Yue Zhao
| Snapshot Date: 2022-03-17 13:55:23 -0400 (Thu, 17 Mar 2022) |
| git_url: https://git.bioconductor.org/packages/animalcules |
| git_branch: master |
| git_last_commit: 66921d7 |
| git_last_commit_date: 2022-01-14 11:36:35 -0400 (Fri, 14 Jan 2022) |
| Back to Multiple platform build/check report for BioC 3.15 |
|
This page was generated on 2022-03-18 11:06:55 -0400 (Fri, 18 Mar 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | R Under development (unstable) (2022-02-17 r81757) -- "Unsuffered Consequences" | 4334 |
| riesling1 | Windows Server 2019 Standard | x64 | R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" | 4097 |
| palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2022-02-17 r81757 ucrt) -- "Unsuffered Consequences" | 4083 |
| merida1 | macOS 10.14.6 Mojave | x86_64 | R Under development (unstable) (2022-03-02 r81842) -- "Unsuffered Consequences" | 4134 |
| 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 | ||||
|
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. |
| Package 53/2090 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| animalcules 1.11.1 (landing page) Yue Zhao
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| riesling1 | Windows Server 2019 Standard / x64 | OK | OK | WARNINGS | OK | |||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | | ||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| Package: animalcules |
| Version: 1.11.1 |
| Command: D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:animalcules.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings animalcules_1.11.1.tar.gz |
| StartedAt: 2022-03-17 18:26:11 -0400 (Thu, 17 Mar 2022) |
| EndedAt: 2022-03-17 18:30:23 -0400 (Thu, 17 Mar 2022) |
| EllapsedTime: 252.5 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: animalcules.Rcheck |
| Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:animalcules.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings animalcules_1.11.1.tar.gz ### ############################################################################## ############################################################################## * using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/animalcules.Rcheck' * using R Under development (unstable) (2021-11-21 r81221) * 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 '1.11.1' * 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 ... 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' See 'D:/biocbuild/bbs-3.15-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 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 * 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 ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 1 WARNING, 1 NOTE See 'D:/biocbuild/bbs-3.15-bioc/meat/animalcules.Rcheck/00check.log' for details.
animalcules.Rcheck/00install.out
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###
### Running command:
###
### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL animalcules
###
##############################################################################
##############################################################################
* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/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'
** 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
Warning: replacing previous import 'SummarizedExperiment::colnames' by 'biomformat::colnames' when loading 'animalcules'
Warning: replacing previous import 'SummarizedExperiment::rownames' by 'biomformat::rownames' 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'
** testing if installed package keeps a record of temporary installation path
* DONE (animalcules)
Making 'packages.html' ... done
animalcules.Rcheck/tests/testthat.Rout
R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences"
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)
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'
>
> test_check("animalcules")
[ FAIL 0 | WARN 5 | SKIP 0 | PASS 38 ]
[ FAIL 0 | WARN 5 | SKIP 0 | PASS 38 ]
>
> proc.time()
user system elapsed
28.23 1.15 30.01
animalcules.Rcheck/animalcules-Ex.timings
| name | user | system | elapsed | |
| alpha_div_boxplot | 0.42 | 0.13 | 0.55 | |
| 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 | 3.56 | 0.06 | 3.63 | |
| dimred_pca | 0.13 | 0.03 | 0.16 | |
| dimred_pcoa | 0.11 | 0.06 | 0.17 | |
| dimred_tsne | 4.03 | 0.11 | 4.14 | |
| dimred_umap | 0.31 | 0.05 | 0.36 | |
| diversities | 0 | 0 | 0 | |
| diversities_help | 0 | 0 | 0 | |
| diversity_beta_boxplot | 0.16 | 0.03 | 0.18 | |
| diversity_beta_heatmap | 0.14 | 0.05 | 0.19 | |
| diversity_beta_test | 0.07 | 0.00 | 0.08 | |
| do_alpha_div_test | 0.05 | 0.00 | 0.05 | |
| filter_categorize | 0.19 | 0.09 | 0.28 | |
| filter_summary_bar_density | 0.24 | 0.02 | 0.25 | |
| filter_summary_pie_box | 0.25 | 0.03 | 0.29 | |
| find_biomarker | 4.34 | 0.07 | 4.42 | |
| find_taxon_mat | 0.13 | 0.02 | 0.83 | |
| find_taxonomy | 0.00 | 0.00 | 0.54 | |
| find_taxonomy_300 | 0.03 | 0.00 | 0.54 | |
| 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 | 0.08 | 0.00 | 0.08 | |
| mae_pick_samples | 0.04 | 0.00 | 0.05 | |
| pct2str | 0 | 0 | 0 | |
| percent | 0 | 0 | 0 | |
| relabu_barplot | 0.72 | 0.03 | 0.75 | |
| relabu_boxplot | 0.10 | 0.03 | 0.12 | |
| relabu_heatmap | 0.11 | 0.01 | 0.13 | |
| run_animalcules | 0 | 0 | 0 | |
| shannon | 0 | 0 | 0 | |
| simpson_index | 0 | 0 | 0 | |
| upsample_counts | 0 | 0 | 0 | |