Yue Zhao
| Snapshot Date: 2023-09-21 14:00:15 -0400 (Thu, 21 Sep 2023) |
| git_url: https://git.bioconductor.org/packages/animalcules |
| git_branch: RELEASE_3_17 |
| git_last_commit: e7416c0 |
| git_last_commit_date: 2023-04-25 11:10:12 -0400 (Tue, 25 Apr 2023) |
| Back to Multiple platform build/check report for BioC 3.17: simplified long |
|
This page was generated on 2023-09-22 11:36:11 -0400 (Fri, 22 Sep 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.2 LTS) | x86_64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4625 |
| palomino3 | Windows Server 2022 Datacenter | x64 | 4.3.1 (2023-06-16 ucrt) -- "Beagle Scouts" | 4378 |
| merida1 | macOS 12.6.4 Monterey | x86_64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4394 |
| 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 | ||||
| Package 64/2230 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| animalcules 1.16.0 (landing page) Yue Zhao
| nebbiolo1 | Linux (Ubuntu 22.04.2 LTS) / x86_64 | OK | OK | ERROR | |||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | | ||||||||
| merida1 | macOS 12.6.4 Monterey / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
|
To the developers/maintainers of the animalcules package: - 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 Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: animalcules |
| Version: 1.16.0 |
| Command: F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:animalcules.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings animalcules_1.16.0.tar.gz |
| StartedAt: 2023-09-21 23:25:53 -0400 (Thu, 21 Sep 2023) |
| EndedAt: 2023-09-21 23:30:17 -0400 (Thu, 21 Sep 2023) |
| EllapsedTime: 264.1 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: animalcules.Rcheck |
| Warnings: 1 |
##############################################################################
##############################################################################
###
### Running command:
###
### F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:animalcules.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings animalcules_1.16.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'F:/biocbuild/bbs-3.17-bioc/meat/animalcules.Rcheck'
* using R version 4.3.1 (2023-06-16 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* R was compiled by
gcc.exe (GCC) 12.2.0
GNU Fortran (GCC) 12.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'animalcules/DESCRIPTION' ... OK
* this is package 'animalcules' version '1.16.0'
* 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::rownames' by 'biomformat::rownames' when loading 'animalcules'
Warning: replacing previous import 'SummarizedExperiment::colnames' by 'biomformat::colnames' when loading 'animalcules'
Warning: replacing previous import 'ape::where' by 'dplyr::where' when loading 'animalcules'
See 'F:/biocbuild/bbs-3.17-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 5.01 0.22 5.26
* 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-3.17-bioc/meat/animalcules.Rcheck/00check.log'
for details.
animalcules.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD INSTALL animalcules ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.17-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::rownames' by 'biomformat::rownames' when loading 'animalcules' Warning: replacing previous import 'SummarizedExperiment::colnames' by 'biomformat::colnames' 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::rownames' by 'biomformat::rownames' when loading 'animalcules' Warning: replacing previous import 'SummarizedExperiment::colnames' by 'biomformat::colnames' 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::rownames' by 'biomformat::rownames' when loading 'animalcules' Warning: replacing previous import 'SummarizedExperiment::colnames' by 'biomformat::colnames' 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 4.3.1 (2023-06-16 ucrt) -- "Beagle Scouts"
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::rownames' by 'biomformat::rownames' when loading 'animalcules'
2: replacing previous import 'SummarizedExperiment::colnames' by 'biomformat::colnames' 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
26.32 1.34 28.26
animalcules.Rcheck/animalcules-Ex.timings
| name | user | system | elapsed | |
| alpha_div_boxplot | 0.61 | 0.06 | 2.10 | |
| alpha_div_test | 0.01 | 0.00 | 0.02 | |
| counts_to_logcpm | 0 | 0 | 0 | |
| counts_to_relabu | 0.01 | 0.00 | 0.02 | |
| df_char_to_factor | 0 | 0 | 0 | |
| differential_abundance | 3.89 | 0.14 | 4.03 | |
| dimred_pca | 0.16 | 0.03 | 0.22 | |
| dimred_pcoa | 0.11 | 0.05 | 0.30 | |
| dimred_tsne | 5.01 | 0.22 | 5.26 | |
| dimred_umap | 0.52 | 0.03 | 0.63 | |
| diversities | 0 | 0 | 0 | |
| diversities_help | 0 | 0 | 0 | |
| diversity_beta_boxplot | 0.20 | 0.03 | 0.45 | |
| diversity_beta_heatmap | 0.25 | 0.03 | 0.74 | |
| diversity_beta_test | 0.08 | 0.02 | 0.09 | |
| do_alpha_div_test | 0.03 | 0.01 | 0.05 | |
| filter_categorize | 0.33 | 0.06 | 0.82 | |
| filter_summary_bar_density | 0.26 | 0.04 | 0.42 | |
| filter_summary_pie_box | 0.19 | 0.03 | 0.41 | |
| find_biomarker | 3.81 | 0.06 | 3.92 | |
| find_taxon_mat | 0.25 | 0.03 | 0.77 | |
| find_taxonomy | 0.00 | 0.00 | 0.51 | |
| 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 | 0.09 | 0.00 | 0.09 | |
| mae_pick_samples | 0.08 | 0.00 | 0.08 | |
| pct2str | 0 | 0 | 0 | |
| percent | 0 | 0 | 0 | |
| relabu_barplot | 1.02 | 0.04 | 1.09 | |
| relabu_boxplot | 0.12 | 0.02 | 0.22 | |
| relabu_heatmap | 0.11 | 0.05 | 0.38 | |
| run_animalcules | 0 | 0 | 0 | |
| shannon | 0 | 0 | 0 | |
| simpson_index | 0 | 0 | 0 | |
| upsample_counts | 0.02 | 0.00 | 0.01 | |