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CHECK report for microbiome on malbec1

This page was generated on 2018-04-12 13:16:37 -0400 (Thu, 12 Apr 2018).

Package 852/1472HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
microbiome 1.0.2
Leo Lahti
Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018)
URL: https://git.bioconductor.org/packages/microbiome
Branch: RELEASE_3_6
Last Commit: 290f0dc
Last Changed Date: 2018-02-22 09:03:04 -0400 (Thu, 22 Feb 2018)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
veracruz1 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: microbiome
Version: 1.0.2
Command: /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings microbiome_1.0.2.tar.gz
StartedAt: 2018-04-12 01:06:07 -0400 (Thu, 12 Apr 2018)
EndedAt: 2018-04-12 01:08:31 -0400 (Thu, 12 Apr 2018)
EllapsedTime: 144.0 seconds
RetCode: 0
Status:  OK 
CheckDir: microbiome.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings microbiome_1.0.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.6-bioc/meat/microbiome.Rcheck’
* using R version 3.4.4 (2018-03-15)
* 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 ‘1.0.2’
* 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 loading without being on the library search path ... 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 installed files from ‘inst/doc’ ... 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


Installation output

microbiome.Rcheck/00install.out

* installing *source* package ‘microbiome’ ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (microbiome)

Tests output

microbiome.Rcheck/tests/testthat.Rout


R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
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 
  8.776   0.120   8.904 

Example timings

microbiome.Rcheck/microbiome-Ex.timings

nameusersystemelapsed
abundances0.0360.0000.034
aggregate_taxa0.3720.0000.371
associate0.0880.0000.088
baseline0.0360.0000.038
bimodality0.1240.0000.122
bimodality_sarle000
boxplot_abundance0.1640.0000.162
chunk_reorder0.0000.0000.001
cmat2table0.2440.0040.250
core0.0160.0000.017
core_abundance0.0120.0000.015
core_matrix0.0000.0000.001
core_members0.0120.0000.010
coverage0.0720.0040.078
densityplot0.0040.0000.000
divergence0.5400.0040.546
diversities0.0160.0000.014
dominance0.0440.0040.048
estimate_stability0.0000.0000.001
evenness0.0040.0040.010
find_optima000
gktau0.0040.0000.006
global0.0760.0000.076
group_age0.0400.0000.038
group_bmi0.0000.0000.001
heat0.0960.0000.094
hotplot0.4480.0000.448
inequality0.3040.0000.305
intermediate_stability0.6560.0040.662
log_modulo_skewness0.1000.0000.098
low_abundance0.0160.0040.020
map_levels0.0520.0040.056
merge_taxa20.0280.0000.027
meta0.0080.0000.009
microbiome-package0.0080.0000.010
multimodality000
neat0.3720.0000.376
neatsort0.160.000.16
noncore_abundance0.0080.0040.014
noncore_members0.0160.0000.016
plot_atlas0.0880.0080.097
plot_composition0.180.000.18
plot_core0.4440.0040.449
plot_density0.0400.0040.043
plot_frequencies0.0480.0000.047
plot_landscape0.0480.0000.048
plot_regression3.0480.0083.058
plot_taxa_prevalence1.3080.0121.321
plot_tipping0.4080.0000.408
potential_analysis0.0360.0000.034
potential_univariate000
prevalence0.0080.0000.006
quiet0.0000.0000.001
rare_members0.0080.0040.011
rarity0.0920.0000.089
read_biom2phyloseq0.0000.0000.001
read_csv2phyloseq0.0000.0000.001
read_mothur2phyloseq0.0000.0000.001
read_phyloseq000
remove_samples0.0160.0000.012
remove_taxa0.0200.0000.021
richness0.0120.0000.010
summarize_phyloseq0.0200.0000.021
taxa0.0080.0000.007
time_normalize0.0240.0000.026
time_sort0.1480.0000.147
top_taxa0.0120.0000.010
transform0.0280.0040.032
variable_members0.0560.0000.054
write_phyloseq0.0000.0000.001
ztransform0.0000.0000.001