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This page was generated on 2024-07-18 11:41 -0400 (Thu, 18 Jul 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.4.1 (2024-06-14) -- "Race for Your Life" 4683
palomino8Windows Server 2022 Datacenterx644.4.1 (2024-06-14 ucrt) -- "Race for Your Life" 4379
lconwaymacOS 12.7.1 Montereyx86_644.4.1 (2024-06-14) -- "Race for Your Life" 4450
kjohnson3macOS 13.6.5 Venturaarm644.4.1 (2024-06-14) -- "Race for Your Life" 4399
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

Package 1231/2248HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
microbiome 1.27.0  (landing page)
Leo Lahti
Snapshot Date: 2024-07-17 14:00 -0400 (Wed, 17 Jul 2024)
git_url: https://git.bioconductor.org/packages/microbiome
git_branch: devel
git_last_commit: b216965
git_last_commit_date: 2024-04-30 11:00:00 -0400 (Tue, 30 Apr 2024)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino8Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.6.5 Ventura / arm64  OK    OK    ERROR    OK  


CHECK results for microbiome on lconway

To the developers/maintainers of the microbiome package:
- 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 Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: microbiome
Version: 1.27.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:microbiome.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings microbiome_1.27.0.tar.gz
StartedAt: 2024-07-17 22:30:55 -0400 (Wed, 17 Jul 2024)
EndedAt: 2024-07-17 22:34:53 -0400 (Wed, 17 Jul 2024)
EllapsedTime: 238.4 seconds
RetCode: 0
Status:   OK  
CheckDir: microbiome.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:microbiome.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings microbiome_1.27.0.tar.gz
###
##############################################################################
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* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/microbiome.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘microbiome/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘microbiome’ version ‘1.27.0’
* 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 ... NOTE
Problems with news in ‘NEWS’:
  Cannot process chunk/lines:
    CHANGES IN VERSION 0.1.2 
    # New features
      o Added plot_abundances function
      o Added Chao1 index in richness function
      o In atlas1006 data set, pseudocount of +1 in otu table has been
        removed to facilitate comparison with sequencing data sets and to
        avoid confusion
      o In atlas1006 data set, only a single replicate per subject-time
        combination is chosen (at random)
      o New function collapse_replicates has been added
    # Major changes
      o Abundance matrices (otu tables) for all example data sets now
        starting from 0 without pseudocount
    # Minor changes
      o Changed the default for the detection argument in the richness function to
        detection=0
      o Color order in plot_landscape legend now follows the factor levels
        of the col argument
      o Various minor fixes; see github commits for many more details
* checking code 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 whether startup messages can be suppressed ... 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 ... NOTE
checkRd: (-1) bimodality.Rd:51-52: Lost braces in \itemize; meant \describe ?
checkRd: (-1) bimodality.Rd:53-54: Lost braces in \itemize; meant \describe ?
checkRd: (-1) bimodality.Rd:55-58: Lost braces in \itemize; meant \describe ?
checkRd: (-1) bimodality.Rd:38-39: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) bimodality.Rd:40-41: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) bimodality.Rd:42-43: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) bimodality.Rd:91-93: Lost braces in \itemize; meant \describe ?
checkRd: (-1) bimodality.Rd:94-95: Lost braces in \itemize; meant \describe ?
checkRd: (-1) bimodality.Rd:96: Lost braces in \itemize; meant \describe ?
checkRd: (-1) bimodality.Rd:97: Lost braces in \itemize; meant \describe ?
checkRd: (-1) bimodality.Rd:98: Lost braces in \itemize; meant \describe ?
checkRd: (-1) bimodality.Rd:99: Lost braces in \itemize; meant \describe ?
checkRd: (-1) bimodality_sarle.Rd:45: Lost braces in \itemize; meant \describe ?
checkRd: (-1) bimodality_sarle.Rd:46: Lost braces in \itemize; meant \describe ?
checkRd: (-1) bimodality_sarle.Rd:47: Lost braces in \itemize; meant \describe ?
checkRd: (-1) bimodality_sarle.Rd:48: Lost braces in \itemize; meant \describe ?
checkRd: (-1) diversity.Rd:28-29: Lost braces in \itemize; meant \describe ?
checkRd: (-1) diversity.Rd:30-32: Lost braces in \itemize; meant \describe ?
checkRd: (-1) diversity.Rd:33: Lost braces in \itemize; meant \describe ?
checkRd: (-1) diversity.Rd:34: Lost braces in \itemize; meant \describe ?
checkRd: (-1) diversity.Rd:35-36: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dominance.Rd:39-43: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dominance.Rd:44-45: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dominance.Rd:46-48: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dominance.Rd:49-51: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dominance.Rd:52-58: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dominance.Rd:59-60: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dominance.Rd:61-62: Lost braces in \itemize; meant \describe ?
checkRd: (-1) multimodality.Rd:33-34: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) multimodality.Rd:35-36: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) multimodality.Rd:37-38: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) multimodality.Rd:55-57: Lost braces in \itemize; meant \describe ?
checkRd: (-1) multimodality.Rd:58-59: Lost braces in \itemize; meant \describe ?
checkRd: (-1) potential_analysis.Rd:30-31: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) potential_analysis.Rd:32-33: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) potential_analysis.Rd:34-35: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) potential_analysis.Rd:36-37: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) potential_analysis.Rd:38: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) potential_analysis.Rd:61-63: Lost braces in \itemize; meant \describe ?
checkRd: (-1) potential_analysis.Rd:64-65: Lost braces in \itemize; meant \describe ?
checkRd: (-1) potential_univariate.Rd:50: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) potential_univariate.Rd:51-52: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) potential_univariate.Rd:53: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) potential_univariate.Rd:54-55: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) potential_univariate.Rd:56-57: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) potential_univariate.Rd:58: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) potential_univariate.Rd:59-60: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) potential_univariate.Rd:61-62: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) potential_univariate.Rd:73-75: Lost braces in \itemize; meant \describe ?
checkRd: (-1) potential_univariate.Rd:76-78: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rarity.Rd:35-41: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rarity.Rd:42-44: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rarity.Rd:45-48: Lost braces in \itemize; meant \describe ?
* 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 19.004  1.693  21.058
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.20-bioc/meat/microbiome.Rcheck/00check.log’
for details.


Installation output

microbiome.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL microbiome
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/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)

Tests output

microbiome.Rcheck/tests/testthat.Rout


R version 4.4.1 (2024-06-14) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

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 (1) ═══════════════════════════════════════════════════════════
• On Bioconductor (1): 'test_divergence.R:5:3'

[ FAIL 0 | WARN 3 | SKIP 1 | PASS 83 ]
> 
> proc.time()
   user  system elapsed 
 14.327   0.846  15.268 

Example timings

microbiome.Rcheck/microbiome-Ex.timings

nameusersystemelapsed
TibbleUtilites0.8050.0090.815
abundances0.0090.0020.010
add_besthit000
add_refseq0.0000.0000.001
aggregate_rare0.3100.0090.320
aggregate_taxa0.1180.0100.129
alpha0.0130.0030.016
associate0.0420.0050.047
baseline0.0440.0040.048
bimodality0.0010.0000.001
bimodality_sarle000
boxplot_abundance0.1260.0120.138
boxplot_alpha0.3990.0060.407
chunk_reorder0.0000.0000.001
cmat2table0.0820.0030.085
collapse_replicates0.0520.0040.057
core0.0420.0040.046
core_abundance0.0370.0050.042
core_matrix0.0000.0010.001
core_members0.0080.0020.010
coverage0.0630.0060.070
default_colors0.0000.0000.001
densityplot000
divergence0.6100.0050.617
diversity0.0120.0020.015
dominance0.0120.0020.014
dominant0.0120.0030.013
estimate_stability000
evenness0.0090.0020.011
find_optima0.0000.0000.001
gktau0.0100.0010.012
group_age0.0200.0010.022
group_bmi0.0010.0000.001
heat0.0680.0070.078
hotplot0.2950.0160.312
inequality0.0240.0040.028
intermediate_stability0.5580.0060.567
is_compositional0.0930.0030.096
log_modulo_skewness0.1030.0040.109
low_abundance0.0160.0020.017
map_levels0.0560.0020.058
merge_taxa20.0330.0010.035
meta0.0070.0010.008
microbiome-package0.0130.0010.014
multimodality0.0000.0000.001
neat0.0830.0030.087
neatsort0.1610.0060.168
overlap19.004 1.69321.058
plot_atlas0.0600.0030.061
plot_composition0.2550.0040.261
plot_core0.0740.0050.079
plot_density0.0440.0020.045
plot_frequencies0.0300.0020.031
plot_landscape0.8400.0350.888
plot_regression0.1750.0030.179
plot_taxa_prevalence0.5210.0100.535
plot_tipping0.1520.0060.159
potential_analysis0.0390.0020.041
potential_univariate0.0000.0010.001
prevalence0.0120.0020.014
psmelt20.0920.0040.095
quiet0.0010.0000.001
rare0.0240.0020.026
rare_abundance0.0360.0020.038
rare_members0.0100.0020.012
rarity0.0860.0020.088
read_biom2phyloseq000
read_csv2phyloseq0.0000.0000.001
read_mothur2phyloseq0.0000.0010.000
read_phyloseq000
readcount0.0070.0020.009
remove_samples0.0160.0020.019
remove_taxa0.0180.0010.020
richness0.0110.0010.013
spreadplot0.0730.0030.076
summarize_phyloseq0.0180.0020.020
taxa0.0060.0020.008
time_normalize0.0380.0020.039
time_sort0.1500.0020.153
timesplit0.1280.0030.132
top0.0070.0010.009
top_taxa0.0070.0010.009
transform0.3460.0220.375
ztransform000