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) |
| Back to Multiple platform build/check report for BioC 3.16: simplified long |
|
This page was generated on 2023-04-12 11:05:24 -0400 (Wed, 12 Apr 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) | x86_64 | 4.2.3 (2023-03-15) -- "Shortstop Beagle" | 4502 |
| palomino4 | Windows Server 2022 Datacenter | x64 | 4.2.3 (2023-03-15 ucrt) -- "Shortstop Beagle" | 4282 |
| lconway | macOS 12.5.1 Monterey | x86_64 | 4.2.3 (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 | ||||
|
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. |
| Package 52/2183 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| animalcules 1.14.0 (landing page) Yue Zhao
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | | ||||||||
| lconway | macOS 12.5.1 Monterey / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| Package: animalcules |
| Version: 1.14.0 |
| Command: F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:animalcules.install-out.txt --library=F:\biocbuild\bbs-3.16-bioc\R\library --no-vignettes --timings animalcules_1.14.0.tar.gz |
| StartedAt: 2023-04-10 22:48:30 -0400 (Mon, 10 Apr 2023) |
| EndedAt: 2023-04-10 22:53:37 -0400 (Mon, 10 Apr 2023) |
| EllapsedTime: 307.6 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: animalcules.Rcheck |
| Warnings: 1 |
##############################################################################
##############################################################################
###
### Running command:
###
### F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:animalcules.install-out.txt --library=F:\biocbuild\bbs-3.16-bioc\R\library --no-vignettes --timings animalcules_1.14.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'F:/biocbuild/bbs-3.16-bioc/meat/animalcules.Rcheck'
* using R version 4.2.3 (2023-03-15 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: UTF-8
* using option '--no-vignettes'
* 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 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 'F:/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 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
dimred_tsne 5.42 0.20 5.63
find_biomarker 5.42 0.06 5.91
* 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
'F:/biocbuild/bbs-3.16-bioc/meat/animalcules.Rcheck/00check.log'
for details.
animalcules.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD INSTALL animalcules ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.16-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' 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)
animalcules.Rcheck/tests/testthat.Rout
R version 4.2.3 (2023-03-15 ucrt) -- "Shortstop Beagle"
Copyright (C) 2023 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'
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
27.64 1.34 29.67
animalcules.Rcheck/animalcules-Ex.timings
| name | user | system | elapsed | |
| alpha_div_boxplot | 1.20 | 0.03 | 2.58 | |
| 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 | 4.27 | 0.10 | 4.36 | |
| dimred_pca | 0.14 | 0.04 | 0.19 | |
| dimred_pcoa | 0.11 | 0.05 | 0.15 | |
| dimred_tsne | 5.42 | 0.20 | 5.63 | |
| dimred_umap | 0.47 | 0.03 | 0.50 | |
| diversities | 0 | 0 | 0 | |
| diversities_help | 0 | 0 | 0 | |
| diversity_beta_boxplot | 0.20 | 0.05 | 0.25 | |
| diversity_beta_heatmap | 0.19 | 0.03 | 0.22 | |
| diversity_beta_test | 0.13 | 0.00 | 0.12 | |
| do_alpha_div_test | 0.04 | 0.00 | 0.05 | |
| filter_categorize | 0.32 | 0.06 | 0.37 | |
| filter_summary_bar_density | 0.34 | 0.04 | 0.38 | |
| filter_summary_pie_box | 0.25 | 0.01 | 0.26 | |
| find_biomarker | 5.42 | 0.06 | 5.91 | |
| find_taxon_mat | 0.17 | 0.02 | 0.83 | |
| find_taxonomy | 0.02 | 0.00 | 0.95 | |
| find_taxonomy_300 | 0.03 | 0.02 | 0.98 | |
| 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 | 0.09 | 0.01 | 0.11 | |
| mae_pick_samples | 0.07 | 0.00 | 0.07 | |
| pct2str | 0 | 0 | 0 | |
| percent | 0 | 0 | 0 | |
| relabu_barplot | 0.98 | 0.05 | 1.04 | |
| relabu_boxplot | 0.16 | 0.01 | 0.18 | |
| relabu_heatmap | 0.19 | 0.03 | 0.22 | |
| run_animalcules | 0 | 0 | 0 | |
| shannon | 0 | 0 | 0 | |
| simpson_index | 0 | 0 | 0 | |
| upsample_counts | 0.02 | 0.00 | 0.02 | |