Multiple platform build/check report for BioC 3.9 - CHECK report for animalcules on tokay2

Package: animalcules

Version: 1.0.6

Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:animalcules.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings animalcules_1.0.6.tar.gz

StartedAt: 2019-10-16 01:54:18 -0400 (Wed, 16 Oct 2019)

EndedAt: 2019-10-16 02:01:11 -0400 (Wed, 16 Oct 2019)

EllapsedTime: 413.6 seconds

RetCode: 0

Status: OK

CheckDir: animalcules.Rcheck

Warnings: 0

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### Running command:
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###   C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:animalcules.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings animalcules_1.0.6.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/animalcules.Rcheck'
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'animalcules/DESCRIPTION' ... OK
* this is package 'animalcules' version '1.0.6'
* 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 'animalcules' 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 ... NOTE
alpha_div_boxplot: no visible binding for global variable 'richness'
differential_abundance: no visible binding for global variable 'padj'
differential_abundance: no visible binding for global variable 'pValue'
differential_abundance: no visible binding for global variable
  'log2FoldChange'
diversities_help: no visible binding for global variable 'x'
find_biomarker: no visible binding for global variable 'rowname'
find_biomarker: no visible binding for global variable 'importance'
find_biomarker: no visible binding for global variable '.'
find_biomarker: no visible binding for global variable 'Overall'
find_biomarker: no visible binding for global variable 'y'
find_biomarker: no visible binding for global variable 'm'
find_biomarker: no visible binding for global variable 'd'
relabu_barplot: no visible binding for global variable '.'
relabu_boxplot: no visible binding for global variable '.'
relabu_heatmap: no visible binding for global variable '.'
upsample_counts: no visible binding for global variable '.'
Undefined global functions or variables:
  . Overall d importance log2FoldChange m pValue padj richness rowname
  x y
* 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                user system elapsed
find_biomarker 10.55   0.70   11.21
dimred_tsne     6.95   0.11    7.87
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                user system elapsed
find_biomarker 12.47   0.14   12.51
dimred_tsne     6.40   0.04    6.69
* 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: 1 NOTE
See
  'C:/Users/biocbuild/bbs-3.9-bioc/meat/animalcules.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/animalcules_1.0.6.tar.gz && rm -rf animalcules.buildbin-libdir && mkdir animalcules.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=animalcules.buildbin-libdir animalcules_1.0.6.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL animalcules_1.0.6.zip && rm animalcules_1.0.6.tar.gz animalcules_1.0.6.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  845k  100  845k    0     0  6972k      0 --:--:-- --:--:-- --:--:-- 7350k

install for i386

* installing *source* package 'animalcules' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'animalcules'
    finding HTML links ... done
    alpha_div_boxplot                       html  
    alpha_div_test                          html  
    animalcules-package                     html  
    counts_to_logcpm                        html  
    counts_to_relabu                        html  
    df_char_to_factor                       html  
    differential_abundance                  html  
    dimred_pca                              html  
    dimred_pcoa                             html  
    dimred_tsne                             html  
    diversities                             html  
    diversities_help                        html  
    diversity_beta_boxplot                  html  
    diversity_beta_heatmap                  html  
    diversity_beta_test                     html  
    do_alpha_div_test                       html  
    filter_categorize                       html  
    filter_summary_bottom                   html  
    filter_summary_top                      html  
    find_biomarker                          html  
    find_taxon_mat                          html  
    find_taxonomy                           html  
    find_taxonomy_300                       html  
    gini_simpson                            html  
    grep_tid                                html  
    inverse_simpson                         html  
    is_categorical                          html  
    is_integer0                             html  
    is_integer1                             html  
    mae_pick_organisms                      html  
    mae_pick_samples                        html  
    pct2str                                 html  
    percent                                 html  
    read_pathoscope_data                    html  
    relabu_barplot                          html  
    relabu_boxplot                          html  
    relabu_heatmap                          html  
    run_animalcules                         html  
    shannon                                 html  
    simpson_index                           html  
    upsample_counts                         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 'animalcules' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'animalcules' as animalcules_1.0.6.zip
* DONE (animalcules)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'animalcules' successfully unpacked and MD5 sums checked


R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 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(animalcules)
> 
> test_check("animalcules")
== testthat results  ===========================================================
[ OK: 39 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
  29.29    1.57   31.39


R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 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(animalcules)
> 
> test_check("animalcules")
== testthat results  ===========================================================
[ OK: 39 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
  31.45    0.95   32.92

name	user	system	elapsed
alpha_div_boxplot	0.83	0.11	3.42
alpha_div_test	0	0	0
counts_to_logcpm	0	0	0
counts_to_relabu	0	0	0
df_char_to_factor	0	0	0
differential_abundance	2.75	0.05	2.80
dimred_pca	0.17	0.03	0.42
dimred_pcoa	0.28	0.06	0.61
dimred_tsne	6.95	0.11	7.87
diversities	0	0	0
diversities_help	0	0	0
diversity_beta_boxplot	0.36	0.02	0.51
diversity_beta_heatmap	0.40	0.01	0.47
diversity_beta_test	0.38	0.00	0.38
do_alpha_div_test	0.05	0.00	0.05
filter_categorize	0.29	0.06	0.71
filter_summary_bottom	0.45	0.03	0.61
filter_summary_top	0.31	0.02	0.59
find_biomarker	10.55	0.70	11.21
find_taxon_mat	0.33	0.02	1.09
find_taxonomy	0.03	0.00	0.59
find_taxonomy_300	0.03	0.00	0.64
gini_simpson	0	0	0
grep_tid	0	0	0
inverse_simpson	0	0	0
is_categorical	0	0	0
is_integer0	0	0	0
is_integer1	0	0	0
mae_pick_organisms	0.14	0.00	0.14
mae_pick_samples	0.11	0.00	0.11
pct2str	0	0	0
percent	0	0	0
relabu_barplot	0.74	0.04	0.89
relabu_boxplot	0.14	0.01	0.42
relabu_heatmap	0.26	0.03	0.44
run_animalcules	0	0	0
shannon	0	0	0
simpson_index	0	0	0
upsample_counts	0.03	0.00	0.09

name	user	system	elapsed
alpha_div_boxplot	0.53	0.07	0.67
alpha_div_test	0	0	0
counts_to_logcpm	0	0	0
counts_to_relabu	0	0	0
df_char_to_factor	0	0	0
differential_abundance	3.69	0.05	3.73
dimred_pca	0.17	0.03	0.20
dimred_pcoa	0.19	0.02	0.25
dimred_tsne	6.40	0.04	6.69
diversities	0	0	0
diversities_help	0	0	0
diversity_beta_boxplot	0.42	0.05	0.47
diversity_beta_heatmap	0.49	0.02	0.50
diversity_beta_test	0.46	0.00	0.46
do_alpha_div_test	0.08	0.00	0.08
filter_categorize	0.39	0.04	0.44
filter_summary_bottom	0.33	0.03	0.35
filter_summary_top	0.20	0.04	0.29
find_biomarker	12.47	0.14	12.51
find_taxon_mat	0.23	0.00	1.17
find_taxonomy	0.02	0.00	0.68
find_taxonomy_300	0.03	0.00	0.64
gini_simpson	0	0	0
grep_tid	0	0	0
inverse_simpson	0	0	0
is_categorical	0	0	0
is_integer0	0	0	0
is_integer1	0	0	0
mae_pick_organisms	0.14	0.00	0.14
mae_pick_samples	0.11	0.00	0.11
pct2str	0	0	0
percent	0	0	0
relabu_barplot	0.87	0.00	0.88
relabu_boxplot	0.09	0.03	0.12
relabu_heatmap	0.19	0.01	0.20
run_animalcules	0	0	0
shannon	0	0	0
simpson_index	0	0	0
upsample_counts	0	0	0

CHECK report for animalcules on tokay2

Summary

Command output

Installation output

Tests output

Example timings