Back to Multiple platform build/check report for BioC 3.15
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This page was generated on 2022-05-16 11:06:31 -0400 (Mon, 16 May 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_644.2.0 (2022-04-22) -- "Vigorous Calisthenics" 4379
palomino3Windows Server 2022 Datacenterx644.2.0 (2022-04-22 ucrt) -- "Vigorous Calisthenics" 4153
merida1macOS 10.14.6 Mojavex86_644.2.0 (2022-04-22) -- "Vigorous Calisthenics" 4220
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

CHECK results for microbiome on palomino3


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? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1171/2140HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
microbiome 1.18.0  (landing page)
Leo Lahti
Snapshot Date: 2022-05-15 13:55:12 -0400 (Sun, 15 May 2022)
git_url: https://git.bioconductor.org/packages/microbiome
git_branch: RELEASE_3_15
git_last_commit: 4887f83
git_last_commit_date: 2022-04-26 11:42:45 -0400 (Tue, 26 Apr 2022)
nebbiolo1Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: microbiome
Version: 1.18.0
Command: F:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:microbiome.install-out.txt --library=F:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings microbiome_1.18.0.tar.gz
StartedAt: 2022-05-16 01:18:59 -0400 (Mon, 16 May 2022)
EndedAt: 2022-05-16 01:22:15 -0400 (Mon, 16 May 2022)
EllapsedTime: 196.0 seconds
RetCode: 0
Status:   OK  
CheckDir: microbiome.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:microbiome.install-out.txt --library=F:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings microbiome_1.18.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.15-bioc/meat/microbiome.Rcheck'
* using R version 4.2.0 (2022-04-22 ucrt)
* using platform: x86_64-w64-mingw32 (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 '1.18.0'
* 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 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 14.36   0.08   14.45
* 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

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL microbiome
###
##############################################################################
##############################################################################


* installing to library 'F:/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
** 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)

Tests output

microbiome.Rcheck/tests/testthat.Rout


R version 4.2.0 (2022-04-22 ucrt) -- "Vigorous Calisthenics"
Copyright (C) 2022 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) 2011-2022 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 3 | SKIP 1 | PASS 83 ]

══ Skipped tests ═══════════════════════════════════════════════════════════════
• On Bioconductor (1)

[ FAIL 0 | WARN 3 | SKIP 1 | PASS 83 ]
> 
> proc.time()
   user  system elapsed 
  12.70    0.68   13.39 

Example timings

microbiome.Rcheck/microbiome-Ex.timings

nameusersystemelapsed
TibbleUtilites0.250.010.27
abundances0.000.020.01
add_besthit000
add_refseq000
aggregate_rare0.460.000.45
aggregate_taxa0.150.000.16
alpha0.020.000.01
associate0.050.000.05
baseline0.640.010.65
bimodality000
bimodality_sarle000
boxplot_abundance0.040.000.05
boxplot_alpha0.270.020.28
chunk_reorder000
cmat2table0.060.000.06
collapse_replicates0.050.000.05
core0.010.020.03
core_abundance0.030.000.03
core_matrix000
core_members0.000.010.01
coverage0.050.000.05
default_colors000
densityplot000
divergence0.440.000.44
diversity0.010.000.01
dominance0.020.000.02
dominant0.020.000.02
estimate_stability000
evenness000
find_optima000
gktau0.000.020.01
group_age0.030.000.03
group_bmi000
heat0.040.000.05
hotplot0.130.000.12
inequality0.030.000.04
intermediate_stability0.480.000.48
is_compositional0.080.000.08
log_modulo_skewness0.190.000.19
low_abundance0.020.000.01
map_levels0.060.000.06
merge_taxa20.030.000.04
meta000
microbiome-package0.000.010.01
multimodality000
neat0.060.000.06
neatsort0.160.020.18
overlap14.36 0.0814.45
plot_atlas0.030.000.03
plot_composition0.170.030.20
plot_core0.060.000.07
plot_density0.050.000.04
plot_frequencies0.020.000.02
plot_landscape0.710.030.75
plot_regression0.270.000.26
plot_taxa_prevalence0.380.000.38
plot_tipping0.120.000.12
potential_analysis0.060.000.06
potential_univariate000
prevalence0.010.010.03
psmelt20.110.000.11
quiet000
rare0.030.000.03
rare_abundance0.040.020.05
rare_members0.010.000.02
rarity0.100.020.11
read_biom2phyloseq000
read_csv2phyloseq000
read_mothur2phyloseq000
read_phyloseq000
readcount0.010.000.01
remove_samples0.020.000.02
remove_taxa0.020.000.02
richness0.010.000.01
spreadplot0.070.030.10
summarize_phyloseq0.010.000.01
taxa0.000.010.02
time_normalize0.030.020.05
time_sort0.110.000.10
timesplit0.10.00.1
top0.010.000.01
top_taxa000
transform0.270.000.27
ztransform000