Back to Multiple platform build/check report for BioC 3.13
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This page was generated on 2021-09-22 15:05:08 -0400 (Wed, 22 Sep 2021).

CHECK results for animalcules on tokay2

To the developers/maintainers of the animalcules package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/animalcules.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 58/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
animalcules 1.8.1  (landing page)
Yue Zhao
Snapshot Date: 2021-09-21 04:50:12 -0400 (Tue, 21 Sep 2021)
git_url: https://git.bioconductor.org/packages/animalcules
git_branch: RELEASE_3_13
git_last_commit: 5a3dc66
git_last_commit_date: 2021-06-02 12:17:59 -0400 (Wed, 02 Jun 2021)
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: animalcules
Version: 1.8.1
Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:animalcules.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings animalcules_1.8.1.tar.gz
StartedAt: 2021-09-21 19:06:56 -0400 (Tue, 21 Sep 2021)
EndedAt: 2021-09-21 19:14:05 -0400 (Tue, 21 Sep 2021)
EllapsedTime: 429.4 seconds
RetCode: 0
Status:   OK  
CheckDir: animalcules.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:animalcules.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings animalcules_1.8.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/animalcules.Rcheck'
* using R version 4.1.1 (2021-08-10)
* 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 '1.8.1'
* 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
differential_abundance 8.18   0.22    8.40
find_biomarker         6.75   0.05    6.79
dimred_tsne            6.06   0.04    6.14
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                       user system elapsed
differential_abundance 8.19   0.08    8.27
find_biomarker         7.44   0.01    7.45
dimred_tsne            6.48   0.05    6.53
* 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-3.13-bioc/meat/animalcules.Rcheck/00check.log'
for details.



Installation output

animalcules.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/animalcules_1.8.1.tar.gz && rm -rf animalcules.buildbin-libdir && mkdir animalcules.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=animalcules.buildbin-libdir animalcules_1.8.1.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL animalcules_1.8.1.zip && rm animalcules_1.8.1.tar.gz animalcules_1.8.1.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 1848k  100 1848k    0     0  2456k      0 --:--:-- --:--:-- --:--:-- 2458k

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_1.8.1.zip
* DONE (animalcules)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'animalcules' successfully unpacked and MD5 sums checked

Tests output

animalcules.Rcheck/tests_i386/testthat.Rout


R version 4.1.1 (2021-08-10) -- "Kick Things"
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)
> library(animalcules)
> 
> test_check("animalcules")
[ FAIL 0 | WARN 1 | SKIP 0 | PASS 38 ]
> 
> proc.time()
   user  system elapsed 
  29.43    1.93   32.71 

animalcules.Rcheck/tests_x64/testthat.Rout


R version 4.1.1 (2021-08-10) -- "Kick Things"
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)
> library(animalcules)
> 
> test_check("animalcules")
[ FAIL 0 | WARN 1 | SKIP 0 | PASS 38 ]
> 
> proc.time()
   user  system elapsed 
  34.84    0.64   36.29 

Example timings

animalcules.Rcheck/examples_i386/animalcules-Ex.timings

nameusersystemelapsed
alpha_div_boxplot0.520.130.65
alpha_div_test000
counts_to_logcpm000
counts_to_relabu000
df_char_to_factor000
differential_abundance8.180.228.40
dimred_pca0.240.050.28
dimred_pcoa0.210.080.34
dimred_tsne6.060.046.14
dimred_umap0.700.020.74
diversities000
diversities_help000
diversity_beta_boxplot0.300.010.31
diversity_beta_heatmap0.220.050.26
diversity_beta_test0.110.000.11
do_alpha_div_test0.060.000.06
filter_categorize0.360.050.42
filter_summary_bar_density0.380.030.41
filter_summary_pie_box0.30.00.3
find_biomarker6.750.056.79
find_taxon_mat0.250.001.42
find_taxonomy0.040.000.68
find_taxonomy_3000.030.000.56
gini_simpson000
grep_tid000
inverse_simpson000
is_categorical000
is_integer0000
is_integer1000
mae_pick_organisms0.220.000.22
mae_pick_samples0.210.000.21
pct2str000
percent000
relabu_barplot1.070.051.12
relabu_boxplot0.100.060.16
relabu_heatmap0.260.020.28
run_animalcules000
shannon000
simpson_index000
upsample_counts0.020.000.03

animalcules.Rcheck/examples_x64/animalcules-Ex.timings

nameusersystemelapsed
alpha_div_boxplot1.170.061.56
alpha_div_test000
counts_to_logcpm000
counts_to_relabu000
df_char_to_factor000
differential_abundance8.190.088.27
dimred_pca0.280.000.62
dimred_pcoa0.220.030.47
dimred_tsne6.480.056.53
dimred_umap0.710.030.75
diversities000
diversities_help000
diversity_beta_boxplot0.250.020.31
diversity_beta_heatmap0.380.040.43
diversity_beta_test0.140.000.14
do_alpha_div_test0.070.000.08
filter_categorize0.460.070.51
filter_summary_bar_density0.440.010.45
filter_summary_pie_box0.280.020.30
find_biomarker7.440.017.45
find_taxon_mat0.300.021.05
find_taxonomy0.010.000.62
find_taxonomy_3000.030.000.64
gini_simpson000
grep_tid000
inverse_simpson000
is_categorical000
is_integer0000
is_integer1000
mae_pick_organisms0.250.000.25
mae_pick_samples0.210.000.20
pct2str0.000.010.02
percent000
relabu_barplot1.150.021.26
relabu_boxplot0.210.010.58
relabu_heatmap0.230.030.27
run_animalcules000
shannon000
simpson_index000
upsample_counts0.020.020.03