Multiple platform build/check report for BioC 3.14 - CHECK results for MicrobiotaProcess on tokay2

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 20.04.4 LTS)	x86_64	4.1.3 (2022-03-10) -- "One Push-Up"	4324
tokay2	Windows Server 2012 R2 Standard	x64	4.1.3 (2022-03-10) -- "One Push-Up"	4077
machv2	macOS 10.14.6 Mojave	x86_64	4.1.3 (2022-03-10) -- "One Push-Up"	4137
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: MicrobiotaProcess

Version: 1.6.6

Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:MicrobiotaProcess.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings MicrobiotaProcess_1.6.6.tar.gz

StartedAt: 2022-04-12 22:51:47 -0400 (Tue, 12 Apr 2022)

EndedAt: 2022-04-12 22:58:42 -0400 (Tue, 12 Apr 2022)

EllapsedTime: 415.0 seconds

RetCode: 0

Status: OK

CheckDir: MicrobiotaProcess.Rcheck

Warnings: 0

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:MicrobiotaProcess.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings MicrobiotaProcess_1.6.6.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/MicrobiotaProcess.Rcheck'
* using R version 4.1.3 (2022-03-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'MicrobiotaProcess/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'MicrobiotaProcess' version '1.6.6'
* 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 whether package 'MicrobiotaProcess' can be installed ... OK
* checking installed package size ... NOTE
  installed size is  5.9Mb
  sub-directories of 1Mb or more:
    R      2.2Mb
    help   1.2Mb
* 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                         user system elapsed
mp_cal_abundance-methods 7.51   0.09    7.61
mp_cal_rarecurve-methods 6.57   0.66    7.22
mp_diff_analysis-methods 5.29   0.23    5.52
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                         user system elapsed
mp_cal_abundance-methods 8.17   0.07    8.25
mp_cal_rarecurve-methods 6.87   0.02    6.92
mp_diff_analysis-methods 6.25   0.03    6.28
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 OK
** running tests for arch 'x64' ...
  Running 'testthat.R'
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... 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
  'C:/Users/biocbuild/bbs-3.14-bioc/meat/MicrobiotaProcess.Rcheck/00check.log'
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/MicrobiotaProcess_1.6.6.tar.gz && rm -rf MicrobiotaProcess.buildbin-libdir && mkdir MicrobiotaProcess.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=MicrobiotaProcess.buildbin-libdir MicrobiotaProcess_1.6.6.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL MicrobiotaProcess_1.6.6.zip && rm MicrobiotaProcess_1.6.6.tar.gz MicrobiotaProcess_1.6.6.zip
###
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##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
 25 2135k   25  539k    0     0  1105k      0  0:00:01 --:--:--  0:00:01 1104k
100 2135k  100 2135k    0     0  1640k      0  0:00:01  0:00:01 --:--:-- 1641k

install for i386

* 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
  converting help for package 'MicrobiotaProcess'
    finding HTML links ... done
    ImportDada2                             html  
    ImportQiime2                            html  
    MPSE-accessors                          html  
    MPSE-class                              html  
    MPSE                                    html  
    alphasample-class                       html  
    as.MPSE                                 html  
REDIRECT:topic	 Previous alias or file overwritten by alias: C:/Users/biocbuild/bbs-3.14-bioc/meat/MicrobiotaProcess.buildbin-libdir/00LOCK-MicrobiotaProcess/00new/MicrobiotaProcess/help/as.mpse.html
    as.phyloseq                             html  
    as.treedata                             html  
    build_tree                              html  
    convert_to_treedata                     html  
    data-hmp_aerobiosis_small               html  
    data-kostic2012crc                      html  
    data-test_otu_data                      html  
    diffAnalysisClass-class                 html  
    diff_analysis                           html  
    dr_extract                              html  
    drop_taxa                               html  
    extract_binary_offspring                html  
    generalizedFC                           html  
    get_NRI_NTI-methods                     html  
    get_alltaxadf                           html  
    get_alphaindex                          html  
    get_clust                               html  
    get_coord                               html  
    get_count                               html  
    get_dist                                html  
    get_mean_median                         html  
    get_pca                                 html  
    get_pcoa                                html  
    get_pvalue                              html  
    get_rarecurve                           html  
    get_sampledflist                        html  
    get_taxadf                              html  
    get_upset                               html  
    get_varct                               html  
    get_vennlist                            html  
    ggbartax                                html  
    ggbox                                   html  
    ggclust                                 html  
    ggdiffbox                               html  
    ggdiffclade                             html  
    ggdifftaxbar                            html  
    ggeffectsize                            html  
    ggordpoint                              html  
    ggrarecurve                             html  
    finding level-2 HTML links ... done

    mouse.time.mpse                         html  
    mp_adonis-methods                       html  
    mp_aggregate-methods                    html  
    mp_aggregate_clade-methods              html  
    mp_anosim-methods                       html  
    mp_balance_clade-methods                html  
    mp_cal_abundance-methods                html  
    mp_cal_alpha-methods                    html  
    mp_cal_cca-methods                      html  
    mp_cal_clust-methods                    html  
    mp_cal_dca-methods                      html  
    mp_cal_dist-methods                     html  
    mp_cal_nmds-methods                     html  
    mp_cal_pca-methods                      html  
    mp_cal_pcoa-methods                     html  
    mp_cal_pd_metric-methods                html  
    mp_cal_rarecurve-methods                html  
    mp_cal_rda-methods                      html  
    mp_cal_upset-methods                    html  
    mp_cal_venn-methods                     html  
    mp_decostand-methods                    html  
    mp_diff_analysis-methods                html  
    mp_diff_clade-methods                   html  
    mp_envfit-methods                       html  
    mp_extract_abundance-methods            html  
    mp_extract_assays-methods               html  
    mp_extract_dist-methods                 html  
    mp_extract_feature-methods              html  
    mp_extract_internal_attr-methods        html  
    mp_extract_rarecurve-methods            html  
    mp_extract_refseq-methods               html  
    mp_extract_sample-methods               html  
    mp_extract_taxonomy-methods             html  
    mp_extract_tree-methods                 html  
    mp_filter_taxa-methods                  html  
    mp_fortify                              html  
    mp_import_metaphlan                     html  
    mp_import_qiime                         html  
    mp_mantel-methods                       html  
    mp_mrpp-methods                         html  
    mp_plot_abundance-methods               html  
    mp_plot_alpha-methods                   html  
    mp_plot_diff_res-methods                html  
    mp_plot_dist-methods                    html  
    mp_plot_ord-methods                     html  
    mp_plot_rarecurve-methods               html  
    mp_plot_upset-methods                   html  
    mp_plot_venn-methods                    html  
    mp_rrarefy-methods                      html  
    mp_select_as_tip-methods                html  
    mp_stat_taxa-methods                    html  
    multi_compare                           html  
    ordplotClass-class                      html  
    pcasample-class                         html  
    pcoa-class                              html  
    prcomp-class                            html  
    print                                   html  
    read_qza                                html  
    reexports                               html  
REDIRECT:topic	 Previous alias or file overwritten by alias: C:/Users/biocbuild/bbs-3.14-bioc/meat/MicrobiotaProcess.buildbin-libdir/00LOCK-MicrobiotaProcess/00new/MicrobiotaProcess/help/as.treedata.html
    set_scale_theme                         html  
    show-methods                            html  
    split_data                              html  
    split_str_to_list                       html  
    theme_taxbar                            html  
** 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

install for x64

* installing *source* package 'MicrobiotaProcess' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'MicrobiotaProcess' as MicrobiotaProcess_1.6.6.zip
* DONE (MicrobiotaProcess)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'MicrobiotaProcess' successfully unpacked and MD5 sums checked


R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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 v1.6.6 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 0 | SKIP 0 | PASS 13 ]
> 
> proc.time()
   user  system elapsed 
  10.98    1.18   12.18


R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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 v1.6.6 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 0 | SKIP 0 | PASS 13 ]
> 
> proc.time()
   user  system elapsed 
  14.92    0.64   15.57

name	user	system	elapsed
ImportDada2	1.69	0.07	1.75
ImportQiime2	4.02	0.14	4.25
MPSE	0.12	0.00	0.12
as.treedata	0.02	0.00	0.00
build_tree	0	0	0
convert_to_treedata	0	0	0
data-hmp_aerobiosis_small	0.01	0.00	0.02
data-kostic2012crc	0.04	0.00	0.03
data-test_otu_data	0.01	0.00	0.01
diff_analysis	0	0	0
dr_extract	0	0	0
drop_taxa	0	0	0
generalizedFC	0	0	0
get_alltaxadf	0	0	0
get_alphaindex	0	0	0
get_clust	0	0	0
get_coord	0	0	0
get_count	0	0	0
get_dist	0	0	0
get_mean_median	0	0	0
get_pca	0	0	0
get_pcoa	0	0	0
get_pvalue	0.12	0.00	0.44
get_rarecurve	0	0	0
get_sampledflist	0	0	0
get_taxadf	0	0	0
get_upset	0	0	0
get_varct	0	0	0
get_vennlist	0	0	0
ggbartax	0	0	0
ggbox	0	0	0
ggclust	0	0	0
ggdiffbox	0	0	0
ggdiffclade	0	0	0
ggdifftaxbar	0	0	0
ggeffectsize	0	0	0
ggordpoint	0	0	0
ggrarecurve	0	0	0
mp_adonis-methods	0.24	0.02	0.25
mp_aggregate-methods	0	0	0
mp_aggregate_clade-methods	0	0	0
mp_anosim-methods	1.31	0.00	1.31
mp_balance_clade-methods	0	0	0
mp_cal_abundance-methods	7.51	0.09	7.61
mp_cal_alpha-methods	1.54	0.00	1.58
mp_cal_cca-methods	0.84	0.00	0.86
mp_cal_clust-methods	0.49	0.00	0.48
mp_cal_dist-methods	1.86	0.02	1.87
mp_cal_nmds-methods	0.27	0.00	0.26
mp_cal_pca-methods	1.67	0.01	1.69
mp_cal_pcoa-methods	0.67	0.00	0.67
mp_cal_pd_metric-methods	0	0	0
mp_cal_rarecurve-methods	6.57	0.66	7.22
mp_cal_rda-methods	0.58	0.02	0.60
mp_cal_upset-methods	1.25	0.01	1.26
mp_cal_venn-methods	1.74	0.10	2.25
mp_decostand-methods	0.60	0.00	0.61
mp_diff_analysis-methods	5.29	0.23	5.52
mp_diff_clade-methods	0	0	0
mp_envfit-methods	1.93	0.11	2.04
mp_filter_taxa-methods	1.19	0.03	1.22
mp_import_metaphlan	4.31	0.00	4.39
mp_mantel-methods	0.36	0.02	0.38
mp_mrpp-methods	0.22	0.00	0.22
mp_plot_abundance-methods	0	0	0
mp_plot_alpha-methods	0	0	0
mp_plot_dist-methods	0	0	0
mp_plot_ord-methods	0	0	0
mp_plot_rarecurve-methods	0	0	0
mp_plot_upset-methods	0	0	0
mp_plot_venn-methods	0	0	0
mp_rrarefy-methods	0.63	0.00	0.62
mp_select_as_tip-methods	0	0	0
mp_stat_taxa-methods	0.96	0.04	1.00
multi_compare	0.01	0.00	0.01
read_qza	0	0	0
show-methods	0	0	0
split_data	0.02	0.00	0.02
split_str_to_list	0	0	0
theme_taxbar	0	0	0

name	user	system	elapsed
ImportDada2	2.66	0.05	2.77
ImportQiime2	3.97	0.05	4.01
MPSE	0.16	0.00	0.16
as.treedata	0	0	0
build_tree	0	0	0
convert_to_treedata	0	0	0
data-hmp_aerobiosis_small	0.01	0.00	0.01
data-kostic2012crc	0.05	0.01	0.07
data-test_otu_data	0	0	0
diff_analysis	0	0	0
dr_extract	0	0	0
drop_taxa	0	0	0
generalizedFC	0.01	0.00	0.01
get_alltaxadf	0	0	0
get_alphaindex	0	0	0
get_clust	0	0	0
get_coord	0	0	0
get_count	0	0	0
get_dist	0	0	0
get_mean_median	0	0	0
get_pca	0	0	0
get_pcoa	0	0	0
get_pvalue	0.18	0.00	0.19
get_rarecurve	0	0	0
get_sampledflist	0	0	0
get_taxadf	0	0	0
get_upset	0.00	0.02	0.02
get_varct	0	0	0
get_vennlist	0	0	0
ggbartax	0	0	0
ggbox	0	0	0
ggclust	0	0	0
ggdiffbox	0	0	0
ggdiffclade	0	0	0
ggdifftaxbar	0	0	0
ggeffectsize	0	0	0
ggordpoint	0	0	0
ggrarecurve	0	0	0
mp_adonis-methods	0.21	0.01	0.23
mp_aggregate-methods	0	0	0
mp_aggregate_clade-methods	0	0	0
mp_anosim-methods	1.47	0.00	1.47
mp_balance_clade-methods	0	0	0
mp_cal_abundance-methods	8.17	0.07	8.25
mp_cal_alpha-methods	1.13	0.01	1.14
mp_cal_cca-methods	0.8	0.0	0.8
mp_cal_clust-methods	0.42	0.00	0.42
mp_cal_dist-methods	1.65	0.02	1.67
mp_cal_nmds-methods	0.29	0.00	0.28
mp_cal_pca-methods	1.42	0.00	1.42
mp_cal_pcoa-methods	0.67	0.01	0.69
mp_cal_pd_metric-methods	0	0	0
mp_cal_rarecurve-methods	6.87	0.02	6.92
mp_cal_rda-methods	0.85	0.00	0.85
mp_cal_upset-methods	1.33	0.00	1.32
mp_cal_venn-methods	1.79	0.05	2.29
mp_decostand-methods	0.63	0.00	0.62
mp_diff_analysis-methods	6.25	0.03	6.28
mp_diff_clade-methods	0	0	0
mp_envfit-methods	2.00	0.01	2.01
mp_filter_taxa-methods	1.16	0.00	1.15
mp_import_metaphlan	3.04	0.00	3.05
mp_mantel-methods	0.33	0.00	0.33
mp_mrpp-methods	0.17	0.02	0.19
mp_plot_abundance-methods	0	0	0
mp_plot_alpha-methods	0	0	0
mp_plot_dist-methods	0	0	0
mp_plot_ord-methods	0	0	0
mp_plot_rarecurve-methods	0	0	0
mp_plot_upset-methods	0	0	0
mp_plot_venn-methods	0	0	0
mp_rrarefy-methods	0.45	0.01	0.47
mp_select_as_tip-methods	0	0	0
mp_stat_taxa-methods	0.85	0.00	0.85
multi_compare	0.01	0.00	0.01
read_qza	0	0	0
show-methods	0	0	0
split_data	0.00	0.02	0.02
split_str_to_list	0	0	0
theme_taxbar	0	0	0

CHECK results for MicrobiotaProcess on tokay2

Summary

Command output

Installation output

Tests output

Example timings