Leo Lahti
| Snapshot Date: 2022-03-17 13:55:23 -0400 (Thu, 17 Mar 2022) |
| git_url: https://git.bioconductor.org/packages/microbiome |
| git_branch: master |
| git_last_commit: dcbc499 |
| git_last_commit_date: 2022-01-11 10:45:26 -0400 (Tue, 11 Jan 2022) |
| Back to Multiple platform build/check report for BioC 3.15 |
|
This page was generated on 2022-03-18 11:08:01 -0400 (Fri, 18 Mar 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | R Under development (unstable) (2022-02-17 r81757) -- "Unsuffered Consequences" | 4334 |
| riesling1 | Windows Server 2019 Standard | x64 | R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" | 4097 |
| palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2022-02-17 r81757 ucrt) -- "Unsuffered Consequences" | 4083 |
| merida1 | macOS 10.14.6 Mojave | x86_64 | R Under development (unstable) (2022-03-02 r81842) -- "Unsuffered Consequences" | 4134 |
| 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 | ||||
|
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 1146/2090 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| microbiome 1.17.1 (landing page) Leo Lahti
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||||
| riesling1 | Windows Server 2019 Standard / x64 | OK | OK | OK | OK | |||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: microbiome |
| Version: 1.17.1 |
| Command: D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:microbiome.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings microbiome_1.17.1.tar.gz |
| StartedAt: 2022-03-17 19:34:32 -0400 (Thu, 17 Mar 2022) |
| EndedAt: 2022-03-17 19:37:30 -0400 (Thu, 17 Mar 2022) |
| EllapsedTime: 178.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: microbiome.Rcheck |
| Warnings: 0 |
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###
### Running command:
###
### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:microbiome.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings microbiome_1.17.1.tar.gz
###
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##############################################################################
* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/microbiome.Rcheck'
* using R Under development (unstable) (2021-11-21 r81221)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'microbiome/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'microbiome' version '1.17.1'
* 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 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 15.9 0.06 15.96
* 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
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###
### Running command:
###
### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL microbiome
###
##############################################################################
##############################################################################
* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'microbiome' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'microbiome'
finding HTML links ... done
abundances html
finding level-2 HTML links ... done
aggregate_rare html
aggregate_taxa html
alpha html
associate html
atlas1006 html
baseline html
bimodality html
bimodality_sarle html
boxplot_abundance html
chunk_reorder html
cmat2table html
collapse_replicates html
core html
core_abundance html
core_heatmap html
core_matrix html
core_members html
coverage html
default_colors html
densityplot html
dietswap html
divergence html
diversity html
dominance html
dominant html
estimate_stability html
evenness html
find_optima html
gktau html
group_age html
group_bmi html
heat html
hitchip.taxonomy html
hotplot html
inequality html
intermediate_stability html
is_compositional html
log_modulo_skewness html
low_abundance html
map_levels html
merge_taxa2 html
meta html
microbiome-package html
multimodality html
neat html
neatsort html
overlap html
peerj32 html
plot_atlas html
plot_composition html
plot_core html
plot_density html
plot_frequencies html
plot_landscape html
plot_regression html
plot_taxa_prevalence html
plot_tipping html
potential_analysis html
potential_univariate html
prevalence html
quiet html
radial_theta html
rare html
rare_abundance html
rare_members html
rarity html
read_biom2phyloseq html
read_csv2phyloseq html
read_mothur2phyloseq html
read_phyloseq html
readcount html
remove_samples html
remove_taxa html
richness html
spreadplot html
summarize_phyloseq html
taxa html
time_normalize html
time_sort html
timesplit html
top html
top_taxa html
transform html
ztransform html
** 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)
Making 'packages.html' ...Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
DESCRIPTION file of package 'XDE' is missing or broken
done
microbiome.Rcheck/tests/testthat.Rout
R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences"
Copyright (C) 2021 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)
> test_check("microbiome")
Loading required package: microbiome
Loading required package: phyloseq
Loading required package: ggplot2
microbiome R package (microbiome.github.com)
Copyright (C) 2011-2021 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
[ FAIL 0 | WARN 5 | SKIP 1 | PASS 82 ]
== Skipped tests ===============================================================
* On Bioconductor (1)
[ FAIL 0 | WARN 5 | SKIP 1 | PASS 82 ]
>
> proc.time()
user system elapsed
10.87 0.76 11.65
microbiome.Rcheck/microbiome-Ex.timings
| name | user | system | elapsed | |
| abundances | 0.01 | 0.00 | 0.01 | |
| aggregate_rare | 0.35 | 0.00 | 0.35 | |
| aggregate_taxa | 0.08 | 0.00 | 0.08 | |
| alpha | 0.01 | 0.00 | 0.02 | |
| associate | 0.04 | 0.00 | 0.03 | |
| baseline | 0.06 | 0.00 | 0.06 | |
| bimodality | 0 | 0 | 0 | |
| bimodality_sarle | 0 | 0 | 0 | |
| boxplot_abundance | 0.04 | 0.02 | 0.04 | |
| chunk_reorder | 0 | 0 | 0 | |
| cmat2table | 0.06 | 0.00 | 0.07 | |
| collapse_replicates | 0.03 | 0.00 | 0.03 | |
| core | 0.47 | 0.01 | 0.48 | |
| core_abundance | 0.03 | 0.00 | 0.03 | |
| core_matrix | 0 | 0 | 0 | |
| core_members | 0.01 | 0.00 | 0.02 | |
| coverage | 0.04 | 0.00 | 0.03 | |
| default_colors | 0.00 | 0.02 | 0.01 | |
| densityplot | 0 | 0 | 0 | |
| divergence | 0.54 | 0.05 | 0.60 | |
| diversity | 0.03 | 0.00 | 0.03 | |
| dominance | 0.02 | 0.00 | 0.02 | |
| dominant | 0.02 | 0.00 | 0.01 | |
| estimate_stability | 0 | 0 | 0 | |
| evenness | 0.01 | 0.00 | 0.02 | |
| find_optima | 0 | 0 | 0 | |
| gktau | 0.00 | 0.01 | 0.01 | |
| group_age | 0.02 | 0.02 | 0.03 | |
| group_bmi | 0.00 | 0.01 | 0.02 | |
| heat | 0.03 | 0.05 | 0.08 | |
| hotplot | 0.17 | 0.00 | 0.17 | |
| inequality | 0.02 | 0.00 | 0.01 | |
| intermediate_stability | 0.35 | 0.02 | 0.38 | |
| is_compositional | 0.04 | 0.01 | 0.05 | |
| log_modulo_skewness | 0.09 | 0.00 | 0.09 | |
| low_abundance | 0.00 | 0.02 | 0.02 | |
| map_levels | 0.03 | 0.00 | 0.03 | |
| merge_taxa2 | 0.03 | 0.00 | 0.03 | |
| meta | 0 | 0 | 0 | |
| microbiome-package | 0.02 | 0.00 | 0.01 | |
| multimodality | 0 | 0 | 0 | |
| neat | 0.03 | 0.01 | 0.05 | |
| neatsort | 0.11 | 0.02 | 0.13 | |
| overlap | 15.90 | 0.06 | 15.96 | |
| plot_atlas | 0.05 | 0.00 | 0.05 | |
| plot_composition | 0.16 | 0.00 | 0.16 | |
| plot_core | 0.06 | 0.00 | 0.06 | |
| plot_density | 0.03 | 0.00 | 0.03 | |
| plot_frequencies | 0.01 | 0.00 | 0.01 | |
| plot_landscape | 0.72 | 0.02 | 0.74 | |
| plot_regression | 0.24 | 0.01 | 0.25 | |
| plot_taxa_prevalence | 0.31 | 0.00 | 0.31 | |
| plot_tipping | 0.11 | 0.03 | 0.14 | |
| potential_analysis | 0.01 | 0.00 | 0.02 | |
| potential_univariate | 0 | 0 | 0 | |
| prevalence | 0 | 0 | 0 | |
| quiet | 0 | 0 | 0 | |
| rare | 0.01 | 0.02 | 0.03 | |
| rare_abundance | 0.02 | 0.00 | 0.02 | |
| rare_members | 0.00 | 0.01 | 0.01 | |
| rarity | 0.03 | 0.02 | 0.05 | |
| read_biom2phyloseq | 0 | 0 | 0 | |
| read_csv2phyloseq | 0 | 0 | 0 | |
| read_mothur2phyloseq | 0 | 0 | 0 | |
| read_phyloseq | 0 | 0 | 0 | |
| readcount | 0 | 0 | 0 | |
| remove_samples | 0.03 | 0.00 | 0.03 | |
| remove_taxa | 0.01 | 0.00 | 0.01 | |
| richness | 0.02 | 0.00 | 0.02 | |
| spreadplot | 0.08 | 0.02 | 0.09 | |
| summarize_phyloseq | 0.01 | 0.01 | 0.03 | |
| taxa | 0.02 | 0.00 | 0.02 | |
| time_normalize | 0.03 | 0.00 | 0.03 | |
| time_sort | 0.09 | 0.02 | 0.11 | |
| timesplit | 0.08 | 0.01 | 0.09 | |
| top | 0.02 | 0.00 | 0.02 | |
| top_taxa | 0.00 | 0.02 | 0.02 | |
| transform | 0.04 | 0.00 | 0.04 | |
| ztransform | 0 | 0 | 0 | |