Back to Multiple platform build/check report for BioC 3.21:   simplified   long
[A]BCDEFGHIJKLMNOPQRSTUVWXYZ

This page was generated on 2025-03-17 11:39 -0400 (Mon, 17 Mar 2025).

HostnameOSArch (*)R versionInstalled pkgs
palomino7Windows Server 2022 Datacenterx64R Under development (unstable) (2025-03-01 r87860 ucrt) -- "Unsuffered Consequences" 4545
lconwaymacOS 12.7.1 Montereyx86_64R Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences" 4576
kjohnson3macOS 13.7.1 Venturaarm64R Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences" 4528
kunpeng2Linux (openEuler 24.03 LTS)aarch64R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" 4459
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 68/2313HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
animalcules 1.23.0  (landing page)
Jessica McClintock
Snapshot Date: 2025-03-16 13:40 -0400 (Sun, 16 Mar 2025)
git_url: https://git.bioconductor.org/packages/animalcules
git_branch: devel
git_last_commit: 1f256fc
git_last_commit_date: 2024-10-29 10:37:18 -0400 (Tue, 29 Oct 2024)
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    ERROR    OK  
kunpeng2Linux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  


CHECK results for animalcules on kjohnson3

To the developers/maintainers of the animalcules package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/animalcules.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: animalcules
Version: 1.23.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:animalcules.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings animalcules_1.23.0.tar.gz
StartedAt: 2025-03-16 18:07:31 -0400 (Sun, 16 Mar 2025)
EndedAt: 2025-03-16 18:09:12 -0400 (Sun, 16 Mar 2025)
EllapsedTime: 100.3 seconds
RetCode: 1
Status:   ERROR  
CheckDir: animalcules.Rcheck
Warnings: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:animalcules.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings animalcules_1.23.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/animalcules.Rcheck’
* using R Under development (unstable) (2025-03-02 r87868)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘animalcules/DESCRIPTION’ ... OK
* this is package ‘animalcules’ version ‘1.23.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 31 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 ‘animalcules’ 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 files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘animalcules-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: find_taxonomy
> ### Title: Find the taxonomy for unlimited tids
> ### Aliases: find_taxonomy
> 
> ### ** Examples
> 
> taxonLevels <- find_taxonomy(tids = 1200)
Error in entrez_check(response) : 
  HTTP failure: 429, too many requests. Functions that contact the NCBI should not be called in parallel. If you are using a shared IP, consider registerring for an API key as described in the rate-limiting section of rentrez tutorial. NCBI message:
 {"error":"API rate limit exceeded","api-key":"170.223.207.78","count":"4","limit":"3"}
Calls: find_taxonomy ... entrez_fetch -> do.call -> <Anonymous> -> entrez_check
Execution halted
* 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: 1 ERROR
See
  ‘/Users/biocbuild/bbs-3.21-bioc/meat/animalcules.Rcheck/00check.log’
for details.


Installation output

animalcules.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL animalcules
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library’
* installing *source* package ‘animalcules’ ...
** this is package ‘animalcules’ version ‘1.23.0’
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** 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 (animalcules)

Tests output

animalcules.Rcheck/tests/testthat.Rout

R Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-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(animalcules)
> 
> test_check("animalcules")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 38 ]
> 
> proc.time()
   user  system elapsed 
  8.720   0.342   9.690 

Example timings

animalcules.Rcheck/animalcules-Ex.timings

nameusersystemelapsed
alpha_div_boxplot0.1880.0210.215
alpha_div_test0.0020.0010.001
counts_to_logcpm0.0010.0000.001
counts_to_relabu0.0010.0000.001
df_char_to_factor0.0000.0000.001
differential_abundance1.1490.0171.174
dimred_pca0.0540.0070.061
dimred_pcoa0.0940.0070.102
dimred_tsne1.8540.0851.948
dimred_umap0.1460.0080.155
diversities0.0010.0000.000
diversities_help000
diversity_beta_boxplot0.0650.0060.072
diversity_beta_heatmap0.0660.0110.076
diversity_beta_test0.0650.0060.070
do_alpha_div_test0.0170.0000.017
filter_categorize0.0890.0140.102
filter_summary_bar_density0.0740.0050.079
filter_summary_pie_box0.0610.0050.065
find_biomarker1.2340.0401.284
find_taxon_mat0.0520.0030.650