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CHECK report for animalcules on tokay1

This page was generated on 2021-01-24 11:53:35 -0500 (Sun, 24 Jan 2021).

TO THE DEVELOPERS/MAINTAINERS OF THE animalcules PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 58/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
animalcules 1.6.0
Yue Zhao
Snapshot Date: 2021-01-23 14:40:16 -0500 (Sat, 23 Jan 2021)
URL: https://git.bioconductor.org/packages/animalcules
Branch: RELEASE_3_12
Last Commit: a95d2e8
Last Changed Date: 2020-12-06 22:41:49 -0500 (Sun, 06 Dec 2020)
malbec1 Linux (Ubuntu 18.04.5 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
nebbiolo1 Linux (Ubuntu 20.04.1 LTS) / x86_64  OK  OK  OK 
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
merida1 macOS 10.14.6 Mojave / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: animalcules
Version: 1.6.0
Command: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:animalcules.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings animalcules_1.6.0.tar.gz
StartedAt: 2021-01-24 00:21:27 -0500 (Sun, 24 Jan 2021)
EndedAt: 2021-01-24 00:29:29 -0500 (Sun, 24 Jan 2021)
EllapsedTime: 482.6 seconds
RetCode: 0
Status:  OK  
CheckDir: animalcules.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:animalcules.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings animalcules_1.6.0.tar.gz
###
##############################################################################
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* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/animalcules.Rcheck'
* using R version 4.0.3 (2020-10-10)
* 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 '1.6.0'
* 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 '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 ... NOTE
Namespace in Imports field not imported from: 'reactable'
  All declared Imports should be used.
* 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 (user + system) or elapsed time > 5s
                       user system elapsed
find_biomarker         9.42   0.08    9.88
dimred_tsne            6.14   0.08    7.45
differential_abundance 5.42   0.29    5.72
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                       user system elapsed
find_biomarker         9.33   0.08    9.41
differential_abundance 6.47   0.11    6.58
dimred_tsne            6.25   0.01    6.59
* 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: 2 NOTEs
See
  'C:/Users/biocbuild/bbs-3.12-bioc/meat/animalcules.Rcheck/00check.log'
for details.



Installation output

animalcules.Rcheck/00install.out

##############################################################################
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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.12/bioc/src/contrib/animalcules_1.6.0.tar.gz && rm -rf animalcules.buildbin-libdir && mkdir animalcules.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=animalcules.buildbin-libdir animalcules_1.6.0.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL animalcules_1.6.0.zip && rm animalcules_1.6.0.tar.gz animalcules_1.6.0.zip
###
##############################################################################
##############################################################################


  % 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 1846k  100 1846k    0     0  20.7M      0 --:--:-- --:--:-- --:--:-- 21.9M

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  
    dimred_umap                             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_bar_density              html  
    filter_summary_pie_box                  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  
    write_to_biom                           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_1.6.0.zip
* DONE (animalcules)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'animalcules' successfully unpacked and MD5 sums checked

Tests output

animalcules.Rcheck/tests_i386/testthat.Rout


R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 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")
== Warnings ====================================================================
-- Warning (test-examples.R:148:5): dimred_tsne() is working -------------------
the condition has length > 1 and only the first element will be used
Backtrace:
 1. animalcules::dimred_tsne(...) test-examples.R:148:4
 2. tsne::tsne(scale(df), k = k, initial_dims = initial_dims, perplexity = perplexity)
 3. tsne:::.x2p(X, perplexity, 1e-05)

[ FAIL 0 | WARN 1 | SKIP 0 | PASS 39 ]
> 
> proc.time()
   user  system elapsed 
  42.54    1.98   45.15 

animalcules.Rcheck/tests_x64/testthat.Rout


R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 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")
== Warnings ====================================================================
-- Warning (test-examples.R:148:5): dimred_tsne() is working -------------------
the condition has length > 1 and only the first element will be used
Backtrace:
 1. animalcules::dimred_tsne(...) test-examples.R:148:4
 2. tsne::tsne(scale(df), k = k, initial_dims = initial_dims, perplexity = perplexity)
 3. tsne:::.x2p(X, perplexity, 1e-05)

[ FAIL 0 | WARN 1 | SKIP 0 | PASS 39 ]
> 
> proc.time()
   user  system elapsed 
  48.45    0.95   50.20 

Example timings

animalcules.Rcheck/examples_i386/animalcules-Ex.timings

nameusersystemelapsed
alpha_div_boxplot0.630.190.93
alpha_div_test000
counts_to_logcpm000
counts_to_relabu000
df_char_to_factor000
differential_abundance5.420.295.72
dimred_pca0.180.040.55
dimred_pcoa0.120.010.23
dimred_tsne6.140.087.45
dimred_umap0.580.081.10
diversities000
diversities_help000
diversity_beta_boxplot0.410.030.59
diversity_beta_heatmap0.370.030.49
diversity_beta_test0.110.000.10
do_alpha_div_test0.080.000.08
filter_categorize0.330.050.50
filter_summary_bar_density0.640.001.00
filter_summary_pie_box0.360.010.51
find_biomarker9.420.089.88
find_taxon_mat0.290.020.98
find_taxonomy0.030.000.61
find_taxonomy_3000.030.000.58
gini_simpson000
grep_tid000
inverse_simpson000
is_categorical000
is_integer0000
is_integer1000
mae_pick_organisms0.190.000.18
mae_pick_samples0.140.000.14
pct2str000
percent000
relabu_barplot1.090.031.13
relabu_boxplot0.160.000.15
relabu_heatmap0.190.010.20
run_animalcules000
shannon000
simpson_index000
upsample_counts0.010.000.02

animalcules.Rcheck/examples_x64/animalcules-Ex.timings

nameusersystemelapsed
alpha_div_boxplot0.580.084.36
alpha_div_test0.010.000.01
counts_to_logcpm000
counts_to_relabu000
df_char_to_factor0.010.000.01
differential_abundance6.470.116.58
dimred_pca0.190.050.27
dimred_pcoa0.120.000.15
dimred_tsne6.250.016.59
dimred_umap0.440.020.82
diversities000
diversities_help000
diversity_beta_boxplot0.250.000.39
diversity_beta_heatmap0.200.060.33
diversity_beta_test0.130.000.12
do_alpha_div_test0.030.000.03
filter_categorize0.280.080.39
filter_summary_bar_density0.360.050.43
filter_summary_pie_box0.240.030.34
find_biomarker9.330.089.41
find_taxon_mat0.280.000.98
find_taxonomy0.030.000.56
find_taxonomy_3000.030.000.55
gini_simpson000
grep_tid000
inverse_simpson000
is_categorical000
is_integer0000
is_integer1000
mae_pick_organisms0.170.000.18
mae_pick_samples0.140.000.14
pct2str000
percent000
relabu_barplot1.110.031.14
relabu_boxplot0.110.030.14
relabu_heatmap0.140.030.17
run_animalcules000
shannon000
simpson_index000
upsample_counts0.030.000.03