Multiple platform build/check report for BioC 3.12 - CHECK report for microbiome on tokay1

Package: microbiome

Version: 1.12.0

Command: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:microbiome.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings microbiome_1.12.0.tar.gz

StartedAt: 2021-05-06 04:38:09 -0400 (Thu, 06 May 2021)

EndedAt: 2021-05-06 04:43:15 -0400 (Thu, 06 May 2021)

EllapsedTime: 305.9 seconds

RetCode: 0

Status: OK

CheckDir: microbiome.Rcheck

Warnings: 0

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### Running command:
###
###   C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:microbiome.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings microbiome_1.12.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/microbiome.Rcheck'
* using R version 4.0.5 (2021-03-31)
* 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 '1.12.0'
* 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 16.42   0.01   16.43
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
         user system elapsed
overlap 21.31      0   21.34
* 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://172.29.0.3/BBS/3.12/bioc/src/contrib/microbiome_1.12.0.tar.gz && rm -rf microbiome.buildbin-libdir && mkdir microbiome.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=microbiome.buildbin-libdir microbiome_1.12.0.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL microbiome_1.12.0.zip && rm microbiome_1.12.0.tar.gz microbiome_1.12.0.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  508k  100  508k    0     0   9.8M      0 --:--:-- --:--:-- --:--:-- 10.1M

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_1.12.0.zip
* DONE (microbiome)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'microbiome' successfully unpacked and MD5 sums checked


R version 4.0.5 (2021-03-31) -- "Shake and Throw"
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 
  12.10    0.73   12.84


R version 4.0.5 (2021-03-31) -- "Shake and Throw"
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 
  12.29    0.42   12.70

name	user	system	elapsed
abundances	0.03	0.00	0.03
aggregate_rare	0.66	0.00	0.66
aggregate_taxa	0.09	0.03	0.12
alpha	0.02	0.00	0.02
associate	0.03	0.03	0.06
baseline	0.05	0.02	0.06
bfratio	0.12	0.05	0.17
bimodality	0	0	0
bimodality_sarle	0	0	0
boxplot_abundance	0.1	0.0	0.1
chunk_reorder	0	0	0
cmat2table	0.06	0.04	0.11
collapse_replicates	0.05	0.04	0.08
core	0.01	0.03	0.04
core_abundance	0.01	0.03	0.04
core_matrix	0	0	0
core_members	0.02	0.00	0.02
coverage	0.06	0.00	0.06
default_colors	0	0	0
densityplot	0	0	0
divergence	0.48	0.00	0.49
diversities	0.02	0.00	0.01
diversity	0.02	0.00	0.02
dominance	0.01	0.00	0.02
dominant	0.02	0.00	0.02
estimate_stability	0	0	0
evenness	0.01	0.00	0.01
find_optima	0	0	0
gktau	0.02	0.00	0.02
global	0.01	0.00	0.01
group_age	0.04	0.00	0.03
group_bmi	0	0	0
heat	0.06	0.00	0.07
hotplot	0.12	0.02	0.14
inequality	0.02	0.03	0.04
intermediate_stability	0.47	0.00	0.47
is_compositional	0.06	0.00	0.06
log_modulo_skewness	0.11	0.00	0.11
low_abundance	0.01	0.02	0.04
map_levels	0.04	0.00	0.03
merge_taxa2	0.02	0.00	0.02
meta	0.01	0.00	0.01
microbiome-package	0.02	0.00	0.02
multimodality	0	0	0
neat	0.06	0.01	0.08
neatsort	0.17	0.05	0.22
overlap	16.42	0.01	16.43
plot_atlas	0.08	0.00	0.08
plot_composition	0.24	0.02	0.25
plot_core	0.08	0.02	0.10
plot_density	0.03	0.01	0.04
plot_frequencies	0.03	0.00	0.03
plot_landscape	0.92	0.05	0.97
plot_regression	0.19	0.01	0.21
plot_taxa_prevalence	0.26	0.03	0.29
plot_tipping	0.1	0.0	0.1
potential_analysis	0.03	0.02	0.04
potential_univariate	0	0	0
prevalence	0.01	0.00	0.02
quiet	0	0	0
rare	0.03	0.00	0.03
rare_abundance	0.05	0.00	0.05
rare_members	0.49	0.00	0.48
rarity	0.07	0.02	0.09
read_biom2phyloseq	0	0	0
read_csv2phyloseq	0	0	0
read_mothur2phyloseq	0	0	0
read_phyloseq	0	0	0
readcount	0.02	0.00	0.02
remove_samples	0.02	0.00	0.02
remove_taxa	0.01	0.00	0.01
richness	0.02	0.01	0.03
spreadplot	0.06	0.00	0.07
summarize_phyloseq	0.01	0.00	0.01
taxa	0.00	0.02	0.02
time_normalize	0.04	0.01	0.04
time_sort	0.14	0.00	0.14
timesplit	0.11	0.00	0.11
top	0	0	0
top_taxa	0.00	0.02	0.01
transform	0.06	0.01	0.08
write_phyloseq	0	0	0
ztransform	0	0	0

name	user	system	elapsed
abundances	0.00	0.01	0.01
aggregate_rare	0.28	0.05	0.33
aggregate_taxa	0.14	0.01	0.16
alpha	0.02	0.00	0.01
associate	0.05	0.00	0.05
baseline	0.03	0.02	0.05
bfratio	0.14	0.00	0.14
bimodality	0	0	0
bimodality_sarle	0	0	0
boxplot_abundance	0.08	0.00	0.08
chunk_reorder	0	0	0
cmat2table	0.1	0.0	0.1
collapse_replicates	0.01	0.03	0.04
core	0.06	0.00	0.06
core_abundance	0.05	0.00	0.05
core_matrix	0	0	0
core_members	0.02	0.00	0.02
coverage	0.03	0.00	0.03
default_colors	0	0	0
densityplot	0	0	0
divergence	0.65	0.01	0.67
diversities	0.04	0.00	0.03
diversity	0.01	0.02	0.03
dominance	0.02	0.00	0.02
dominant	0.01	0.02	0.03
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	0.02	0.01	0.03
group_age	0.03	0.00	0.03
group_bmi	0	0	0
heat	0.06	0.00	0.07
hotplot	0.13	0.00	0.12
inequality	0.05	0.00	0.05
intermediate_stability	0.65	0.02	0.67
is_compositional	0.11	0.00	0.11
log_modulo_skewness	0.2	0.0	0.2
low_abundance	0.04	0.00	0.03
map_levels	0.06	0.00	0.07
merge_taxa2	0.03	0.00	0.03
meta	0.05	0.00	0.05
microbiome-package	0.02	0.00	0.02
multimodality	0	0	0
neat	0.09	0.00	0.09
neatsort	0.24	0.01	0.25
overlap	21.31	0.00	21.34
plot_atlas	0.06	0.00	0.07
plot_composition	0.36	0.00	0.35
plot_core	0.08	0.00	0.08
plot_density	0.04	0.02	0.07
plot_frequencies	0.03	0.00	0.03
plot_landscape	1.41	0.01	1.42
plot_regression	0.26	0.00	0.30
plot_taxa_prevalence	0.5	0.0	0.5
plot_tipping	0.18	0.00	0.17
potential_analysis	0.06	0.00	0.07
potential_univariate	0	0	0
prevalence	0.03	0.00	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	0.00	0.02	0.02
remove_samples	0.03	0.00	0.03
remove_taxa	0.03	0.00	0.03
richness	0.02	0.00	0.01
spreadplot	0.10	0.00	0.09
summarize_phyloseq	0.04	0.00	0.05
taxa	0.02	0.00	0.02
time_normalize	0.04	0.01	0.06
time_sort	0.19	0.00	0.19
timesplit	0.19	0.00	0.18
top	0.02	0.00	0.02
top_taxa	0.01	0.00	0.02
transform	0.09	0.02	0.10
write_phyloseq	0	0	0
ztransform	0	0	0

CHECK report for microbiome on tokay1

Summary

Command output

Installation output

Tests output

Example timings