Multiple platform build/check report for BioC 3.13 - CHECK results for MicrobiotaProcess on tokay2

Package: MicrobiotaProcess

Version: 1.4.4

Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:MicrobiotaProcess.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings MicrobiotaProcess_1.4.4.tar.gz

StartedAt: 2021-10-15 01:54:38 -0400 (Fri, 15 Oct 2021)

EndedAt: 2021-10-15 02:02:23 -0400 (Fri, 15 Oct 2021)

EllapsedTime: 464.4 seconds

RetCode: 0

Status: OK

CheckDir: MicrobiotaProcess.Rcheck

Warnings: 0

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### Running command:
###
###   C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:MicrobiotaProcess.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings MicrobiotaProcess_1.4.4.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/MicrobiotaProcess.Rcheck'
* using R version 4.1.1 (2021-08-10)
* 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 '1.4.4'
* 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 ... 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
* 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_rarecurve-methods 8.12   0.11    8.24
mp_cal_venn-methods      1.68   0.34   10.31
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                         user system elapsed
mp_cal_rarecurve-methods 7.67   0.11    7.78
mp_cal_abundance-methods 5.99   0.11    6.11
mp_diff_analysis-methods 5.20   0.10    5.32
mp_cal_venn-methods      1.88   0.11    5.86
* 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: OK

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/MicrobiotaProcess_1.4.4.tar.gz && rm -rf MicrobiotaProcess.buildbin-libdir && mkdir MicrobiotaProcess.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=MicrobiotaProcess.buildbin-libdir MicrobiotaProcess_1.4.4.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL MicrobiotaProcess_1.4.4.zip && rm MicrobiotaProcess_1.4.4.tar.gz MicrobiotaProcess_1.4.4.zip
###
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                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 1496k  100 1496k    0     0  2565k      0 --:--:-- --:--:-- --:--:-- 2571k

install for i386

* installing *source* package 'MicrobiotaProcess' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Creating a generic function for 'rownames<-' from package 'base' in package 'MicrobiotaProcess'
** 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  
    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  
    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_anosim-methods                       html  
    mp_cal_NRI_NTI-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_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_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_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_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-3.13-bioc/meat/MicrobiotaProcess.buildbin-libdir/00LOCK-MicrobiotaProcess/00new/MicrobiotaProcess/help/as.treedata.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_1.4.4.zip
* DONE (MicrobiotaProcess)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'MicrobiotaProcess' successfully unpacked and MD5 sums checked


R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 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")

Attaching package: 'MicrobiotaProcess'

The following object is masked from 'package:stats':

    filter

> test_check("MicrobiotaProcess")
Processing map file...
Processing otu/tax file...
Reading file into memory prior to parsing...
Detecting first header line...
Header is on line 2  
Converting input file to a table...
Defining OTU table... 
Parsing taxonomy table...
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 12 ]
> 
> proc.time()
   user  system elapsed 
  20.17    1.26   21.45


R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 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")

Attaching package: 'MicrobiotaProcess'

The following object is masked from 'package:stats':

    filter

> test_check("MicrobiotaProcess")
Processing map file...
Processing otu/tax file...
Reading file into memory prior to parsing...
Detecting first header line...
Header is on line 2  
Converting input file to a table...
Defining OTU table... 
Parsing taxonomy table...
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 12 ]
> 
> proc.time()
   user  system elapsed 
  22.79    0.73   23.57

name	user	system	elapsed
ImportDada2	1.00	0.11	1.11
ImportQiime2	3.12	0.25	3.42
as.MPSE	0.63	0.00	0.63
as.treedata	0.33	0.00	0.33
build_tree	0	0	0
convert_to_treedata	0	0	0
data-hmp_aerobiosis_small	0.01	0.00	0.01
data-kostic2012crc	0.08	0.07	0.14
data-test_otu_data	0.02	0.00	0.02
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	0.10	0.00	0.24
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	0.34	0.14	0.49
mp_aggregate-methods	0	0	0
mp_anosim-methods	1.85	0.14	1.98
mp_cal_abundance-methods	4.78	0.08	4.86
mp_cal_alpha-methods	1.34	0.11	1.49
mp_cal_cca-methods	0.75	0.02	0.78
mp_cal_clust-methods	0.57	0.12	0.68
mp_cal_dist-methods	0.67	0.17	0.85
mp_cal_nmds-methods	0.34	0.13	0.47
mp_cal_pca-methods	1.31	0.11	1.42
mp_cal_pcoa-methods	0.66	0.08	0.73
mp_cal_rarecurve-methods	8.12	0.11	8.24
mp_cal_rda-methods	0.54	0.01	0.54
mp_cal_upset-methods	0.86	0.16	1.02
mp_cal_venn-methods	1.68	0.34	10.31
mp_decostand-methods	0.57	0.17	0.74
mp_diff_analysis-methods	3.96	0.52	4.48
mp_envfit-methods	1.86	0.08	1.94
mp_filter_taxa-methods	1.08	0.12	1.20
mp_import_metaphlan	2.79	0.02	2.84
mp_mantel-methods	0.38	0.00	0.38
mp_mrpp-methods	0.35	0.18	0.56
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	0.40	0.18	0.58
mp_stat_taxa-methods	0.94	0.15	1.11
multi_compare	0.02	0.00	0.02
read_qza	0	0	0
show-methods	0	0	0
split_data	0.01	0.00	0.01
split_str_to_list	0	0	0
theme_taxbar	0	0	0

name	user	system	elapsed
ImportDada2	2.00	0.04	2.05
ImportQiime2	3.03	0.04	3.06
as.MPSE	0.77	0.00	0.76
as.treedata	0.42	0.06	0.49
build_tree	0	0	0
convert_to_treedata	0	0	0
data-hmp_aerobiosis_small	0.00	0.01	0.01
data-kostic2012crc	0.19	0.11	0.30
data-test_otu_data	0.00	0.02	0.01
diff_analysis	0	0	0
dr_extract	0	0	0
drop_taxa	0	0	0
generalizedFC	0.02	0.00	0.02
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	0.10	0.00	2.53
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	0.32	0.12	0.46
mp_aggregate-methods	0	0	0
mp_anosim-methods	1.58	0.11	1.68
mp_cal_abundance-methods	5.99	0.11	6.11
mp_cal_alpha-methods	1.12	0.05	1.17
mp_cal_cca-methods	0.74	0.02	0.75
mp_cal_clust-methods	0.56	0.10	0.68
mp_cal_dist-methods	0.78	0.10	0.87
mp_cal_nmds-methods	0.36	0.11	0.47
mp_cal_pca-methods	1.30	0.11	1.41
mp_cal_pcoa-methods	0.62	0.04	0.67
mp_cal_rarecurve-methods	7.67	0.11	7.78
mp_cal_rda-methods	0.55	0.02	0.56
mp_cal_upset-methods	0.95	0.09	1.05
mp_cal_venn-methods	1.88	0.11	5.86
mp_decostand-methods	0.53	0.21	0.73
mp_diff_analysis-methods	5.20	0.10	5.32
mp_envfit-methods	3.25	0.05	3.29
mp_filter_taxa-methods	1.56	0.14	1.70
mp_import_metaphlan	4.11	0.02	4.13
mp_mantel-methods	0.39	0.00	0.39
mp_mrpp-methods	0.31	0.09	0.40
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	0.41	0.10	0.50
mp_stat_taxa-methods	0.72	0.09	0.82
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

CHECK results for MicrobiotaProcess on tokay2

Summary

Command output

Installation output

Tests output

Example timings