Multiple platform build/check report for BioC 3.18 - CHECK results for MicrobiotaProcess on nebbiolo2

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 22.04.3 LTS)	x86_64	4.3.3 (2024-02-29) -- "Angel Food Cake"	4669
palomino4	Windows Server 2022 Datacenter	x64	4.3.3 (2024-02-29 ucrt) -- "Angel Food Cake"	4404
merida1	macOS 12.7.1 Monterey	x86_64	4.3.3 (2024-02-29) -- "Angel Food Cake"	4427
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*

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### Running command:
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###   /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --install=check:MicrobiotaProcess.install-out.txt --library=/home/biocbuild/bbs-3.18-bioc/R/site-library --timings MicrobiotaProcess_1.14.1.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/MicrobiotaProcess.Rcheck’
* using R version 4.3.3 (2024-02-29)
* using platform: x86_64-pc-linux-gnu (64-bit)
* 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 ‘MicrobiotaProcess/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘MicrobiotaProcess’ version ‘1.14.1’
* 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 ‘MicrobiotaProcess’ can be installed ... OK
* checking installed package size ... NOTE
  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 R 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 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 ... 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                              user system elapsed
mp_cal_abundance-methods     9.342  0.268   9.331
mp_cal_rarecurve-methods     5.602  0.099   5.702
mp_plot_diff_boxplot-methods 5.229  0.024   5.074
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘MicrobiotaProcess.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.18-bioc/meat/MicrobiotaProcess.Rcheck/00check.log’
for details.

Installation output

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### Running command:
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###   /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD INSTALL MicrobiotaProcess
###
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* installing to library ‘/home/biocbuild/bbs-3.18-bioc/R/site-library’
* installing *source* package ‘MicrobiotaProcess’ ...
** 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


R version 4.3.3 (2024-02-29) -- "Angel Food Cake"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

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 v1.14.1 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 
 12.414   0.708  13.015

Example timings

name	user	system	elapsed
ImportDada2	1.808	0.157	1.965
ImportQiime2	3.068	0.043	3.116
MPSE	0.121	0.001	0.121
as.treedata	0	0	0
build_tree	0	0	0
convert_to_treedata	0	0	0
data-hmp_aerobiosis_small	0.012	0.000	0.011
data-kostic2012crc	0.018	0.011	0.030
data-test_otu_data	0.002	0.000	0.002
diff_analysis	0	0	0
dr_extract	0	0	0
drop_taxa	0	0	0
generalizedFC	0.006	0.001	0.005
get_alltaxadf	0	0	0
get_alphaindex	0	0	0
get_clust	0	0	0
get_coord	0	0	0
get_count	0.000	0.000	0.001
get_dist	0	0	0
get_mean_median	0	0	0
get_pca	0	0	0
get_pcoa	0	0	0
get_pvalue	0.061	0.003	0.065
get_rarecurve	0	0	0
get_sampledflist	0	0	0
get_taxadf	0.001	0.001	0.000
get_upset	0	0	0
get_varct	0	0	0
get_vennlist	0	0	0
ggbartax	0	0	0
ggbox	0.000	0.001	0.001
ggclust	0	0	0
ggdiffbox	0.000	0.001	0.000
ggdiffclade	0	0	0
ggdifftaxbar	0	0	0
ggeffectsize	0	0	0
ggordpoint	0	0	0
ggrarecurve	0.000	0.000	0.001
mp_adonis-methods	0.127	0.004	0.131
mp_aggregate-methods	0	0	0
mp_aggregate_clade-methods	0	0	0
mp_anosim-methods	1.109	0.004	1.114
mp_balance_clade-methods	0.000	0.000	0.001
mp_cal_abundance-methods	9.342	0.268	9.331
mp_cal_alpha-methods	1.023	0.056	1.081
mp_cal_cca-methods	0.882	0.004	0.887
mp_cal_clust-methods	0.363	0.004	0.368
mp_cal_dist-methods	2.166	0.008	2.173
mp_cal_divergence-methods	0.001	0.000	0.000
mp_cal_nmds-methods	0.268	0.012	0.280
mp_cal_pca-methods	1.435	0.007	1.442
mp_cal_pcoa-methods	0.526	0.008	0.534
mp_cal_pd_metric-methods	0	0	0
mp_cal_rarecurve-methods	5.602	0.099	5.702
mp_cal_rda-methods	0.653	0.012	0.665
mp_cal_upset-methods	1.378	0.008	1.370
mp_cal_venn-methods	0.449	0.000	0.435
mp_decostand-methods	0.310	0.003	0.314
mp_diff_analysis-methods	4.163	0.029	4.074
mp_diff_clade-methods	0	0	0
mp_dmn-methods	0	0	0
mp_dmngroup-methods	0	0	0
mp_envfit-methods	1.796	0.032	1.827
mp_filter_taxa-methods	0.885	0.004	0.889
mp_import_metaphlan	2.749	0.036	2.786
mp_mantel-methods	0.250	0.004	0.255
mp_mrpp-methods	0.155	0.004	0.159
mp_plot_abundance-methods	0.001	0.000	0.000
mp_plot_alpha-methods	0	0	0
mp_plot_diff_boxplot-methods	5.229	0.024	5.074
mp_plot_diff_cladogram	0	0	0
mp_plot_diff_manhattan-methods	2.776	0.012	2.668
mp_plot_dist-methods	0	0	0
mp_plot_ord-methods	0	0	0
mp_plot_rarecurve-methods	0.001	0.000	0.000
mp_plot_upset-methods	0	0	0
mp_plot_venn-methods	0	0	0
mp_rrarefy-methods	0.310	0.008	0.317
mp_select_as_tip-methods	0	0	0
mp_stat_taxa-methods	0.886	0.019	0.799
multi_compare	0.009	0.000	0.008
read_qza	0	0	0
show-methods	0	0	0
split_data	0.002	0.001	0.002
split_str_to_list	0	0	0
theme_taxbar	0	0	0

CHECK results for MicrobiotaProcess on nebbiolo2

Summary

Command output

Installation output

Tests output

Example timings