Multiple platform build/check report for BioC 3.6 - CHECK report for microbiome on tokay1

Package: microbiome

Version: 1.0.2

Command: rm -rf microbiome.buildbin-libdir microbiome.Rcheck && mkdir microbiome.buildbin-libdir microbiome.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=microbiome.buildbin-libdir microbiome_1.0.2.tar.gz >microbiome.Rcheck\00install.out 2>&1 && cp microbiome.Rcheck\00install.out microbiome-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=microbiome.buildbin-libdir --install="check:microbiome-install.out" --force-multiarch --no-vignettes --timings microbiome_1.0.2.tar.gz

StartedAt: 2018-04-12 01:26:58 -0400 (Thu, 12 Apr 2018)

EndedAt: 2018-04-12 01:31:10 -0400 (Thu, 12 Apr 2018)

EllapsedTime: 251.8 seconds

RetCode: 0

Status: OK

CheckDir: microbiome.Rcheck

Warnings: 0

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### Running command:
###
###   rm -rf microbiome.buildbin-libdir microbiome.Rcheck && mkdir microbiome.buildbin-libdir microbiome.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=microbiome.buildbin-libdir microbiome_1.0.2.tar.gz >microbiome.Rcheck\00install.out 2>&1 && cp microbiome.Rcheck\00install.out microbiome-install.out  &&  C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=microbiome.buildbin-libdir --install="check:microbiome-install.out" --force-multiarch --no-vignettes --timings microbiome_1.0.2.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/microbiome.Rcheck'
* using R version 3.4.4 (2018-03-15)
* 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 '1.0.2'
* 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
** checking loading without being on the library search path ... 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 loading without being on the library search path ... 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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* 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


install for i386

* installing *source* package 'microbiome' ...
** R
** data
** inst
** preparing 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_taxa                          html  
    associate                               html  
    atlas1006                               html  
    baseline                                html  
    bimodality                              html  
    bimodality_sarle                        html  
    boxplot_abundance                       html  
    chunk_reorder                           html  
    cmat2table                              html  
    core                                    html  
    core_abundance                          html  
    core_heatmap                            html  
    core_matrix                             html  
    core_members                            html  
    coverage                                html  
    densityplot                             html  
    dietswap                                html  
    divergence                              html  
    diversities                             html  
    dominance                               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  
    log_modulo_skewness                     html  
    low_abundance                           html  
    map_levels                              html  
    merge_taxa2                             html  
    meta                                    html  
    microbiome-package                      html  
    multimodality                           html  
    neat                                    html  
    neatsort                                html  
    noncore_abundance                       html  
    noncore_members                         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_members                            html  
    rarity                                  html  
    read_biom2phyloseq                      html  
    read_csv2phyloseq                       html  
    read_mothur2phyloseq                    html  
    read_phyloseq                           html  
    remove_samples                          html  
    remove_taxa                             html  
    richness                                html  
    summarize_phyloseq                      html  
    taxa                                    html  
    time_normalize                          html  
    time_sort                               html  
    top_taxa                                html  
    transform                               html  
    variable_members                        html  
    write_phyloseq                          html  
    ztransform                              html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'microbiome' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'microbiome' as microbiome_1.0.2.zip
* DONE (microbiome)
In R CMD INSTALL
In R CMD INSTALL


R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 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) 2011-2018 Leo Lahti et al. <microbiome.github.io>


Attaching package: 'microbiome'

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

    transform

== testthat results  ===========================================================
OK: 69 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
  11.45    0.43   11.85


R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 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) 2011-2018 Leo Lahti et al. <microbiome.github.io>


Attaching package: 'microbiome'

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

    transform

== testthat results  ===========================================================
OK: 69 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
  11.75    0.28   12.01

name	user	system	elapsed
abundances	0.03	0.00	0.04
aggregate_taxa	0.34	0.00	0.34
associate	0.09	0.00	0.09
baseline	0.04	0.00	0.03
bimodality	0.09	0.00	0.10
bimodality_sarle	0	0	0
boxplot_abundance	0.15	0.00	0.16
chunk_reorder	0	0	0
cmat2table	0.41	0.00	0.41
core	0.01	0.00	0.01
core_abundance	0.01	0.00	0.01
core_matrix	0	0	0
core_members	0.02	0.00	0.02
coverage	0.08	0.00	0.08
densityplot	0	0	0
divergence	0.47	0.00	0.47
diversities	0.02	0.00	0.02
dominance	0.05	0.02	0.06
estimate_stability	0	0	0
evenness	0	0	0
find_optima	0	0	0
gktau	0.01	0.00	0.01
global	0.08	0.00	0.08
group_age	0.05	0.00	0.05
group_bmi	0	0	0
heat	0.07	0.00	0.08
hotplot	0.38	0.00	0.38
inequality	0.03	0.00	0.03
intermediate_stability	0.58	0.02	0.59
log_modulo_skewness	0.11	0.00	0.11
low_abundance	0.03	0.00	0.03
map_levels	0.06	0.02	0.08
merge_taxa2	0.03	0.00	0.03
meta	0.02	0.00	0.02
microbiome-package	0.01	0.00	0.01
multimodality	0	0	0
neat	0.36	0.00	0.36
neatsort	0.35	0.03	0.38
noncore_abundance	0.01	0.00	0.01
noncore_members	0.03	0.00	0.04
plot_atlas	0.10	0.00	0.09
plot_composition	0.19	0.00	0.19
plot_core	0.23	0.00	0.23
plot_density	0.03	0.00	0.03
plot_frequencies	0.05	0.01	0.07
plot_landscape	0.04	0.00	0.04
plot_regression	3.47	0.00	3.47
plot_taxa_prevalence	1.00	0.02	1.02
plot_tipping	0.39	0.00	0.39
potential_analysis	0.04	0.01	0.04
potential_univariate	0	0	0
prevalence	0	0	0
quiet	0	0	0
rare_members	0.02	0.00	0.02
rarity	0.09	0.00	0.09
read_biom2phyloseq	0	0	0
read_csv2phyloseq	0	0	0
read_mothur2phyloseq	0	0	0
read_phyloseq	0	0	0
remove_samples	0.02	0.00	0.01
remove_taxa	0.01	0.02	0.04
richness	0.02	0.00	0.01
summarize_phyloseq	0.03	0.01	0.05
taxa	0	0	0
time_normalize	0.02	0.02	0.04
time_sort	0.12	0.02	0.14
top_taxa	0.00	0.01	0.01
transform	0.04	0.00	0.03
variable_members	0.06	0.00	0.06
write_phyloseq	0	0	0
ztransform	0	0	0

name	user	system	elapsed
abundances	0.03	0.02	0.05
aggregate_taxa	0.38	0.02	0.39
associate	0.10	0.00	0.09
baseline	0.03	0.00	0.03
bimodality	0.16	0.00	0.16
bimodality_sarle	0	0	0
boxplot_abundance	0.18	0.00	0.19
chunk_reorder	0	0	0
cmat2table	0.25	0.00	0.25
core	0.02	0.00	0.02
core_abundance	0.03	0.00	0.03
core_matrix	0	0	0
core_members	0	0	0
coverage	0.11	0.00	0.11
densityplot	0	0	0
divergence	0.59	0.01	0.61
diversities	0.02	0.00	0.01
dominance	0.05	0.00	0.05
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	0.09	0.00	0.09
group_age	0.03	0.02	0.05
group_bmi	0	0	0
heat	0.10	0.00	0.09
hotplot	0.57	0.01	0.60
inequality	0.04	0.00	0.03
intermediate_stability	1.03	0.04	1.06
log_modulo_skewness	0.11	0.00	0.11
low_abundance	0.04	0.00	0.05
map_levels	0.07	0.00	0.06
merge_taxa2	0.03	0.00	0.03
meta	0	0	0
microbiome-package	0	0	0
multimodality	0.02	0.00	0.01
neat	0.47	0.00	0.47
neatsort	0.18	0.00	0.19
noncore_abundance	0.02	0.00	0.01
noncore_members	0.02	0.00	0.02
plot_atlas	0.10	0.00	0.11
plot_composition	0.21	0.00	0.20
plot_core	0.23	0.01	0.25
plot_density	0.05	0.00	0.05
plot_frequencies	0.06	0.00	0.06
plot_landscape	0.06	0.00	0.06
plot_regression	3.77	0.03	3.80
plot_taxa_prevalence	1.16	0.02	1.17
plot_tipping	0.45	0.00	0.46
potential_analysis	0.05	0.00	0.04
potential_univariate	0	0	0
prevalence	0.01	0.00	0.02
quiet	0	0	0
rare_members	0.02	0.00	0.01
rarity	0.09	0.00	0.10
read_biom2phyloseq	0	0	0
read_csv2phyloseq	0	0	0
read_mothur2phyloseq	0	0	0
read_phyloseq	0	0	0
remove_samples	0.02	0.00	0.01
remove_taxa	0.03	0.00	0.03
richness	0.02	0.00	0.02
summarize_phyloseq	0.01	0.00	0.01
taxa	0.00	0.01	0.02
time_normalize	0.04	0.00	0.03
time_sort	0.17	0.00	0.17
top_taxa	0.01	0.00	0.02
transform	0.03	0.00	0.03
variable_members	0.07	0.00	0.06
write_phyloseq	0	0	0
ztransform	0	0	0

CHECK report for microbiome on tokay1

Summary

Command output

Installation output

Tests output

Example timings