Leo Lahti
| Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019) |
| URL: https://git.bioconductor.org/packages/microbiome |
| Branch: RELEASE_3_8 |
| Last Commit: d4437ff |
| Last Changed Date: 2018-11-30 13:56:03 -0400 (Fri, 30 Nov 2018) |
| Back to Multiple platform build/check report for BioC 3.8 |
|
This page was generated on 2019-04-16 11:52:58 -0400 (Tue, 16 Apr 2019).
| Package 954/1649 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| microbiome 1.4.2 Leo Lahti
| malbec1 | Linux (Ubuntu 16.04.6 LTS) / x86_64 | OK | OK | [ OK ] | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: microbiome |
| Version: 1.4.2 |
| Command: /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:microbiome.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings microbiome_1.4.2.tar.gz |
| StartedAt: 2019-04-16 01:25:20 -0400 (Tue, 16 Apr 2019) |
| EndedAt: 2019-04-16 01:28:19 -0400 (Tue, 16 Apr 2019) |
| EllapsedTime: 179.3 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: microbiome.Rcheck |
| Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:microbiome.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings microbiome_1.4.2.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.8-bioc/meat/microbiome.Rcheck’ * using R version 3.5.3 (2019-03-11) * using platform: x86_64-pc-linux-gnu (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘microbiome/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘microbiome’ version ‘1.4.2’ * 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 ‘microbiome’ 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 ... OK * 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 contents of ‘data’ directory ... OK * checking data for non-ASCII characters ... OK * checking data for ASCII and uncompressed saves ... 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: OK
microbiome.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD INSTALL microbiome ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.8-bioc/R/library’ * installing *source* package ‘microbiome’ ... ** R ** data ** 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 * DONE (microbiome)
microbiome.Rcheck/tests/testthat.Rout
R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 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)
> test_check("microbiome")
Loading required package: microbiome
Loading required package: phyloseq
Loading required package: ggplot2
microbiome R package (microbiome.github.com)
Copyright (C) 2011-2018 Leo Lahti et al. <microbiome.github.io>
Attaching package: 'microbiome'
The following object is masked from 'package:base':
transform
══ testthat results ═══════════════════════════════════════════════════════════
OK: 69 SKIPPED: 0 FAILED: 0
>
> proc.time()
user system elapsed
8.296 0.176 8.483
microbiome.Rcheck/microbiome-Ex.timings
| name | user | system | elapsed | |
| abundances | 0.012 | 0.000 | 0.015 | |
| aggregate_taxa | 1.012 | 0.060 | 1.072 | |
| associate | 0.032 | 0.004 | 0.036 | |
| baseline | 0.020 | 0.000 | 0.022 | |
| bimodality | 0.004 | 0.004 | 0.011 | |
| bimodality_sarle | 0 | 0 | 0 | |
| boxplot_abundance | 0.036 | 0.008 | 0.043 | |
| chunk_reorder | 0 | 0 | 0 | |
| cmat2table | 0.068 | 0.016 | 0.085 | |
| core | 0.012 | 0.004 | 0.015 | |
| core_abundance | 0.012 | 0.000 | 0.014 | |
| core_matrix | 0 | 0 | 0 | |
| core_members | 0.012 | 0.000 | 0.009 | |
| coverage | 0.032 | 0.000 | 0.031 | |
| densityplot | 0 | 0 | 0 | |
| divergence | 0.772 | 0.000 | 0.773 | |
| diversities | 0.032 | 0.000 | 0.031 | |
| dominance | 0.016 | 0.000 | 0.017 | |
| estimate_stability | 0.000 | 0.000 | 0.001 | |
| evenness | 0.016 | 0.000 | 0.014 | |
| find_optima | 0 | 0 | 0 | |
| gktau | 0.012 | 0.000 | 0.008 | |
| global | 0.036 | 0.000 | 0.039 | |
| group_age | 0.044 | 0.004 | 0.050 | |
| group_bmi | 0.000 | 0.000 | 0.001 | |
| heat | 0.084 | 0.004 | 0.091 | |
| hotplot | 0.216 | 0.008 | 0.225 | |
| inequality | 0.524 | 0.000 | 0.525 | |
| intermediate_stability | 0.696 | 0.012 | 0.709 | |
| log_modulo_skewness | 0.172 | 0.004 | 0.173 | |
| low_abundance | 0.020 | 0.000 | 0.021 | |
| map_levels | 0.060 | 0.000 | 0.059 | |
| merge_taxa2 | 0.040 | 0.000 | 0.042 | |
| meta | 0.012 | 0.000 | 0.013 | |
| microbiome-package | 0.012 | 0.000 | 0.034 | |
| multimodality | 0 | 0 | 0 | |
| neat | 0.084 | 0.000 | 0.084 | |
| neatsort | 0.192 | 0.004 | 0.198 | |
| noncore_abundance | 0.012 | 0.000 | 0.013 | |
| noncore_members | 0.016 | 0.000 | 0.014 | |
| plot_atlas | 0.064 | 0.000 | 0.066 | |
| plot_composition | 3.548 | 0.004 | 3.561 | |
| plot_core | 0.172 | 0.008 | 0.181 | |
| plot_density | 0.048 | 0.000 | 0.048 | |
| plot_frequencies | 0.016 | 0.000 | 0.017 | |
| plot_landscape | 0.052 | 0.000 | 0.050 | |
| plot_regression | 4.064 | 0.004 | 4.087 | |
| plot_taxa_prevalence | 0.384 | 0.008 | 0.392 | |
| plot_tipping | 0.144 | 0.008 | 0.151 | |
| potential_analysis | 0.016 | 0.000 | 0.014 | |
| potential_univariate | 0 | 0 | 0 | |
| prevalence | 0.004 | 0.000 | 0.005 | |
| quiet | 0.000 | 0.000 | 0.001 | |
| rare_members | 0.012 | 0.000 | 0.010 | |
| rarity | 0.072 | 0.000 | 0.072 | |
| read_biom2phyloseq | 0 | 0 | 0 | |
| read_csv2phyloseq | 0.000 | 0.000 | 0.001 | |
| read_mothur2phyloseq | 0 | 0 | 0 | |
| read_phyloseq | 0 | 0 | 0 | |
| remove_samples | 0.012 | 0.000 | 0.011 | |
| remove_taxa | 0.016 | 0.000 | 0.019 | |
| richness | 0.004 | 0.004 | 0.010 | |
| summarize_phyloseq | 0.020 | 0.000 | 0.019 | |
| taxa | 0.008 | 0.000 | 0.009 | |
| time_normalize | 0.028 | 0.000 | 0.027 | |
| time_sort | 0.232 | 0.004 | 0.237 | |
| top_taxa | 0.016 | 0.000 | 0.014 | |
| transform | 0.044 | 0.000 | 0.043 | |
| variable_members | 0.068 | 0.000 | 0.068 | |
| write_phyloseq | 0 | 0 | 0 | |
| ztransform | 0.000 | 0.000 | 0.001 | |