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### Running command:
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###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:MicrobiotaProcess.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings MicrobiotaProcess_1.11.3.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/MicrobiotaProcess.Rcheck’
* using R Under development (unstable) (2023-01-14 r83615)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
    GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.1 LTS
* using session charset: UTF-8
* checking for file ‘MicrobiotaProcess/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘MicrobiotaProcess’ version ‘1.11.3’
* 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 ... 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 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 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 RareA…¹ time  Kingdom Phylum Class Order Family Genus
   <chr>  <chr>      <int>   <int> <chr> <chr>   <chr>  <chr> <chr> <chr>  <chr>
 1 OTU_1  F3D0         579     214 Early k__Bac… p__Ba… c__B… o__B… f__Mu… g__u…
 2 OTU_2  F3D0         345     116 Early k__Bac… p__Ba… c__B… o__B… f__Mu… g__u…
 3 OTU_3  F3D0         449     179 Early k__Bac… p__Ba… c__B… o__B… f__Mu… g__u…
 4 OTU_4  F3D0         430     167 Early k__Bac… p__Ba… c__B… o__B… f__Mu… g__u…
 5 OTU_5  F3D0         154      54 Early k__Bac… p__Ba… c__B… o__B… f__Ba… g__B…
 6 OTU_6  F3D0         470     174 Early k__Bac… p__Ba… c__B… o__B… f__Mu… g__u…
 7 OTU_7  F3D0         282     115 Early k__Bac… p__Ba… c__B… o__B… f__Mu… g__u…
 8 OTU_8  F3D0         184      74 Early k__Bac… p__Ba… c__B… o__B… f__Ri… g__A…
 9 OTU_9  F3D0          45      16 Early k__Bac… p__Ba… c__B… o__B… f__Mu… g__u…
10 OTU_10 F3D0         158      59 Early k__Bac… p__Ba… c__B… o__B… f__Mu… g__u…
# … with 4,132 more rows, 1 more variable: Species <chr>, and abbreviated
#   variable name ¹​RareAbundance
> 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
> p <- p + 
+      scale_fill_manual(
+        aesthetics = "fill_new", # The fill aes was renamed to "fill_new" for the abundance dotplot layer
+        values = c("skyblue", "orange")
+      )  + 
+      scale_fill_manual(
+        values=c("skyblue", "orange") # The LDA barplot layer
+      )
Scale for fill_new is already present.
Adding another scale for fill_new, which will replace the existing scale.
> ### and the fill aes for hight light layer of tree was renamed to 'fill_new_new'
> p <- p + 
+      scale_fill_manual(
+        aesthetics = "fill_new_new",
+        values = c("#E41A1C", "#377EB8", "#4DAF4A", 
+                   "#984EA3", "#FF7F00", "#FFFF33", 
+                   "#A65628", "#F781BF", "#999999")
+      )
Scale for fill_new_new is already present.
Adding another scale for fill_new_new, which will replace the existing scale.
> p
Warning: Duplicated aesthetics after name standardisation: fill_new
Killed
* 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 ... ERROR
Error(s) in re-building vignettes:
  ...
--- re-building ‘MicrobiotaProcess.Rmd’ using rmarkdown
Killed

* checking PDF version of manual ... OK
* DONE

Status: 2 ERRORs
See
  ‘/home/biocbuild/bbs-3.17-bioc/meat/MicrobiotaProcess.Rcheck/00check.log’
for details.

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### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL MicrobiotaProcess
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* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/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 Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences"
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 v1.11.3 For help:
https://github.com/YuLab-SMU/MicrobiotaProcess/issues

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

S Xu, L Zhan, W Tang, Z Dai, L Zhou, T Feng, M Chen, S Liu, X Fu, T Wu,
E Hu, G Yu. MicrobiotaProcess: A comprehensive R package for managing
and analyzing microbiome and other ecological data within the tidy
framework. 04 February 2022, PREPRINT (Version 1) available at Research
Square [https://doi.org/10.21203/rs.3.rs-1284357/v1]

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 
 17.258   0.746  23.204