Multiple platform build/check report for BioC 3.20 - CHECK results for microbiome on kjohnson3

Hostname	OS	Arch (*)	R version	Installed pkgs
teran2	Linux (Ubuntu 24.04.1 LTS)	x86_64	4.4.1 (2024-06-14) -- "Race for Your Life"	4505
palomino8	Windows Server 2022 Datacenter	x64	4.4.1 (2024-06-14 ucrt) -- "Race for Your Life"	4506
lconway	macOS 12.7.1 Monterey	x86_64	4.4.1 (2024-06-14) -- "Race for Your Life"	4538
kjohnson3	macOS 13.6.5 Ventura	arm64	4.4.1 (2024-06-14) -- "Race for Your Life"	4486
kunpeng2	Linux (openEuler 22.03 LTS-SP1)	aarch64	4.4.1 (2024-06-14) -- "Race for Your Life"	4493
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: 1.28.0

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_1.28.0.tar.gz

StartedAt: 2024-11-09 07:02:39 -0500 (Sat, 09 Nov 2024)

EndedAt: 2024-11-09 07:07:26 -0500 (Sat, 09 Nov 2024)

EllapsedTime: 286.8 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_1.28.0.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: 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 13.6.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘microbiome/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘microbiome’ version ‘1.28.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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 5.289  0.645   5.939
* 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-3.20-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-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 4.4.1 (2024-06-14) -- "Race for Your Life"
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	0.224	0.002	0.226
abundances	0.003	0.000	0.002
add_besthit	0	0	0
add_refseq	0	0	0
aggregate_rare	0.067	0.003	0.068
aggregate_taxa	0.023	0.003	0.026
alpha	0.004	0.001	0.005
associate	0.011	0.001	0.013
baseline	0.014	0.001	0.014
bimodality	0.000	0.000	0.001
bimodality_sarle	0	0	0
boxplot_abundance	0.035	0.002	0.038
boxplot_alpha	0.089	0.002	0.090
chunk_reorder	0	0	0
cmat2table	0.018	0.001	0.019
collapse_replicates	0.016	0.001	0.016
core	0.010	0.001	0.011
core_abundance	0.008	0.001	0.010
core_matrix	0.000	0.000	0.001
core_members	0.002	0.001	0.003
coverage	0.015	0.002	0.017
default_colors	0	0	0
densityplot	0	0	0
divergence	0.110	0.001	0.111
diversity	0.004	0.001	0.005
dominance	0.003	0.000	0.004
dominant	0.003	0.001	0.003
estimate_stability	0	0	0
evenness	0.002	0.001	0.003
find_optima	0.001	0.000	0.000
gktau	0.005	0.000	0.006
group_age	0.009	0.000	0.010
group_bmi	0	0	0
heat	0.017	0.002	0.019
hotplot	0.069	0.004	0.073
inequality	0.007	0.001	0.008
intermediate_stability	0.116	0.001	0.117
is_compositional	0.020	0.000	0.021
log_modulo_skewness	0.024	0.001	0.025
low_abundance	0.004	0.001	0.005
map_levels	0.012	0.001	0.012
merge_taxa2	0.006	0.001	0.007
meta	0.003	0.000	0.003
microbiome-package	0.003	0.001	0.004
multimodality	0	0	0
neat	0.022	0.001	0.023
neatsort	0.056	0.002	0.057
overlap	5.289	0.645	5.939
plot_atlas	0.015	0.001	0.016
plot_composition	0.051	0.001	0.053
plot_core	0.016	0.002	0.017
plot_density	0.009	0.001	0.011
plot_frequencies	0.006	0.000	0.007
plot_landscape	0.261	0.016	0.277
plot_regression	0.040	0.002	0.041
plot_taxa_prevalence	0.106	0.010	0.116
plot_tipping	0.033	0.003	0.035
potential_analysis	0.010	0.001	0.010
potential_univariate	0	0	0
prevalence	0.004	0.000	0.005
psmelt2	0.020	0.002	0.021
quiet	0.000	0.000	0.001
rare	0.005	0.001	0.005
rare_abundance	0.008	0.001	0.008
rare_members	0.002	0.000	0.003
rarity	0.017	0.001	0.018
read_biom2phyloseq	0.001	0.000	0.000
read_csv2phyloseq	0	0	0
read_mothur2phyloseq	0	0	0
read_phyloseq	0	0	0
readcount	0.002	0.000	0.003
remove_samples	0.004	0.001	0.004
remove_taxa	0.004	0.000	0.004
richness	0.003	0.000	0.003
spreadplot	0.015	0.002	0.017
summarize_phyloseq	0.004	0.001	0.004
taxa	0.002	0.000	0.003
time_normalize	0.009	0.001	0.009
time_sort	0.035	0.000	0.036
timesplit	0.026	0.000	0.027
top	0.003	0.001	0.003
top_taxa	0.002	0.000	0.003
transform	0.090	0.007	0.097
ztransform	0	0	0