
read_data1.1620.6891.865
recipe 1.014 0.04417.961
required_deps0.0500.0050.054
sample_data0.0320.0070.038
step_aldex15.237 0.97216.236
step_ancom11.493 0.48012.055
step_corncob2.9100.1153.028
step_deseq6.4150.0386.456
step_filter_by_abundance0.0420.0000.042
step_filter_by_prevalence0.0410.0000.042
step_filter_by_rarity0.0430.0020.045
step_filter_by_variance0.0420.0020.043
step_filter_taxa0.0430.0010.044
step_lefse0.0680.0030.070
step_maaslin4.6250.1134.754
step_metagenomeseq3.6370.0149.333
step_rarefaction0.0480.0020.049
step_subset_taxa0.0390.0010.041
step_wilcox1.7410.0151.756
steps_ids0.0170.0000.017
tax_table0.0470.0010.048
tidyeval0.0150.0020.018
to_tibble0.3880.0010.388
use_rarefy0.0140.0010.015
zero_otu0.3940.0010.396