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This page was generated on 2025-09-29 11:41 -0400 (Mon, 29 Sep 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4827
merida1macOS 12.7.5 Montereyx86_644.5.1 RC (2025-06-05 r88288) -- "Great Square Root" 4608
kjohnson1macOS 13.6.6 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4549
kunpeng2Linux (openEuler 24.03 LTS)aarch64R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" 4580
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 1282/2341HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MicrobiotaProcess 1.20.2  (landing page)
Shuangbin Xu
Snapshot Date: 2025-09-25 13:40 -0400 (Thu, 25 Sep 2025)
git_url: https://git.bioconductor.org/packages/MicrobiotaProcess
git_branch: RELEASE_3_21
git_last_commit: a0e37d8
git_last_commit_date: 2025-09-17 02:26:41 -0400 (Wed, 17 Sep 2025)
nebbiolo1Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.5 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  


CHECK results for MicrobiotaProcess on kunpeng2

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: 1.20.2
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_1.20.2.tar.gz
StartedAt: 2025-09-26 12:35:34 -0000 (Fri, 26 Sep 2025)
EndedAt: 2025-09-26 12:42:42 -0000 (Fri, 26 Sep 2025)
EllapsedTime: 427.4 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_1.20.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/MicrobiotaProcess.Rcheck’
* using R Under development (unstable) (2025-02-19 r87757)
* 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-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘MicrobiotaProcess/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘MicrobiotaProcess’ version ‘1.20.2’
* 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     12.113  0.208  12.292
mp_cal_rarecurve-methods      9.139  0.176   9.330
mp_envfit-methods             8.537  0.044   8.619
mp_plot_diff_boxplot-methods  7.581  0.008   7.604
mp_diff_analysis-methods      6.568  0.075   6.647
* 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-3.21-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-devel_2025-02-19/site-library’
* installing *source* package ‘MicrobiotaProcess’ ...
** this is package ‘MicrobiotaProcess’ version ‘1.20.2’
** 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 Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences"
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 v1.20.2 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 
 17.403   0.640  18.053 

Example timings

MicrobiotaProcess.Rcheck/MicrobiotaProcess-Ex.timings

nameusersystemelapsed
ImportDada22.7170.1512.875
ImportQiime24.5420.1004.660
MPSE0.1080.0040.113
as.treedata000
build_tree0.0010.0000.000
convert_to_treedata000
data-hmp_aerobiosis_small0.010.000.01
data-kostic2012crc0.0190.0040.024
data-test_otu_data0.0000.0020.003
diff_analysis000
dr_extract0.0000.0010.000
drop_taxa000
generalizedFC0.0070.0000.006
get_alltaxadf000
get_alphaindex000
get_clust000
get_coord0.0000.0000.001
get_count000
get_dist0.0000.0000.001
get_mean_median000
get_pca0.0000.0000.001
get_pcoa000
get_pvalue0.0720.0000.075
get_rarecurve0.0000.0000.001
get_sampledflist000
get_taxadf000
get_upset000
get_varct000
get_vennlist000
ggbartax000
ggbox0.0010.0000.000
ggclust000
ggdiffbox0.0000.0000.001
ggdiffclade000
ggdifftaxbar000
ggeffectsize000
ggordpoint000
ggrarecurve000
mp_adonis-methods0.1320.0000.132
mp_aggregate-methods000
mp_aggregate_clade-methods000
mp_anosim-methods1.5050.0241.530
mp_balance_clade-methods000
mp_cal_abundance-methods12.113 0.20812.292
mp_cal_alpha-methods1.4150.0401.459
mp_cal_cca-methods1.2770.0321.314
mp_cal_clust-methods0.5390.0040.544
mp_cal_dist-methods2.8770.0122.894
mp_cal_divergence-methods000
mp_cal_nmds-methods0.3610.0040.367
mp_cal_pca-methods2.1620.0162.182
mp_cal_pcoa-methods0.7470.0160.764
mp_cal_pd_metric-methods0.0000.0000.001
mp_cal_rarecurve-methods9.1390.1769.330
mp_cal_rda-methods1.0580.0041.064
mp_cal_upset-methods1.4160.0041.422
mp_cal_venn-methods0.6330.0080.643
mp_decostand-methods0.4670.0040.472
mp_diff_analysis-methods6.5680.0756.647
mp_diff_clade-methods0.0000.0000.001
mp_dmn-methods000
mp_dmngroup-methods000
mp_envfit-methods8.5370.0448.619
mp_filter_taxa-methods1.1380.0041.145
mp_import_metaphlan4.4630.0204.499
mp_mantel-methods0.4420.0000.443
mp_mrpp-methods0.2410.0000.241
mp_plot_abundance-methods000
mp_plot_alpha-methods000
mp_plot_diff_boxplot-methods7.5810.0087.604
mp_plot_diff_cladogram000
mp_plot_diff_manhattan-methods3.8740.0403.907
mp_plot_dist-methods0.0010.0000.000
mp_plot_ord-methods0.0000.0000.001
mp_plot_rarecurve-methods000
mp_plot_upset-methods000
mp_plot_venn-methods000
mp_rrarefy-methods0.4390.0000.440
mp_select_as_tip-methods000
mp_stat_taxa-methods1.1530.0081.141
multi_compare0.0060.0040.011
read_qza000
show-methods000
split_data0.0030.0000.002
split_str_to_list000
theme_taxbar000