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### Running command:
###
###   /home/biocbuild/R/R-4.3.0/bin/R CMD check --install=check:MicrobiotaProcess.install-out.txt --library=/home/biocbuild/R/R-4.3.0/site-library --timings MicrobiotaProcess_1.13.1.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/MicrobiotaProcess.Rcheck’
* using R version 4.3.0 (2023-04-21)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
    gcc (GCC) 10.3.1
    GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* checking for file ‘MicrobiotaProcess/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘MicrobiotaProcess’ version ‘1.13.1’
* 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  5.7Mb
  sub-directories of 1Mb or more:
    R         2.5Mb
    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 ... ERROR
Running examples in ‘MicrobiotaProcess-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: mp_diff_analysis
> ### Title: Differential expression analysis for MPSE or tbl_mpse object
> ### Aliases: mp_diff_analysis mp_diff_analysis,MPSE-method
> ###   mp_diff_analysis,MPSE mp_diff_analysis,tbl_mpse-method
> ###   mp_diff_analysis,tbl_mpse mp_diff_analysis,grouped_df_mpse-method
> ###   mp_diff_analysis,grouped_df_mpse
> 
> ### ** Examples
> 
> data(mouse.time.mpse)
> mouse.time.mpse %<>%
+   mp_rrarefy() 
> mouse.time.mpse
# A MPSE-tibble (MPSE object) abstraction: 4,142 × 12
# OTU=218 | Samples=19 | Assays=Abundance, RareAbundance | Taxonomy=Kingdom,
#   Phylum, Class, Order, Family, Genus, Species
   OTU    Sample Abundance RareAbundance time  Kingdom Phylum Class Order Family
   <chr>  <chr>      <int>         <int> <chr> <chr>   <chr>  <chr> <chr> <chr> 
 1 OTU_1  F3D0         579           214 Early k__Bac… p__Ba… c__B… o__B… f__Mu…
 2 OTU_2  F3D0         345           116 Early k__Bac… p__Ba… c__B… o__B… f__Mu…
 3 OTU_3  F3D0         449           179 Early k__Bac… p__Ba… c__B… o__B… f__Mu…
 4 OTU_4  F3D0         430           167 Early k__Bac… p__Ba… c__B… o__B… f__Mu…
 5 OTU_5  F3D0         154            54 Early k__Bac… p__Ba… c__B… o__B… f__Ba…
 6 OTU_6  F3D0         470           174 Early k__Bac… p__Ba… c__B… o__B… f__Mu…
 7 OTU_7  F3D0         282           115 Early k__Bac… p__Ba… c__B… o__B… f__Mu…
 8 OTU_8  F3D0         184            74 Early k__Bac… p__Ba… c__B… o__B… f__Ri…
 9 OTU_9  F3D0          45            16 Early k__Bac… p__Ba… c__B… o__B… f__Mu…
10 OTU_10 F3D0         158            59 Early k__Bac… p__Ba… c__B… o__B… f__Mu…
# ℹ 4,132 more rows
# ℹ 2 more variables: Genus <chr>, Species <chr>
> mouse.time.mpse %<>%
+   mp_diff_analysis(.abundance=RareAbundance, 
+                    .group=time, 
+                    first.test.alpha=0.01,
+                    action="add") 
> library(ggplot2)
> p <- mouse.time.mpse %>% mp_plot_diff_res()
Warning: Duplicated aesthetics after name standardisation: fill
Error in new_stat$default_aes[[new_aes]] : no such index at level 1
Calls: %>% -> mp_plot_diff_res -> mp_plot_diff_res
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 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 ERROR, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.18-bioc/meat/MicrobiotaProcess.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/R/R-4.3.0/bin/R CMD INSTALL MicrobiotaProcess
###
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* installing to library ‘/home/biocbuild/R/R-4.3.0/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)

R version 4.3.0 (2023-04-21) -- "Already Tomorrow"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-unknown-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 v1.13.1 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 
 17.391   0.679  18.068