Multiple platform build/check report for BioC 3.19 - CHECK results for microbiome on kjohnson3

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo1	Linux (Ubuntu 22.04.3 LTS)	x86_64	4.4.0 (2024-04-24) -- "Puppy Cup"	4757
palomino3	Windows Server 2022 Datacenter	x64	4.4.0 (2024-04-24 ucrt) -- "Puppy Cup"	4491
lconway	macOS 12.7.1 Monterey	x86_64	4.4.0 (2024-04-24) -- "Puppy Cup"	4522
kjohnson3	macOS 13.6.5 Ventura	arm64	4.4.0 (2024-04-24) -- "Puppy Cup"	4468
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 kjohnson3

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: 1.26.0

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_1.26.0.tar.gz

StartedAt: 2024-06-10 21:51:07 -0400 (Mon, 10 Jun 2024)

EndedAt: 2024-06-10 21:56:53 -0400 (Mon, 10 Jun 2024)

EllapsedTime: 346.6 seconds

RetCode: 1

Status: ERROR

CheckDir: microbiome.Rcheck

Warnings: NA

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_1.26.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/microbiome.Rcheck’
* using R version 4.4.0 (2024-04-24)
* using platform: aarch64-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 Ventura 13.6.5
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘microbiome/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘microbiome’ version ‘1.26.0’
* 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 19.76  1.307  31.764
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  [ FAIL 1 | WARN 3 | SKIP 1 | PASS 82 ]
  
  ══ Skipped tests (1) ═══════════════════════════════════════════════════════════
  • On Bioconductor (1): 'test_divergence.R:5:3'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test_transformations.R:47:3'): transform works correctly ──────────
  ... < 1e-15 is not TRUE
  
  `actual`:   FALSE
  `expected`: TRUE 
  
  [ FAIL 1 | WARN 3 | SKIP 1 | PASS 82 ]
  Error: Test failures
  Execution halted
* 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: 1 ERROR, 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.19-bioc/meat/microbiome.Rcheck/00check.log’
for details.

Installation output

microbiome.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/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.fail


R version 4.4.0 (2024-04-24) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-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 1 | WARN 3 | SKIP 1 | PASS 82 ]

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

══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test_transformations.R:47:3'): transform works correctly ──────────
... < 1e-15 is not TRUE

`actual`:   FALSE
`expected`: TRUE 

[ FAIL 1 | WARN 3 | SKIP 1 | PASS 82 ]
Error: Test failures
Execution halted

Example timings

microbiome.Rcheck/microbiome-Ex.timings

name	user	system	elapsed
TibbleUtilites	1.061	0.014	1.614
abundances	0.006	0.002	0.013
add_besthit	0.000	0.000	0.001
add_refseq	0	0	0
aggregate_rare	0.288	0.011	0.464
aggregate_taxa	0.100	0.010	0.181
alpha	0.012	0.003	0.026
associate	0.033	0.005	0.058
baseline	0.037	0.004	0.042
bimodality	0.001	0.000	0.001
bimodality_sarle	0	0	0
boxplot_abundance	0.124	0.010	0.197
boxplot_alpha	0.340	0.008	0.526
chunk_reorder	0.000	0.001	0.000
cmat2table	0.062	0.003	0.108
collapse_replicates	0.044	0.004	0.065
core	0.039	0.004	0.054
core_abundance	0.032	0.005	0.054
core_matrix	0	0	0
core_members	0.008	0.002	0.015
coverage	0.067	0.006	0.123
default_colors	0	0	0
densityplot	0.001	0.000	0.000
divergence	0.572	0.008	0.903
diversity	0.011	0.002	0.017
dominance	0.009	0.002	0.020
dominant	0.009	0.003	0.022
estimate_stability	0	0	0
evenness	0.007	0.002	0.015
find_optima	0.000	0.000	0.001
gktau	0.010	0.002	0.017
group_age	0.021	0.003	0.028
group_bmi	0.001	0.001	0.001
heat	0.059	0.006	0.101
hotplot	0.286	0.018	0.428
inequality	0.021	0.005	0.048
intermediate_stability	0.513	0.009	0.809
is_compositional	0.918	0.008	1.355
log_modulo_skewness	0.091	0.004	0.153
low_abundance	0.013	0.003	0.028
map_levels	0.047	0.003	0.074
merge_taxa2	0.023	0.002	0.034
meta	0.006	0.002	0.013
microbiome-package	0.010	0.002	0.021
multimodality	0	0	0
neat	0.064	0.003	0.096
neatsort	0.119	0.004	0.188
overlap	19.760	1.307	31.764
plot_atlas	0.048	0.002	0.067
plot_composition	0.263	0.009	0.271
plot_core	0.045	0.005	0.050
plot_density	0.041	0.002	0.069
plot_frequencies	0.028	0.003	0.052
plot_landscape	0.700	0.029	1.176
plot_regression	0.129	0.004	0.132
plot_taxa_prevalence	0.413	0.009	0.687
plot_tipping	0.093	0.005	0.098
potential_analysis	0.029	0.002	0.031
potential_univariate	0	0	0
prevalence	0.009	0.002	0.011
psmelt2	0.072	0.007	0.080
quiet	0.001	0.000	0.001
rare	0.017	0.002	0.020
rare_abundance	0.026	0.005	0.031
rare_members	0.007	0.003	0.009
rarity	0.092	0.011	0.103
read_biom2phyloseq	0.001	0.000	0.000
read_csv2phyloseq	0	0	0
read_mothur2phyloseq	0.000	0.000	0.001
read_phyloseq	0	0	0
readcount	0.006	0.001	0.008
remove_samples	0.013	0.002	0.015
remove_taxa	0.014	0.001	0.016
richness	0.008	0.001	0.010
spreadplot	0.057	0.003	0.060
summarize_phyloseq	0.011	0.003	0.014
taxa	0.005	0.002	0.007
time_normalize	0.027	0.002	0.029
time_sort	0.105	0.003	0.107
timesplit	0.088	0.002	0.092
top	0.007	0.002	0.009
top_taxa	0.006	0.002	0.007
transform	0.330	0.019	0.567
ztransform	0	0	0