Yue Zhao
| Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019) |
| URL: https://git.bioconductor.org/packages/animalcules |
| Branch: RELEASE_3_9 |
| Last Commit: d57e352 |
| Last Changed Date: 2019-06-28 19:53:58 -0400 (Fri, 28 Jun 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-10-16 13:05:03 -0400 (Wed, 16 Oct 2019).
| Package 55/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| animalcules 1.0.6 Yue Zhao
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK | |
| Package: animalcules |
| Version: 1.0.6 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:animalcules.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings animalcules_1.0.6.tar.gz |
| StartedAt: 2019-10-16 00:30:29 -0400 (Wed, 16 Oct 2019) |
| EndedAt: 2019-10-16 00:37:09 -0400 (Wed, 16 Oct 2019) |
| EllapsedTime: 399.6 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: animalcules.Rcheck |
| Warnings: 0 |
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:animalcules.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings animalcules_1.0.6.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/animalcules.Rcheck’
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘animalcules/DESCRIPTION’ ... OK
* this is package ‘animalcules’ version ‘1.0.6’
* 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 ... 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
* 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 or elapsed time > 5s
user system elapsed
find_biomarker 47.643 28.700 14.730
dimred_tsne 12.264 0.615 12.882
* 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 NOTE
See
‘/Users/biocbuild/bbs-3.9-bioc/meat/animalcules.Rcheck/00check.log’
for details.
animalcules.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL animalcules ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’ * installing *source* package ‘animalcules’ ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** 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 * DONE (animalcules)
animalcules.Rcheck/tests/testthat.Rout
R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (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")
══ testthat results ═══════════════════════════════════════════════════════════
[ OK: 39 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
>
> proc.time()
user system elapsed
87.741 32.733 53.150
animalcules.Rcheck/animalcules-Ex.timings
| name | user | system | elapsed | |
| alpha_div_boxplot | 1.854 | 0.135 | 1.999 | |
| alpha_div_test | 0.006 | 0.001 | 0.006 | |
| counts_to_logcpm | 0.002 | 0.000 | 0.003 | |
| counts_to_relabu | 0.004 | 0.000 | 0.005 | |
| df_char_to_factor | 0.001 | 0.000 | 0.001 | |
| differential_abundance | 4.492 | 0.056 | 4.548 | |
| dimred_pca | 0.316 | 0.048 | 0.366 | |
| dimred_pcoa | 0.251 | 0.048 | 0.303 | |
| dimred_tsne | 12.264 | 0.615 | 12.882 | |
| diversities | 0.001 | 0.000 | 0.001 | |
| diversities_help | 0.001 | 0.000 | 0.001 | |
| diversity_beta_boxplot | 0.364 | 0.050 | 0.420 | |
| diversity_beta_heatmap | 0.448 | 0.071 | 0.523 | |
| diversity_beta_test | 0.491 | 0.005 | 0.495 | |
| do_alpha_div_test | 0.083 | 0.001 | 0.084 | |
| filter_categorize | 2.060 | 0.206 | 0.677 | |
| filter_summary_bottom | 0.465 | 0.087 | 0.554 | |
| filter_summary_top | 0.402 | 0.094 | 0.500 | |
| find_biomarker | 47.643 | 28.700 | 14.730 | |
| find_taxon_mat | 0.360 | 0.018 | 1.071 | |
| find_taxonomy | 0.056 | 0.002 | 0.730 | |
| find_taxonomy_300 | 0.046 | 0.003 | 0.694 | |
| gini_simpson | 0.001 | 0.000 | 0.001 | |
| grep_tid | 0 | 0 | 0 | |
| inverse_simpson | 0.001 | 0.001 | 0.001 | |
| is_categorical | 0.000 | 0.000 | 0.001 | |
| is_integer0 | 0.000 | 0.000 | 0.001 | |
| is_integer1 | 0 | 0 | 0 | |
| mae_pick_organisms | 0.135 | 0.000 | 0.136 | |
| mae_pick_samples | 0.162 | 0.001 | 0.163 | |
| pct2str | 0.001 | 0.000 | 0.000 | |
| percent | 0.000 | 0.000 | 0.001 | |
| relabu_barplot | 1.447 | 0.043 | 1.493 | |
| relabu_boxplot | 0.173 | 0.040 | 0.217 | |
| relabu_heatmap | 0.237 | 0.042 | 0.282 | |
| run_animalcules | 0.001 | 0.000 | 0.000 | |
| shannon | 0.001 | 0.001 | 0.001 | |
| simpson_index | 0.001 | 0.000 | 0.000 | |
| upsample_counts | 0.019 | 0.002 | 0.021 | |