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This page was generated on 2025-10-09 12:07 -0400 (Thu, 09 Oct 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4854
lconwaymacOS 12.7.1 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4642
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4587
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4584
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 1289/2341HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MicrobiotaProcess 1.21.2  (landing page)
Shuangbin Xu
Snapshot Date: 2025-10-08 14:17 -0400 (Wed, 08 Oct 2025)
git_url: https://git.bioconductor.org/packages/MicrobiotaProcess
git_branch: devel
git_last_commit: 0822a21
git_last_commit_date: 2025-09-23 21:22:57 -0400 (Tue, 23 Sep 2025)
nebbiolo2Linux (Ubuntu 24.04.3 LTS) / x86_64  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 13.7.7 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  


CHECK results for MicrobiotaProcess on taishan

To the developers/maintainers of the MicrobiotaProcess package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/MicrobiotaProcess.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: MicrobiotaProcess
Version: 1.21.2
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:MicrobiotaProcess.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings MicrobiotaProcess_1.21.2.tar.gz
StartedAt: 2025-10-07 09:40:00 -0000 (Tue, 07 Oct 2025)
EndedAt: 2025-10-07 09:47:06 -0000 (Tue, 07 Oct 2025)
EllapsedTime: 425.4 seconds
RetCode: 0
Status:   OK  
CheckDir: MicrobiotaProcess.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:MicrobiotaProcess.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings MicrobiotaProcess_1.21.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/MicrobiotaProcess.Rcheck’
* using R version 4.5.0 (2025-04-11)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘MicrobiotaProcess/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘MicrobiotaProcess’ version ‘1.21.2’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 29 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 ‘MicrobiotaProcess’ can be installed ... OK
* checking installed package size ... INFO
  installed size is  5.8Mb
  sub-directories of 1Mb or more:
    R         2.6Mb
    figures   1.9Mb
* 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 whether startup messages can be suppressed ... 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 ... NOTE
Non-topic package-anchored link(s) in Rd file 'reexports.Rd':
  ‘[magrittr:compound]{%<>%}’ ‘[magrittr:pipe]{%>%}’
  ‘[magrittr:aliases]{extract}’

See section 'Cross-references' in the 'Writing R Extensions' manual.

Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  ggrarecurve.Rd: ggplot2
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                               user system elapsed
mp_cal_abundance-methods     13.441  0.064  13.500
mp_cal_rarecurve-methods      8.829  0.071   8.929
mp_plot_diff_boxplot-methods  8.734  0.016   8.754
mp_envfit-methods             8.611  0.040   8.677
mp_diff_analysis-methods      6.765  0.028   6.791
* 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 NOTE
See
  ‘/home/biocbuild/bbs-3.22-bioc/meat/MicrobiotaProcess.Rcheck/00check.log’
for details.


Installation output

MicrobiotaProcess.Rcheck/00install.out

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


* installing to library ‘/home/biocbuild/R/R-4.5.0/site-library’
* installing *source* package ‘MicrobiotaProcess’ ...
** this is package ‘MicrobiotaProcess’ version ‘1.21.2’
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
in method for ‘taxonomy<-’ with signature ‘x="MPSE",value="taxonomyTable"’: no definition for class “taxonomyTable”
Creating a generic function for ‘rownames<-’ from package ‘base’ in package ‘MicrobiotaProcess’
in method for ‘get_alltaxadf’ with signature ‘"phyloseq"’: no definition for class “phyloseq”
in method for ‘get_taxadf’ with signature ‘"phyloseq"’: no definition for class “phyloseq”
in method for ‘get_alphaindex’ with signature ‘"phyloseq"’: no definition for class “phyloseq”
in method for ‘get_NRI_NTI’ with signature ‘"phyloseq"’: no definition for class “phyloseq”
in method for ‘get_rarecurve’ with signature ‘"phyloseq"’: no definition for class “phyloseq”
in method for ‘get_upset’ with signature ‘"phyloseq"’: no definition for class “phyloseq”
in method for ‘get_vennlist’ with signature ‘"phyloseq"’: no definition for class “phyloseq”
in method for ‘drop_taxa’ with signature ‘"phyloseq"’: no definition for class “phyloseq”
** 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 (MicrobiotaProcess)

Tests output

MicrobiotaProcess.Rcheck/tests/testthat.Rout


R version 4.5.0 (2025-04-11) -- "How About a Twenty-Six"
Copyright (C) 2025 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("MicrobiotaProcess")
MicrobiotaProcess v1.21.2 For help:
https://github.com/YuLab-SMU/MicrobiotaProcess/issues

If you use MicrobiotaProcess in published research, please cite the
paper:

Shuangbin Xu, Li Zhan, Wenli Tang, Qianwen Wang, Zehan Dai, Lang Zhou,
Tingze Feng, Meijun Chen, Tianzhi Wu, Erqiang Hu, Guangchuang Yu.
MicrobiotaProcess: A comprehensive R package for deep mining
microbiome. The Innovation. 2023, 4(2):100388. doi:
10.1016/j.xinn.2023.100388

Export the citation to BibTex by citation('MicrobiotaProcess')

This message can be suppressed by:
suppressPackageStartupMessages(library(MicrobiotaProcess))

Attaching package: 'MicrobiotaProcess'

The following object is masked from 'package:stats':

    filter

> test_check("MicrobiotaProcess")
[ FAIL 0 | WARN 9 | SKIP 0 | PASS 13 ]

[ FAIL 0 | WARN 9 | SKIP 0 | PASS 13 ]
> 
> proc.time()
   user  system elapsed 
 17.248   0.815  18.075 

Example timings

MicrobiotaProcess.Rcheck/MicrobiotaProcess-Ex.timings

nameusersystemelapsed
ImportDada21.7520.0641.823
ImportQiime24.4190.0634.511
MPSE0.8110.0040.817
as.treedata000
build_tree000
convert_to_treedata000
data-hmp_aerobiosis_small0.010.000.01
data-kostic2012crc0.0240.0000.024
data-test_otu_data0.0000.0020.002
diff_analysis000
dr_extract000
drop_taxa0.0000.0000.001
generalizedFC0.0070.0000.007
get_alltaxadf000
get_alphaindex000
get_clust000
get_coord000
get_count0.0010.0000.000
get_dist000
get_mean_median0.0010.0000.000
get_pca000
get_pcoa000
get_pvalue0.0730.0000.076
get_rarecurve000
get_sampledflist0.0010.0000.000
get_taxadf000
get_upset0.0000.0000.001
get_varct000
get_vennlist000
ggbartax000
ggbox000
ggclust0.0010.0000.000
ggdiffbox000
ggdiffclade0.0000.0000.001
ggdifftaxbar000
ggeffectsize000
ggordpoint0.0010.0000.000
ggrarecurve000
mp_adonis-methods0.1270.0000.128
mp_aggregate-methods000
mp_aggregate_clade-methods0.0000.0000.001
mp_anosim-methods1.6120.0241.641
mp_balance_clade-methods000
mp_cal_abundance-methods13.441 0.06413.500
mp_cal_alpha-methods1.7820.0001.787
mp_cal_cca-methods1.3940.0001.400
mp_cal_clust-methods0.7870.0000.790
mp_cal_dist-methods4.1980.0764.287
mp_cal_divergence-methods000
mp_cal_nmds-methods0.4650.0080.475
mp_cal_pca-methods2.8700.0082.888
mp_cal_pcoa-methods0.8640.0000.867
mp_cal_pd_metric-methods000
mp_cal_rarecurve-methods8.8290.0718.929
mp_cal_rda-methods1.8550.0481.909
mp_cal_upset-methods1.6830.0001.688
mp_cal_venn-methods0.6950.0080.704
mp_decostand-methods0.4290.0000.430
mp_diff_analysis-methods6.7650.0286.791
mp_diff_clade-methods000
mp_dmn-methods0.0000.0000.001
mp_dmngroup-methods000
mp_envfit-methods8.6110.0408.677
mp_filter_taxa-methods1.1720.0001.176
mp_import_metaphlan4.1510.0244.192
mp_mantel-methods0.4330.0000.434
mp_mrpp-methods0.2570.0000.262
mp_plot_abundance-methods0.0010.0000.000
mp_plot_alpha-methods000
mp_plot_diff_boxplot-methods8.7340.0168.754
mp_plot_diff_cladogram000
mp_plot_diff_manhattan-methods3.9520.0644.006
mp_plot_dist-methods000
mp_plot_ord-methods000
mp_plot_rarecurve-methods000
mp_plot_upset-methods0.0000.0000.001
mp_plot_venn-methods000
mp_rrarefy-methods0.4410.0000.442
mp_select_as_tip-methods000
mp_stat_taxa-methods1.2320.0161.227
multi_compare0.0090.0040.013
read_qza0.0010.0000.000
show-methods000
split_data0.0030.0000.003
split_str_to_list000
theme_taxbar000