Back to Multiple platform build/check report for BioC 3.19:   simplified   long
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This page was generated on 2024-05-04 11:36:27 -0400 (Sat, 04 May 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" 4753
palomino3Windows Server 2022 Datacenterx644.4.0 beta (2024-04-15 r86425 ucrt) -- "Puppy Cup" 4486
lconwaymacOS 12.7.1 Montereyx86_644.4.0 beta (2024-04-14 r86421) -- "Puppy Cup" 4519
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch644.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" 4479
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 510/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
dar 1.0.0  (landing page)
Francesc Catala-Moll
Snapshot Date: 2024-05-03 14:00:19 -0400 (Fri, 03 May 2024)
git_url: https://git.bioconductor.org/packages/dar
git_branch: RELEASE_3_19
git_last_commit: 1d07d5f
git_last_commit_date: 2024-04-30 11:53:50 -0400 (Tue, 30 Apr 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows 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
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    OK  
kjohnson3macOS 13.6.5 Ventura / arm64see weekly results here

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: 1.0.0
Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:dar.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings dar_1.0.0.tar.gz
StartedAt: 2024-05-03 22:23:04 -0400 (Fri, 03 May 2024)
EndedAt: 2024-05-03 22:36:12 -0400 (Fri, 03 May 2024)
EllapsedTime: 787.7 seconds
RetCode: 0
Status:   OK  
CheckDir: dar.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:dar.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings dar_1.0.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/dar.Rcheck’
* using R version 4.4.0 beta (2024-04-15 r86425)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* checking for file ‘dar/DESCRIPTION’ ... OK
* this is package ‘dar’ version ‘1.0.0’
* 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 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_ancom         15.895  0.620  16.531
step_aldex         15.163  1.092  16.270
step_deseq          6.600  0.849   8.056
step_metagenomeseq  4.951  0.145  11.482
prep                2.845  0.186  36.803
import_steps        2.072  0.146  34.538
export_steps        1.861  0.104  12.334
recipe              1.100  0.106  18.738
* 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-3.19-bioc/R/bin/R CMD INSTALL dar
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.19-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 version 4.4.0 beta (2024-04-15 r86425) -- "Puppy Cup"
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 
215.393   8.959 314.135 

Example timings

dar.Rcheck/dar-Ex.timings

nameusersystemelapsed
abundance_plt2.1430.1482.293
add_tax0.1510.0000.151
add_var0.1360.0080.144
bake0.4500.0000.449
contains_rarefaction0.2370.0280.267
cool0.2990.0080.307
corr_heatmap3.6570.0733.733
exclusion_plt0.8470.0080.856
export_steps 1.861 0.10412.334
find_intersections0.1880.0000.188
get_comparisons0.0280.0000.028
get_phy0.0220.0000.022
get_tax0.0250.0000.025
get_var0.0270.0000.027
import_steps 2.072 0.14634.538
intersection_df0.1910.0120.203
intersection_plt1.5760.0721.648
mutual_plt1.8830.0161.900
otu_table0.3960.0120.408
overlap_df0.2460.0040.250
phy_qc1.1020.0321.134
prep 2.845 0.18636.803
rand_id000
read_data1.6140.6892.115
recipe 1.100 0.10618.738
required_deps0.0520.0040.056
sample_data0.0400.0080.048
step_aldex15.163 1.09216.270
step_ancom15.895 0.62016.531
step_corncob3.1320.0563.200
step_deseq6.6000.8498.056
step_filter_by_abundance0.0410.0000.041
step_filter_by_prevalence0.0330.0070.041
step_filter_by_rarity0.0410.0010.041
step_filter_by_variance0.1490.0030.153
step_filter_taxa0.0430.0010.043
step_lefse0.0650.0120.077
step_maaslin3.0760.0563.135
step_metagenomeseq 4.951 0.14511.482
step_rarefaction0.0490.0000.050
step_subset_taxa0.0380.0000.038
step_wilcox1.7190.0041.724
steps_ids0.0130.0040.017
tax_table0.0460.0000.046
tidyeval0.0160.0000.017
to_tibble0.3960.0000.397
use_rarefy0.0160.0000.016
zero_otu0.3910.0000.392