Multiple platform build/check report for BioC 3.14 - CHECK results for microbiome 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: microbiome

Version: 1.16.0

Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:microbiome.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings microbiome_1.16.0.tar.gz

StartedAt: 2022-04-12 22:50:04 -0400 (Tue, 12 Apr 2022)

EndedAt: 2022-04-12 22:54:43 -0400 (Tue, 12 Apr 2022)

EllapsedTime: 278.6 seconds

RetCode: 0

Status: OK

CheckDir: microbiome.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:microbiome.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings microbiome_1.16.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/microbiome.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 'microbiome/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'microbiome' version '1.16.0'
* 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 17.5   0.01   17.54
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
         user system elapsed
overlap 15.11   0.05   15.16
* 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://155.52.207.166/BBS/3.14/bioc/src/contrib/microbiome_1.16.0.tar.gz && rm -rf microbiome.buildbin-libdir && mkdir microbiome.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=microbiome.buildbin-libdir microbiome_1.16.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL microbiome_1.16.0.zip && rm microbiome_1.16.0.tar.gz microbiome_1.16.0.zip
###
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  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100  505k  100  505k    0     0   501k      0  0:00:01  0:00:01 --:--:--  502k
100  505k  100  505k    0     0   501k      0  0:00:01  0:00:01 --:--:--  502k

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  
    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  
    diversity                               html  
    dominance                               html  
    dominant                                html  
    estimate_stability                      html  
    evenness                                html  
    find_optima                             html  
    gktau                                   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  
    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_1.16.0.zip
* DONE (microbiome)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'microbiome' 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)
> test_check("microbiome")
Loading required package: microbiome
Loading required package: phyloseq
Loading required package: ggplot2

microbiome R package (microbiome.github.com)
    


 Copyright (C) 2011-2021 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

[ FAIL 0 | WARN 5 | SKIP 1 | PASS 82 ]

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

[ FAIL 0 | WARN 5 | SKIP 1 | PASS 82 ]
> 
> proc.time()
   user  system elapsed 
  11.10    0.85   11.98


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

microbiome R package (microbiome.github.com)
    


 Copyright (C) 2011-2021 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

[ FAIL 0 | WARN 5 | SKIP 1 | PASS 82 ]

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

[ FAIL 0 | WARN 5 | SKIP 1 | PASS 82 ]
> 
> proc.time()
   user  system elapsed 
  11.76    0.48   12.23

name	user	system	elapsed
abundances	0.02	0.00	0.02
aggregate_rare	0.33	0.02	0.34
aggregate_taxa	0.09	0.00	0.09
alpha	0.01	0.02	0.03
associate	0.05	0.00	0.05
baseline	0.06	0.00	0.06
bfratio	0.11	0.00	0.11
bimodality	0.02	0.00	0.01
bimodality_sarle	0	0	0
boxplot_abundance	0.05	0.01	0.07
chunk_reorder	0	0	0
cmat2table	0.07	0.00	0.08
collapse_replicates	0.07	0.00	0.06
core	0.04	0.02	0.06
core_abundance	0.03	0.00	0.03
core_matrix	0	0	0
core_members	0.00	0.01	0.02
coverage	0.07	0.02	0.08
default_colors	0	0	0
densityplot	0	0	0
divergence	0.59	0.00	0.59
diversity	0.02	0.01	0.03
dominance	0.01	0.00	0.02
dominant	0.02	0.00	0.01
estimate_stability	0	0	0
evenness	0.01	0.00	0.02
find_optima	0	0	0
gktau	0.02	0.00	0.01
group_age	0.01	0.04	0.05
group_bmi	0	0	0
heat	0.07	0.00	0.06
hotplot	0.10	0.06	0.15
inequality	0.09	0.00	0.10
intermediate_stability	0.59	0.00	0.59
is_compositional	0.07	0.00	0.06
log_modulo_skewness	0.14	0.00	0.14
low_abundance	0.01	0.00	0.02
map_levels	0.05	0.00	0.05
merge_taxa2	0.05	0.00	0.04
meta	0.01	0.00	0.02
microbiome-package	0	0	0
multimodality	0	0	0
neat	0.06	0.03	0.09
neatsort	0.24	0.00	0.24
overlap	17.50	0.01	17.54
plot_atlas	0.05	0.02	0.07
plot_composition	0.2	0.0	0.2
plot_core	0.08	0.00	0.08
plot_density	0.04	0.00	0.05
plot_frequencies	0.04	0.00	0.03
plot_landscape	0.89	0.03	0.92
plot_regression	0.21	0.00	0.22
plot_taxa_prevalence	0.27	0.00	0.26
plot_tipping	0.09	0.02	0.11
potential_analysis	0.04	0.00	0.03
potential_univariate	0	0	0
prevalence	0.01	0.00	0.01
quiet	0	0	0
rare	0.03	0.00	0.04
rare_abundance	0.03	0.00	0.03
rare_members	0.00	0.02	0.01
rarity	0.07	0.01	0.08
read_biom2phyloseq	0	0	0
read_csv2phyloseq	0	0	0
read_mothur2phyloseq	0	0	0
read_phyloseq	0	0	0
readcount	0.01	0.00	0.02
remove_samples	0.02	0.00	0.01
remove_taxa	0.01	0.00	0.02
richness	0.00	0.02	0.02
spreadplot	0.11	0.00	0.11
summarize_phyloseq	0.01	0.00	0.01
taxa	0.00	0.02	0.02
time_normalize	0.03	0.00	0.03
time_sort	0.13	0.00	0.12
timesplit	0.10	0.00	0.11
top	0.02	0.00	0.02
top_taxa	0.02	0.00	0.01
transform	0.04	0.00	0.05
ztransform	0	0	0

name	user	system	elapsed
abundances	0.02	0.00	0.01
aggregate_rare	0.31	0.01	0.33
aggregate_taxa	0.10	0.00	0.11
alpha	0.00	0.02	0.01
associate	0.07	0.00	0.07
baseline	0.06	0.00	0.06
bfratio	0.14	0.00	0.14
bimodality	0	0	0
bimodality_sarle	0	0	0
boxplot_abundance	0.05	0.01	0.06
chunk_reorder	0	0	0
cmat2table	0.08	0.00	0.08
collapse_replicates	0.53	0.02	0.55
core	0.03	0.00	0.03
core_abundance	0.01	0.03	0.04
core_matrix	0	0	0
core_members	0	0	0
coverage	0.03	0.02	0.05
default_colors	0	0	0
densityplot	0	0	0
divergence	0.54	0.03	0.56
diversity	0.01	0.01	0.04
dominance	0.02	0.00	0.01
dominant	0	0	0
estimate_stability	0	0	0
evenness	0	0	0
find_optima	0	0	0
gktau	0.03	0.00	0.03
group_age	0.02	0.00	0.01
group_bmi	0	0	0
heat	0.08	0.00	0.08
hotplot	0.14	0.04	0.17
inequality	0.01	0.01	0.03
intermediate_stability	0.47	0.02	0.49
is_compositional	0.07	0.00	0.06
log_modulo_skewness	0.12	0.00	0.13
low_abundance	0.00	0.01	0.01
map_levels	0.05	0.00	0.05
merge_taxa2	0.03	0.00	0.03
meta	0.00	0.02	0.02
microbiome-package	0	0	0
multimodality	0	0	0
neat	0.06	0.01	0.07
neatsort	0.22	0.00	0.22
overlap	15.11	0.05	15.16
plot_atlas	0.05	0.00	0.05
plot_composition	0.2	0.0	0.2
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	0.84	0.00	0.84
plot_regression	0.22	0.00	0.22
plot_taxa_prevalence	0.28	0.01	0.29
plot_tipping	0.18	0.00	0.18
potential_analysis	0.04	0.02	0.06
potential_univariate	0	0	0
prevalence	0.02	0.01	0.03
quiet	0	0	0
rare	0.03	0.00	0.03
rare_abundance	0.05	0.02	0.06
rare_members	0.01	0.00	0.02
rarity	0.13	0.00	0.12
read_biom2phyloseq	0	0	0
read_csv2phyloseq	0	0	0
read_mothur2phyloseq	0	0	0
read_phyloseq	0	0	0
readcount	0.01	0.00	0.02
remove_samples	0.03	0.00	0.03
remove_taxa	0.02	0.00	0.02
richness	0.02	0.00	0.02
spreadplot	0.06	0.01	0.08
summarize_phyloseq	0.03	0.00	0.03
taxa	0	0	0
time_normalize	0.04	0.02	0.04
time_sort	0.14	0.02	0.16
timesplit	0.12	0.00	0.13
top	0.00	0.01	0.01
top_taxa	0.02	0.00	0.02
transform	0.06	0.00	0.06
ztransform	0	0	0

CHECK results for microbiome on tokay2

Summary

Command output

Installation output

Tests output

Example timings