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This page was generated on 2023-04-12 11:04:57 -0400 (Wed, 12 Apr 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.5 LTS)x86_644.2.3 (2023-03-15) -- "Shortstop Beagle" 4502
palomino4Windows Server 2022 Datacenterx644.2.3 (2023-03-15 ucrt) -- "Shortstop Beagle" 4282
lconwaymacOS 12.5.1 Montereyx86_644.2.3 (2023-03-15) -- "Shortstop Beagle" 4310
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

CHECK results for animalcules on nebbiolo2


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? 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 52/2183HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
animalcules 1.14.0  (landing page)
Yue Zhao
Snapshot Date: 2023-04-10 14:00:05 -0400 (Mon, 10 Apr 2023)
git_url: https://git.bioconductor.org/packages/animalcules
git_branch: RELEASE_3_16
git_last_commit: bac5a33
git_last_commit_date: 2022-11-01 11:19:53 -0400 (Tue, 01 Nov 2022)
nebbiolo2Linux (Ubuntu 20.04.5 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
lconwaymacOS 12.5.1 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

Package: animalcules
Version: 1.14.0
Command: /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:animalcules.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/site-library --timings animalcules_1.14.0.tar.gz
StartedAt: 2023-04-10 18:57:26 -0400 (Mon, 10 Apr 2023)
EndedAt: 2023-04-10 19:02:42 -0400 (Mon, 10 Apr 2023)
EllapsedTime: 316.0 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: animalcules.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:animalcules.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/site-library --timings animalcules_1.14.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.16-bioc/meat/animalcules.Rcheck’
* using R version 4.2.3 (2023-03-15)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* checking for file ‘animalcules/DESCRIPTION’ ... OK
* this is package ‘animalcules’ version ‘1.14.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘animalcules’ can be installed ... WARNING
Found the following significant warnings:
  Warning: replacing previous import ‘SummarizedExperiment::colnames’ by ‘biomformat::colnames’ when loading ‘animalcules’
  Warning: replacing previous import ‘SummarizedExperiment::rownames’ by ‘biomformat::rownames’ when loading ‘animalcules’
  Warning: replacing previous import ‘ape::where’ by ‘dplyr::where’ when loading ‘animalcules’
See ‘/home/biocbuild/bbs-3.16-bioc/meat/animalcules.Rcheck/00install.out’ for details.
* 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
* 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 ... 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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
                        user system elapsed
differential_abundance 4.883  0.332   5.215
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘animalcules.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.16-bioc/meat/animalcules.Rcheck/00check.log’
for details.



Installation output

animalcules.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD INSTALL animalcules
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.16-bioc/R/site-library’
* installing *source* package ‘animalcules’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
Warning: replacing previous import ‘SummarizedExperiment::colnames’ by ‘biomformat::colnames’ when loading ‘animalcules’
Warning: replacing previous import ‘SummarizedExperiment::rownames’ by ‘biomformat::rownames’ when loading ‘animalcules’
Warning: replacing previous import ‘ape::where’ by ‘dplyr::where’ when loading ‘animalcules’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning: replacing previous import ‘SummarizedExperiment::colnames’ by ‘biomformat::colnames’ when loading ‘animalcules’
Warning: replacing previous import ‘SummarizedExperiment::rownames’ by ‘biomformat::rownames’ when loading ‘animalcules’
Warning: replacing previous import ‘ape::where’ by ‘dplyr::where’ when loading ‘animalcules’
** testing if installed package can be loaded from final location
Warning: replacing previous import ‘SummarizedExperiment::colnames’ by ‘biomformat::colnames’ when loading ‘animalcules’
Warning: replacing previous import ‘SummarizedExperiment::rownames’ by ‘biomformat::rownames’ when loading ‘animalcules’
Warning: replacing previous import ‘ape::where’ by ‘dplyr::where’ when loading ‘animalcules’
** testing if installed package keeps a record of temporary installation path
* DONE (animalcules)

Tests output

animalcules.Rcheck/tests/testthat.Rout


R version 4.2.3 (2023-03-15) -- "Shortstop Beagle"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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)
Warning messages:
1: replacing previous import 'SummarizedExperiment::colnames' by 'biomformat::colnames' when loading 'animalcules' 
2: replacing previous import 'SummarizedExperiment::rownames' by 'biomformat::rownames' when loading 'animalcules' 
3: replacing previous import 'ape::where' by 'dplyr::where' when loading 'animalcules' 
> 
> test_check("animalcules")
[ FAIL 0 | WARN 7 | SKIP 0 | PASS 38 ]

[ FAIL 0 | WARN 7 | SKIP 0 | PASS 38 ]
> 
> proc.time()
   user  system elapsed 
 26.065   0.943  27.692 

Example timings

animalcules.Rcheck/animalcules-Ex.timings

nameusersystemelapsed
alpha_div_boxplot0.4880.0920.580
alpha_div_test0.0030.0000.004
counts_to_logcpm0.0010.0000.001
counts_to_relabu0.0020.0000.002
df_char_to_factor0.0000.0000.001
differential_abundance4.8830.3325.215
dimred_pca0.1570.0080.165
dimred_pcoa0.1040.0160.119
dimred_tsne4.2260.1044.331
dimred_umap0.3360.0320.368
diversities000
diversities_help0.0000.0000.001
diversity_beta_boxplot0.1600.0160.175
diversity_beta_heatmap0.1820.0120.194
diversity_beta_test0.0920.0040.095
do_alpha_div_test0.0670.0000.066
filter_categorize0.2620.0200.281
filter_summary_bar_density0.2720.0120.284
filter_summary_pie_box0.1780.0080.187
find_biomarker3.5190.1403.660
find_taxon_mat0.1640.0160.868
find_taxonomy0.0280.0040.632
find_taxonomy_3000.0340.0000.664
gini_simpson0.0000.0000.001
grep_tid000
inverse_simpson000
is_categorical0.0000.0000.001
is_integer00.0010.0000.000
is_integer1000
mae_pick_organisms0.1280.0120.141
mae_pick_samples0.0620.0000.062
pct2str0.0010.0000.000
percent000
relabu_barplot0.9690.0881.057
relabu_boxplot0.0940.0120.105
relabu_heatmap0.1100.0080.118
run_animalcules000
shannon000
simpson_index000
upsample_counts0.0120.0000.012