Leo Lahti
| Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018) |
| URL: https://git.bioconductor.org/packages/microbiome |
| Branch: RELEASE_3_7 |
| Last Commit: ce71c09 |
| Last Changed Date: 2018-05-23 09:21:39 -0400 (Wed, 23 May 2018) |
| Back to Multiple platform build/check report for BioC 3.7 |
|
This page was generated on 2018-10-17 08:30:36 -0400 (Wed, 17 Oct 2018).
| Package 902/1561 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| microbiome 1.2.1 Leo Lahti
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | [ OK ] | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: microbiome |
| Version: 1.2.1 |
| Command: /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:microbiome.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings microbiome_1.2.1.tar.gz |
| StartedAt: 2018-10-16 02:00:51 -0400 (Tue, 16 Oct 2018) |
| EndedAt: 2018-10-16 02:02:50 -0400 (Tue, 16 Oct 2018) |
| EllapsedTime: 119.9 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: microbiome.Rcheck |
| Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:microbiome.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings microbiome_1.2.1.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.7-bioc/meat/microbiome.Rcheck’ * using R version 3.5.1 Patched (2018-07-12 r74967) * 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 ‘1.2.1’ * 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 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-3.7-bioc/R/bin/R CMD INSTALL microbiome ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.7-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 3.5.1 Patched (2018-07-12 r74967) -- "Feather Spray"
Copyright (C) 2018 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
6.532 0.152 6.682
microbiome.Rcheck/microbiome-Ex.timings
| name | user | system | elapsed | |
| abundances | 0.016 | 0.000 | 0.016 | |
| aggregate_taxa | 0.876 | 0.072 | 0.951 | |
| associate | 0.024 | 0.008 | 0.034 | |
| baseline | 0.032 | 0.004 | 0.033 | |
| bimodality | 0.012 | 0.000 | 0.011 | |
| bimodality_sarle | 0 | 0 | 0 | |
| boxplot_abundance | 0.044 | 0.000 | 0.042 | |
| chunk_reorder | 0.000 | 0.000 | 0.001 | |
| cmat2table | 0.068 | 0.008 | 0.078 | |
| core | 0.020 | 0.000 | 0.017 | |
| core_abundance | 0.016 | 0.000 | 0.015 | |
| core_matrix | 0 | 0 | 0 | |
| core_members | 0.012 | 0.000 | 0.011 | |
| coverage | 0.032 | 0.000 | 0.031 | |
| densityplot | 0.000 | 0.000 | 0.001 | |
| divergence | 0.420 | 0.004 | 0.424 | |
| diversities | 0.02 | 0.00 | 0.02 | |
| dominance | 0.012 | 0.000 | 0.012 | |
| estimate_stability | 0.004 | 0.000 | 0.001 | |
| evenness | 0.008 | 0.000 | 0.009 | |
| find_optima | 0.004 | 0.000 | 0.001 | |
| gktau | 0.004 | 0.000 | 0.006 | |
| global | 0.024 | 0.000 | 0.021 | |
| group_age | 0.028 | 0.000 | 0.031 | |
| group_bmi | 0.000 | 0.000 | 0.001 | |
| heat | 0.048 | 0.000 | 0.048 | |
| hotplot | 0.120 | 0.008 | 0.126 | |
| inequality | 0.404 | 0.000 | 0.405 | |
| intermediate_stability | 0.556 | 0.000 | 0.557 | |
| log_modulo_skewness | 0.108 | 0.000 | 0.111 | |
| low_abundance | 0.012 | 0.000 | 0.013 | |
| map_levels | 0.036 | 0.000 | 0.034 | |
| merge_taxa2 | 0.024 | 0.000 | 0.026 | |
| meta | 0.008 | 0.000 | 0.009 | |
| microbiome-package | 0.012 | 0.000 | 0.022 | |
| multimodality | 0 | 0 | 0 | |
| neat | 0.052 | 0.000 | 0.051 | |
| neatsort | 0.120 | 0.004 | 0.124 | |
| noncore_abundance | 0.012 | 0.000 | 0.012 | |
| noncore_members | 0.008 | 0.004 | 0.013 | |
| plot_atlas | 0.060 | 0.000 | 0.061 | |
| plot_composition | 2.180 | 0.000 | 2.187 | |
| plot_core | 0.140 | 0.016 | 0.155 | |
| plot_density | 0.044 | 0.000 | 0.044 | |
| plot_frequencies | 0.016 | 0.000 | 0.015 | |
| plot_landscape | 0.048 | 0.000 | 0.047 | |
| plot_regression | 2.668 | 0.008 | 2.681 | |
| plot_taxa_prevalence | 0.392 | 0.004 | 0.396 | |
| plot_tipping | 0.132 | 0.004 | 0.137 | |
| potential_analysis | 0.012 | 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 | 0.009 | |
| rarity | 0.064 | 0.004 | 0.069 | |
| read_biom2phyloseq | 0.000 | 0.000 | 0.001 | |
| read_csv2phyloseq | 0.000 | 0.000 | 0.001 | |
| read_mothur2phyloseq | 0.000 | 0.000 | 0.001 | |
| read_phyloseq | 0.000 | 0.004 | 0.001 | |
| remove_samples | 0.012 | 0.000 | 0.011 | |
| remove_taxa | 0.016 | 0.000 | 0.016 | |
| richness | 0.008 | 0.000 | 0.010 | |
| summarize_phyloseq | 0.016 | 0.000 | 0.019 | |
| taxa | 0.008 | 0.000 | 0.007 | |
| time_normalize | 0.024 | 0.000 | 0.025 | |
| time_sort | 0.148 | 0.000 | 0.148 | |
| top_taxa | 0.004 | 0.004 | 0.009 | |
| transform | 0.364 | 0.000 | 0.365 | |
| variable_members | 0.04 | 0.00 | 0.04 | |
| write_phyloseq | 0.004 | 0.000 | 0.001 | |
| ztransform | 0 | 0 | 0 | |