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

Package: microbiome

Version: 1.14.0

Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:microbiome.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings microbiome_1.14.0.tar.gz

StartedAt: 2021-10-15 01:53:47 -0400 (Fri, 15 Oct 2021)

EndedAt: 2021-10-15 01:58:24 -0400 (Fri, 15 Oct 2021)

EllapsedTime: 276.9 seconds

RetCode: 0

Status: OK

CheckDir: microbiome.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:microbiome.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings microbiome_1.14.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/microbiome.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 'microbiome/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'microbiome' version '1.14.0'
* 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 'microbiome' 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
overlap 13.19      0   13.19
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
         user system elapsed
overlap 15.29      0    15.3
* 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/microbiome_1.14.0.tar.gz && rm -rf microbiome.buildbin-libdir && mkdir microbiome.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=microbiome.buildbin-libdir microbiome_1.14.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL microbiome_1.14.0.zip && rm microbiome_1.14.0.tar.gz microbiome_1.14.0.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
100  505k  100  505k    0     0  1141k      0 --:--:-- --:--:-- --:--:-- 1144k

install for i386

* installing *source* package 'microbiome' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'microbiome'
    finding HTML links ... done
    abundances                              html  
    finding level-2 HTML links ... done

    aggregate_rare                          html  
    aggregate_taxa                          html  
    aggregate_top_taxa                      html  
    alpha                                   html  
    associate                               html  
    atlas1006                               html  
    baseline                                html  
    bfratio                                 html  
    bimodality                              html  
    bimodality_sarle                        html  
    boxplot_abundance                       html  
    chunk_reorder                           html  
    cmat2table                              html  
    collapse_replicates                     html  
    core                                    html  
    core_abundance                          html  
    core_heatmap                            html  
    core_matrix                             html  
    core_members                            html  
    coverage                                html  
    default_colors                          html  
    densityplot                             html  
    dietswap                                html  
    divergence                              html  
    diversities                             html  
    diversity                               html  
    dominance                               html  
    dominant                                html  
    estimate_stability                      html  
    evenness                                html  
    find_optima                             html  
    gktau                                   html  
    global                                  html  
    group_age                               html  
    group_bmi                               html  
    heat                                    html  
    hitchip.taxonomy                        html  
    hotplot                                 html  
    inequality                              html  
    intermediate_stability                  html  
    is_compositional                        html  
    log_modulo_skewness                     html  
    low_abundance                           html  
    map_levels                              html  
    merge_taxa2                             html  
    meta                                    html  
    microbiome-package                      html  
    multimodality                           html  
    neat                                    html  
    neatsort                                html  
    overlap                                 html  
    peerj32                                 html  
    plot_atlas                              html  
    plot_composition                        html  
    plot_core                               html  
    plot_density                            html  
    plot_frequencies                        html  
    plot_landscape                          html  
    plot_regression                         html  
    plot_taxa_prevalence                    html  
    plot_tipping                            html  
    potential_analysis                      html  
    potential_univariate                    html  
    prevalence                              html  
    quiet                                   html  
    radial_theta                            html  
    rare                                    html  
    rare_abundance                          html  
    rare_members                            html  
    rarity                                  html  
    read_biom2phyloseq                      html  
    read_csv2phyloseq                       html  
    read_mothur2phyloseq                    html  
    read_phyloseq                           html  
    readcount                               html  
    remove_samples                          html  
    remove_taxa                             html  
    richness                                html  
    spreadplot                              html  
    summarize_phyloseq                      html  
    taxa                                    html  
    time_normalize                          html  
    time_sort                               html  
    timesplit                               html  
    top                                     html  
    top_taxa                                html  
    transform                               html  
    write_phyloseq                          html  
    ztransform                              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 'microbiome' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'microbiome' as microbiome_1.14.0.zip
* DONE (microbiome)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'microbiome' 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)
> test_check("microbiome")
Loading required package: microbiome
Loading required package: phyloseq
Loading required package: ggplot2

microbiome R package (microbiome.github.com)
    


 Copyright (C) 2011-2020 Leo Lahti, 
    Sudarshan Shetty et al. <microbiome.github.io>


Attaching package: 'microbiome'

The following object is masked from 'package:ggplot2':

    alpha

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

    transform

== Skipped tests ===============================================================
* On Bioconductor (1)

[ FAIL 0 | WARN 2 | SKIP 1 | PASS 75 ]
> 
> proc.time()
   user  system elapsed 
  12.34    0.81   13.12


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)
> test_check("microbiome")
Loading required package: microbiome
Loading required package: phyloseq
Loading required package: ggplot2

microbiome R package (microbiome.github.com)
    


 Copyright (C) 2011-2020 Leo Lahti, 
    Sudarshan Shetty et al. <microbiome.github.io>


Attaching package: 'microbiome'

The following object is masked from 'package:ggplot2':

    alpha

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

    transform

== Skipped tests ===============================================================
* On Bioconductor (1)

[ FAIL 0 | WARN 2 | SKIP 1 | PASS 75 ]
> 
> proc.time()
   user  system elapsed 
  12.59    0.51   13.09

name	user	system	elapsed
abundances	0.01	0.00	0.01
aggregate_rare	0.30	0.05	0.35
aggregate_taxa	0.09	0.01	0.11
alpha	0.02	0.00	0.02
associate	0.01	0.05	0.06
baseline	0.08	0.00	0.08
bfratio	0.12	0.01	0.14
bimodality	0	0	0
bimodality_sarle	0	0	0
boxplot_abundance	0.06	0.02	0.08
chunk_reorder	0	0	0
cmat2table	0.08	0.02	0.10
collapse_replicates	0.08	0.00	0.07
core	0.03	0.00	0.03
core_abundance	0.03	0.00	0.04
core_matrix	0	0	0
core_members	0.02	0.00	0.01
coverage	0.03	0.00	0.03
default_colors	0	0	0
densityplot	0	0	0
divergence	0.40	0.00	0.41
diversities	0	0	0
diversity	0.02	0.00	0.02
dominance	0.01	0.00	0.02
dominant	0.00	0.01	0.01
estimate_stability	0	0	0
evenness	0.02	0.00	0.02
find_optima	0	0	0
gktau	0.01	0.00	0.01
global	0.00	0.02	0.02
group_age	0.03	0.00	0.03
group_bmi	0	0	0
heat	0.07	0.00	0.06
hotplot	0.12	0.00	0.13
inequality	0.02	0.00	0.01
intermediate_stability	0.34	0.03	0.38
is_compositional	0.05	0.00	0.04
log_modulo_skewness	0.11	0.00	0.11
low_abundance	0.01	0.00	0.02
map_levels	0.05	0.00	0.05
merge_taxa2	0.03	0.00	0.03
meta	0	0	0
microbiome-package	0.02	0.00	0.01
multimodality	0	0	0
neat	0.06	0.00	0.07
neatsort	0.15	0.00	0.15
overlap	13.19	0.00	13.19
plot_atlas	0.05	0.00	0.05
plot_composition	0.19	0.00	0.18
plot_core	0.03	0.03	0.07
plot_density	0.03	0.00	0.03
plot_frequencies	0.02	0.00	0.02
plot_landscape	0.80	0.03	0.83
plot_regression	0.14	0.00	0.14
plot_taxa_prevalence	0.23	0.02	0.25
plot_tipping	0.08	0.00	0.08
potential_analysis	0.03	0.00	0.03
potential_univariate	0	0	0
prevalence	0.02	0.01	0.03
quiet	0	0	0
rare	0.01	0.00	0.01
rare_abundance	0.03	0.00	0.04
rare_members	0.02	0.00	0.01
rarity	0.06	0.00	0.06
read_biom2phyloseq	0	0	0
read_csv2phyloseq	0	0	0
read_mothur2phyloseq	0	0	0
read_phyloseq	0	0	0
readcount	0.00	0.02	0.02
remove_samples	0.02	0.00	0.01
remove_taxa	0.01	0.00	0.02
richness	0.02	0.00	0.02
spreadplot	0.05	0.01	0.06
summarize_phyloseq	0.01	0.02	0.03
taxa	0	0	0
time_normalize	0.03	0.01	0.05
time_sort	0.11	0.00	0.11
timesplit	0.10	0.00	0.09
top	0.00	0.02	0.02
top_taxa	0.01	0.00	0.01
transform	0.06	0.00	0.06
write_phyloseq	0	0	0
ztransform	0	0	0

name	user	system	elapsed
abundances	0.03	0.00	0.04
aggregate_rare	0.63	0.00	0.63
aggregate_taxa	0.12	0.00	0.12
alpha	0.02	0.00	0.02
associate	0.05	0.00	0.05
baseline	0.06	0.00	0.06
bfratio	0.15	0.00	0.14
bimodality	0	0	0
bimodality_sarle	0	0	0
boxplot_abundance	0.08	0.02	0.09
chunk_reorder	0	0	0
cmat2table	0.08	0.00	0.08
collapse_replicates	0.04	0.00	0.05
core	0.05	0.00	0.05
core_abundance	0.14	0.00	0.14
core_matrix	0	0	0
core_members	0.03	0.00	0.03
coverage	0.05	0.00	0.04
default_colors	0	0	0
densityplot	0	0	0
divergence	0.72	0.04	0.77
diversities	0.64	0.00	0.64
diversity	0.01	0.02	0.03
dominance	0.02	0.00	0.02
dominant	0.00	0.01	0.01
estimate_stability	0	0	0
evenness	0.02	0.00	0.01
find_optima	0	0	0
gktau	0.01	0.00	0.02
global	0.03	0.00	0.03
group_age	0.05	0.00	0.05
group_bmi	0	0	0
heat	0.09	0.00	0.09
hotplot	0.11	0.03	0.14
inequality	0.02	0.02	0.03
intermediate_stability	0.50	0.01	0.52
is_compositional	0.07	0.00	0.07
log_modulo_skewness	0.12	0.02	0.14
low_abundance	0.02	0.00	0.01
map_levels	0.04	0.00	0.05
merge_taxa2	0.02	0.01	0.03
meta	0.02	0.00	0.02
microbiome-package	0	0	0
multimodality	0	0	0
neat	0.06	0.00	0.07
neatsort	0.19	0.01	0.20
overlap	15.29	0.00	15.30
plot_atlas	0.05	0.00	0.04
plot_composition	0.22	0.00	0.22
plot_core	0.08	0.00	0.08
plot_density	0.03	0.00	0.03
plot_frequencies	0.01	0.02	0.03
plot_landscape	0.88	0.00	0.88
plot_regression	0.15	0.00	0.15
plot_taxa_prevalence	0.25	0.02	0.27
plot_tipping	0.10	0.00	0.09
potential_analysis	0.04	0.00	0.05
potential_univariate	0	0	0
prevalence	0.02	0.00	0.01
quiet	0	0	0
rare	0.02	0.00	0.02
rare_abundance	0.01	0.01	0.03
rare_members	0.03	0.02	0.05
rarity	0.08	0.00	0.08
read_biom2phyloseq	0	0	0
read_csv2phyloseq	0	0	0
read_mothur2phyloseq	0	0	0
read_phyloseq	0	0	0
readcount	0	0	0
remove_samples	0.02	0.01	0.03
remove_taxa	0.01	0.00	0.01
richness	0.02	0.00	0.02
spreadplot	0.11	0.00	0.11
summarize_phyloseq	0.03	0.00	0.03
taxa	0.01	0.00	0.02
time_normalize	0.05	0.02	0.06
time_sort	0.2	0.0	0.2
timesplit	0.14	0.00	0.14
top	0.02	0.00	0.02
top_taxa	0.02	0.00	0.01
transform	0.07	0.00	0.08
write_phyloseq	0	0	0
ztransform	0	0	0

CHECK results for microbiome on tokay2

Summary

Command output

Installation output

Tests output

Example timings