Back to Multiple platform build/check report for BioC 3.20:   simplified   long
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This page was generated on 2024-11-20 12:07 -0500 (Wed, 20 Nov 2024).

HostnameOSArch (*)R versionInstalled pkgs
teran2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4481
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4479
palomino8Windows Server 2022 Datacenterx644.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" 4359
lconwaymacOS 12.7.1 Montereyx86_644.4.1 (2024-06-14) -- "Race for Your Life" 4539
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch644.4.1 (2024-06-14) -- "Race for Your Life" 4493
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 67/2289HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
animalcules 1.22.0  (landing page)
Jessica McClintock
Snapshot Date: 2024-11-19 13:40 -0500 (Tue, 19 Nov 2024)
git_url: https://git.bioconductor.org/packages/animalcules
git_branch: RELEASE_3_20
git_last_commit: 7d67c79
git_last_commit_date: 2024-10-29 10:37:18 -0500 (Tue, 29 Oct 2024)
teran2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
nebbiolo2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    ERROR  
palomino8Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    ERROR    OK  
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    OK  


CHECK results for animalcules on kunpeng2

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.
- See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host.

raw results


Summary

Package: animalcules
Version: 1.22.0
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:animalcules.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings animalcules_1.22.0.tar.gz
StartedAt: 2024-11-20 05:07:13 -0000 (Wed, 20 Nov 2024)
EndedAt: 2024-11-20 05:13:03 -0000 (Wed, 20 Nov 2024)
EllapsedTime: 349.8 seconds
RetCode: 0
Status:   OK  
CheckDir: animalcules.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:animalcules.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings animalcules_1.22.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/animalcules.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    gcc (GCC) 12.2.1 20220819 (openEuler 12.2.1-14)
    GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘animalcules/DESCRIPTION’ ... OK
* this is package ‘animalcules’ version ‘1.22.0’
* 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 ‘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 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                        user system elapsed
dimred_tsne            8.742  0.053   8.815
find_biomarker         5.620  0.097   5.810
differential_abundance 5.314  0.148   5.474
* 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

animalcules.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL animalcules
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-4.4.1/site-library’
* installing *source* package ‘animalcules’ ...
** 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 version 4.4.1 (2024-06-14) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-unknown-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(animalcules)
> 
> test_check("animalcules")
[ FAIL 0 | WARN 1 | SKIP 0 | PASS 38 ]

[ FAIL 0 | WARN 1 | SKIP 0 | PASS 38 ]
> 
> proc.time()
   user  system elapsed 
 37.787   1.314  40.316 

Example timings

animalcules.Rcheck/animalcules-Ex.timings

nameusersystemelapsed
alpha_div_boxplot0.7130.0240.739
alpha_div_test0.0040.0000.004
counts_to_logcpm0.0010.0000.001
counts_to_relabu0.0000.0030.003
df_char_to_factor0.0000.0000.001
differential_abundance5.3140.1485.474
dimred_pca0.2940.0120.222
dimred_pcoa0.1630.0140.177
dimred_tsne8.7420.0538.815
dimred_umap0.5360.0080.544
diversities000
diversities_help000
diversity_beta_boxplot0.2780.0080.286
diversity_beta_heatmap0.2810.0080.290
diversity_beta_test0.2310.0000.231
do_alpha_div_test0.0590.0000.059
filter_categorize0.3400.0160.356
filter_summary_bar_density0.3470.0120.359
filter_summary_pie_box0.2760.0110.288
find_biomarker5.6200.0975.810
find_taxon_mat0.2390.0042.115
find_taxonomy0.0330.0000.815
find_taxonomy_3000.0330.0040.795
gini_simpson000
grep_tid000
inverse_simpson000
is_categorical0.0010.0000.001
is_integer00.0010.0000.001
is_integer10.0010.0000.000
mae_pick_organisms0.1300.0080.186
mae_pick_samples0.1660.0080.174
pct2str000
percent0.0000.0000.001
relabu_barplot1.5180.0641.585
relabu_boxplot0.1440.0160.161
relabu_heatmap0.1640.0240.188
run_animalcules000
shannon000
simpson_index000
upsample_counts0.0160.0000.017