Leo Lahti
| Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020) |
| URL: https://git.bioconductor.org/packages/microbiome |
| Branch: RELEASE_3_10 |
| Last Commit: 11ae6af |
| Last Changed Date: 2019-10-29 13:10:41 -0400 (Tue, 29 Oct 2019) |
| Back to Multiple platform build/check report for BioC 3.10 |
|
This page was generated on 2020-04-15 12:13:05 -0400 (Wed, 15 Apr 2020).
| Package 1039/1823 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| microbiome 1.8.0 Leo Lahti
| malbec1 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | [ WARNINGS ] | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | WARNINGS | OK | |
| Package: microbiome |
| Version: 1.8.0 |
| Command: /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:microbiome.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings microbiome_1.8.0.tar.gz |
| StartedAt: 2020-04-15 05:03:36 -0400 (Wed, 15 Apr 2020) |
| EndedAt: 2020-04-15 05:07:01 -0400 (Wed, 15 Apr 2020) |
| EllapsedTime: 204.8 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: microbiome.Rcheck |
| Warnings: 3 |
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### Running command:
###
### /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:microbiome.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings microbiome_1.8.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.10-bioc/meat/microbiome.Rcheck’
* using R version 3.6.3 (2020-02-29)
* 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 ‘1.8.0’
* 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 ... WARNING
Documented arguments not in \usage in documentation object 'core':
‘...’
Documented arguments not in \usage in documentation object 'rare':
‘...’
Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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 ... WARNING
Note: significantly better compression could be obtained
by using R CMD build --resave-data
old_size new_size compress
atlas1006.rda 233Kb 128Kb xz
dietswap.rda 45Kb 28Kb xz
hitchip.taxonomy.rda 402Kb 115Kb xz
peerj32.rda 113Kb 87Kb xz
* checking files in ‘vignettes’ ... OK
* checking examples ... WARNING
Found the following significant warnings:
Warning: 'noncore_abundance' is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
* 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: 3 WARNINGs
See
‘/home/biocbuild/bbs-3.10-bioc/meat/microbiome.Rcheck/00check.log’
for details.
microbiome.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD INSTALL microbiome ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.10-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 ** 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 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 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) 2011-2019 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
══ testthat results ═══════════════════════════════════════════════════════════
[ OK: 74 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
>
> proc.time()
user system elapsed
14.172 0.232 14.616
microbiome.Rcheck/microbiome-Ex.timings
| name | user | system | elapsed | |
| abundances | 0.428 | 0.000 | 0.428 | |
| aggregate_taxa | 0.296 | 0.000 | 0.297 | |
| aggregate_top_taxa | 0.348 | 0.028 | 0.375 | |
| alpha | 0.016 | 0.000 | 0.018 | |
| associate | 0.064 | 0.000 | 0.065 | |
| baseline | 0.024 | 0.004 | 0.027 | |
| bfratio | 0.144 | 0.000 | 0.145 | |
| bimodality | 0.012 | 0.000 | 0.013 | |
| bimodality_sarle | 0 | 0 | 0 | |
| boxplot_abundance | 0.072 | 0.000 | 0.074 | |
| chunk_reorder | 0 | 0 | 0 | |
| cmat2table | 0.084 | 0.000 | 0.087 | |
| collapse_replicates | 0.040 | 0.000 | 0.041 | |
| core | 0.048 | 0.000 | 0.046 | |
| core_abundance | 0.044 | 0.008 | 0.054 | |
| core_matrix | 0.004 | 0.000 | 0.000 | |
| core_members | 0.004 | 0.004 | 0.008 | |
| coverage | 0.036 | 0.000 | 0.036 | |
| default_colors | 0.000 | 0.000 | 0.001 | |
| densityplot | 0 | 0 | 0 | |
| divergence | 0.636 | 0.024 | 0.661 | |
| diversities | 0.008 | 0.008 | 0.013 | |
| diversity | 0.008 | 0.004 | 0.013 | |
| dominance | 0.008 | 0.000 | 0.010 | |
| dominant | 0.012 | 0.000 | 0.009 | |
| estimate_stability | 0.000 | 0.000 | 0.001 | |
| evenness | 0.008 | 0.000 | 0.007 | |
| find_optima | 0 | 0 | 0 | |
| gktau | 0.024 | 0.000 | 0.024 | |
| global | 0.008 | 0.000 | 0.008 | |
| group_age | 0.016 | 0.000 | 0.019 | |
| group_bmi | 0.000 | 0.000 | 0.001 | |
| heat | 0.060 | 0.000 | 0.061 | |
| hotplot | 0.120 | 0.004 | 0.122 | |
| inequality | 0.028 | 0.000 | 0.025 | |
| intermediate_stability | 0.840 | 0.000 | 0.842 | |
| is.compositional | 0.040 | 0.004 | 0.044 | |
| log_modulo_skewness | 0.652 | 0.000 | 0.651 | |
| low_abundance | 0.008 | 0.004 | 0.014 | |
| map_levels | 0.060 | 0.000 | 0.061 | |
| merge_taxa2 | 0.028 | 0.004 | 0.031 | |
| meta | 0.004 | 0.000 | 0.005 | |
| microbiome-package | 0.016 | 0.000 | 0.056 | |
| multimodality | 0 | 0 | 0 | |
| neat | 0.084 | 0.000 | 0.122 | |
| neatsort | 0.232 | 0.000 | 0.234 | |
| noncore_abundance | 0.040 | 0.004 | 0.045 | |
| noncore_members | 0 | 0 | 0 | |
| plot_atlas | 0.044 | 0.000 | 0.046 | |
| plot_composition | 0.296 | 0.008 | 0.334 | |
| plot_core | 0.088 | 0.004 | 0.091 | |
| plot_density | 0.048 | 0.000 | 0.047 | |
| plot_frequencies | 0.016 | 0.000 | 0.016 | |
| plot_landscape | 1.704 | 0.008 | 1.712 | |
| plot_regression | 0.172 | 0.000 | 0.172 | |
| plot_taxa_prevalence | 0.532 | 0.004 | 0.539 | |
| plot_tipping | 0.108 | 0.008 | 0.116 | |
| potential_analysis | 0.044 | 0.012 | 0.055 | |
| potential_univariate | 0 | 0 | 0 | |
| prevalence | 0.008 | 0.000 | 0.008 | |
| quiet | 0.000 | 0.000 | 0.001 | |
| rare | 0.024 | 0.004 | 0.027 | |
| rare_abundance | 0.052 | 0.004 | 0.057 | |
| rare_members | 0.008 | 0.000 | 0.007 | |
| rarity | 0.068 | 0.000 | 0.069 | |
| read_biom2phyloseq | 0 | 0 | 0 | |
| read_csv2phyloseq | 0 | 0 | 0 | |
| read_mothur2phyloseq | 0 | 0 | 0 | |
| read_phyloseq | 0.000 | 0.000 | 0.001 | |
| readcount | 0.008 | 0.000 | 0.006 | |
| remove_samples | 0.016 | 0.000 | 0.014 | |
| remove_taxa | 0.016 | 0.000 | 0.018 | |
| richness | 0.012 | 0.000 | 0.009 | |
| spreadplot | 0.052 | 0.004 | 0.055 | |
| summarize_phyloseq | 0.016 | 0.000 | 0.017 | |
| taxa | 0.008 | 0.000 | 0.005 | |
| time_normalize | 0.028 | 0.000 | 0.031 | |
| time_sort | 0.144 | 0.004 | 0.149 | |
| timesplit | 0.12 | 0.00 | 0.12 | |
| top_taxa | 0.008 | 0.000 | 0.006 | |
| transform | 0.028 | 0.000 | 0.026 | |
| write_phyloseq | 0 | 0 | 0 | |
| ztransform | 0 | 0 | 0 | |