* using log directory ‘/srv/hornik/tmp/CRAN_pretest/ggpicrust2.Rcheck’ * using R Under development (unstable) (2026-02-10 r89394) * using platform: x86_64-pc-linux-gnu * R was compiled by Debian clang version 21.1.8 (1+b1) Debian flang version 21.1.8 (1+b1) * running under: Debian GNU/Linux forky/sid * using session charset: UTF-8 * current time: 2026-02-11 14:58:11 UTC * checking for file ‘ggpicrust2/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘ggpicrust2’ version ‘2.5.7’ * package encoding: UTF-8 * checking CRAN incoming feasibility ... [5s/7s] NOTE Maintainer: ‘Chen Yang ’ Suggests or Enhances not in mainstream repositories: Maaslin2 Availability using Additional_repositories specification: Maaslin2 no ? ? ? https://bioconductor.org/packages/release/bioc * checking package namespace information ... OK * checking package dependencies ... INFO Package suggested but not available for checking: ‘Maaslin2’ * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for executable files ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘ggpicrust2’ can be installed ... [6s/6s] OK * checking package directory ... OK * checking for future file timestamps ... 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 code files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... [1s/1s] OK * checking whether the package can be loaded with stated dependencies ... [1s/1s] OK * checking whether the package can be unloaded cleanly ... [1s/1s] OK * checking whether the namespace can be loaded with stated dependencies ... [1s/1s] OK * checking whether the namespace can be unloaded cleanly ... [1s/1s] OK * checking loading without being on the library search path ... [1s/1s] OK * checking whether startup messages can be suppressed ... [1s/1s] OK * checking use of S3 registration ... 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 ... [9s/9s] OK * checking Rd files ... [0s/0s] OK * checking Rd metadata ... OK * checking Rd line widths ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... WARNING Data codoc mismatches from Rd file 'metacyc_reference.Rd': Variables in data frame 'metacyc_reference' Code: description id Docs: category description id * 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 ... [1s/1s] OK * checking LazyData ... OK * checking data for ASCII and uncompressed saves ... OK * checking installed files from ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... [5s/5s] OK * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... [24s/24s] ERROR Running ‘testthat.R’ [24s/24s] Running the tests in ‘tests/testthat.R’ failed. Complete output: > library(testthat) > library(ggpicrust2) Loading required package: ggpicrust2 To cite ggpicrust2 in publications use: Chen Yang, Jiahao Mai, Xuan Cao, Aaron Burberry, Fabio Cominelli, Liangliang Zhang, ggpicrust2: an R package for PICRUSt2 predicted functional profile analysis and visualization, Bioinformatics, Volume 39, Issue 8, August 2023, btad470, https://doi.org/10.1093/bioinformatics/btad470 > > test_check("ggpicrust2") Note: Preranked GSEA methods (fgsea, clusterProfiler) do not account for inter-gene correlations, which may lead to unreliable p-values (Wu et al., 2012). Consider using method='camera' or method='fry' for more reliable statistical inference. 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computing center with all features converting counts to integer mode gene-wise dispersion estimates mean-dispersion relationship -- note: fitType='parametric', but the dispersion trend was not well captured by the function: y = a/x + b, and a local regression fit was automatically substituted. specify fitType='local' or 'mean' to avoid this message next time. final dispersion estimates Disp = 1e-04 , BCV = 0.01 0 features are filtered! The filtered data has 10 samples and 3 features will be tested! Fit linear models ... Completed. Saving _problems/test-pathway_daa-85.R conditions vector supplied operating in serial mode computing center with all features conditions vector supplied operating in serial mode computing center with all features conditions vector supplied operating in serial mode computing center with all features conditions vector supplied operating in serial mode computing center with all features conditions vector supplied operating in serial mode computing center with all features conditions vector supplied operating in serial mode computing center with all features Excluded 1 rows with missing 'pathway_name' annotations. conditions vector supplied operating in serial mode computing center with all features Note: Preranked GSEA methods (fgsea, clusterProfiler) do not account for inter-gene correlations, which may lead to unreliable p-values (Wu et al., 2012). Consider using method='camera' or method='fry' for more reliable statistical inference. 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═══════════════════════════════════════════════════════════ • On CRAN (6): 'test-ggpicrust2-return-structure.R:4:3', 'test-pathway_annotation.R:36:3', 'test-pathway_ridgeplot.R:25:3', 'test-pathway_ridgeplot.R:42:3', 'test-pathway_ridgeplot.R:65:3', 'test-pathway_volcano.R:82:3' ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test-pathway_daa.R:85:5'): pathway_daa methods produce expected results ── Error in `require_package(method_packages[[daa_method]], purpose = daa_method)`: Package 'Maaslin2' is required for Maaslin2. Install with: BiocManager::install('Maaslin2') Backtrace: ▆ 1. └─ggpicrust2::pathway_daa(abundance, metadata, "group", daa_method = method) at test-pathway_daa.R:85:5 2. └─ggpicrust2:::require_package(method_packages[[daa_method]], purpose = daa_method) [ FAIL 1 | WARN 4 | SKIP 6 | PASS 192 ] Error: ! Test failures. Execution halted * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... [1s/1s] OK * checking PDF version of manual ... [3s/3s] OK * checking HTML version of manual ... [2s/2s] OK * checking for non-standard things in the check directory ... OK * checking for detritus in the temp directory ... OK * DONE Status: 1 ERROR, 1 WARNING, 1 NOTE