Back to Multiple platform build/check report for BioC 3.13 |
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This page was generated on 2021-10-15 15:06:42 -0400 (Fri, 15 Oct 2021).
To the developers/maintainers of the microbiome package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/microbiome.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 1127/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
microbiome 1.14.0 (landing page) Leo Lahti
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | OK | |||||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | |||||||||
machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | |||||||||
Package: microbiome |
Version: 1.14.0 |
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:microbiome.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings microbiome_1.14.0.tar.gz |
StartedAt: 2021-10-14 21:06:30 -0400 (Thu, 14 Oct 2021) |
EndedAt: 2021-10-14 21:10:47 -0400 (Thu, 14 Oct 2021) |
EllapsedTime: 256.4 seconds |
RetCode: 0 |
Status: OK |
CheckDir: microbiome.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:microbiome.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings microbiome_1.14.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.13-bioc/meat/microbiome.Rcheck’ * using R version 4.1.1 (2021-08-10) * using platform: x86_64-apple-darwin17.0 (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 ‘1.14.0’ * 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 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 Examples with CPU (user + system) or elapsed time > 5s user system elapsed overlap 23.751 1.774 25.544 * 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: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL microbiome ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library’ * installing *source* package ‘microbiome’ ... ** using staged installation ** 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 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 (microbiome)
microbiome.Rcheck/tests/testthat.Rout
R version 4.1.1 (2021-08-10) -- "Kick Things" Copyright (C) 2021 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin17.0 (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) > test_check("microbiome") Loading required package: microbiome Loading required package: phyloseq Loading required package: ggplot2 microbiome R package (microbiome.github.com) Copyright (C) 2011-2020 Leo Lahti, Sudarshan Shetty et al. <microbiome.github.io> Attaching package: 'microbiome' The following object is masked from 'package:ggplot2': alpha The following object is masked from 'package:base': transform ══ Skipped tests ═══════════════════════════════════════════════════════════════ • On Bioconductor (1) [ FAIL 0 | WARN 2 | SKIP 1 | PASS 75 ] > > proc.time() user system elapsed 15.528 0.749 16.262
microbiome.Rcheck/microbiome-Ex.timings
name | user | system | elapsed | |
abundances | 0.021 | 0.003 | 0.024 | |
aggregate_rare | 0.349 | 0.014 | 0.363 | |
aggregate_taxa | 0.111 | 0.002 | 0.113 | |
alpha | 0.015 | 0.002 | 0.018 | |
associate | 0.060 | 0.002 | 0.062 | |
baseline | 0.100 | 0.003 | 0.102 | |
bfratio | 0.193 | 0.002 | 0.196 | |
bimodality | 0.002 | 0.000 | 0.002 | |
bimodality_sarle | 0 | 0 | 0 | |
boxplot_abundance | 0.071 | 0.003 | 0.075 | |
chunk_reorder | 0.000 | 0.000 | 0.001 | |
cmat2table | 0.087 | 0.003 | 0.090 | |
collapse_replicates | 0.511 | 0.005 | 0.515 | |
core | 0.039 | 0.001 | 0.041 | |
core_abundance | 0.042 | 0.003 | 0.045 | |
core_matrix | 0.000 | 0.001 | 0.000 | |
core_members | 0.011 | 0.002 | 0.013 | |
coverage | 0.045 | 0.003 | 0.047 | |
default_colors | 0 | 0 | 0 | |
densityplot | 0 | 0 | 0 | |
divergence | 0.807 | 0.031 | 0.839 | |
diversities | 0.015 | 0.003 | 0.018 | |
diversity | 0.015 | 0.004 | 0.018 | |
dominance | 0.011 | 0.002 | 0.012 | |
dominant | 0.015 | 0.003 | 0.018 | |
estimate_stability | 0.000 | 0.000 | 0.001 | |
evenness | 0.009 | 0.001 | 0.011 | |
find_optima | 0 | 0 | 0 | |
gktau | 0.016 | 0.002 | 0.018 | |
global | 0.012 | 0.002 | 0.015 | |
group_age | 0.025 | 0.002 | 0.026 | |
group_bmi | 0.000 | 0.000 | 0.001 | |
heat | 0.078 | 0.009 | 0.088 | |
hotplot | 0.177 | 0.005 | 0.182 | |
inequality | 0.041 | 0.006 | 0.048 | |
intermediate_stability | 0.657 | 0.005 | 0.662 | |
is_compositional | 0.089 | 0.003 | 0.092 | |
log_modulo_skewness | 0.205 | 0.005 | 0.210 | |
low_abundance | 0.018 | 0.002 | 0.022 | |
map_levels | 0.046 | 0.002 | 0.048 | |
merge_taxa2 | 0.025 | 0.001 | 0.027 | |
meta | 0.006 | 0.001 | 0.007 | |
microbiome-package | 0.012 | 0.001 | 0.014 | |
multimodality | 0.000 | 0.001 | 0.000 | |
neat | 0.100 | 0.003 | 0.104 | |
neatsort | 0.249 | 0.005 | 0.254 | |
overlap | 23.751 | 1.774 | 25.544 | |
plot_atlas | 0.059 | 0.002 | 0.062 | |
plot_composition | 0.246 | 0.003 | 0.248 | |
plot_core | 0.082 | 0.005 | 0.086 | |
plot_density | 0.040 | 0.002 | 0.043 | |
plot_frequencies | 0.031 | 0.002 | 0.033 | |
plot_landscape | 1.271 | 0.016 | 1.290 | |
plot_regression | 0.197 | 0.004 | 0.201 | |
plot_taxa_prevalence | 0.408 | 0.006 | 0.413 | |
plot_tipping | 0.132 | 0.004 | 0.135 | |
potential_analysis | 0.057 | 0.002 | 0.058 | |
potential_univariate | 0 | 0 | 0 | |
prevalence | 0.013 | 0.001 | 0.015 | |
quiet | 0.000 | 0.000 | 0.001 | |
rare | 0.032 | 0.002 | 0.034 | |
rare_abundance | 0.037 | 0.001 | 0.038 | |
rare_members | 0.015 | 0.002 | 0.017 | |
rarity | 0.126 | 0.003 | 0.129 | |
read_biom2phyloseq | 0.000 | 0.000 | 0.001 | |
read_csv2phyloseq | 0.000 | 0.001 | 0.001 | |
read_mothur2phyloseq | 0.001 | 0.001 | 0.000 | |
read_phyloseq | 0.000 | 0.000 | 0.001 | |
readcount | 0.032 | 0.003 | 0.034 | |
remove_samples | 0.019 | 0.002 | 0.020 | |
remove_taxa | 0.024 | 0.001 | 0.025 | |
richness | 0.015 | 0.002 | 0.016 | |
spreadplot | 0.074 | 0.002 | 0.077 | |
summarize_phyloseq | 0.026 | 0.003 | 0.028 | |
taxa | 0.007 | 0.002 | 0.009 | |
time_normalize | 0.045 | 0.002 | 0.047 | |
time_sort | 0.188 | 0.003 | 0.191 | |
timesplit | 0.189 | 0.002 | 0.192 | |
top | 0.012 | 0.002 | 0.014 | |
top_taxa | 0.009 | 0.001 | 0.010 | |
transform | 0.094 | 0.003 | 0.096 | |
write_phyloseq | 0 | 0 | 0 | |
ztransform | 0 | 0 | 0 | |