############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD check --install=check:microbiome.install-out.txt --library=/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library --no-vignettes --timings microbiome_1.26.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/microbiome.Rcheck’ * using R version 4.4.0 beta (2024-04-15 r86425) * using platform: aarch64-unknown-linux-gnu * R was compiled by gcc (GCC) 10.3.1 GNU Fortran (GCC) 10.3.1 * running under: openEuler 22.03 (LTS-SP1) * 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 loading without being on the library search path ... 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 21.92 0.148 22.114 * 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 ‘/home/biocbuild/bbs-3.19-bioc/meat/microbiome.Rcheck/00check.log’ for details.