Movatterモバイル変換

################################################################################################################################################################## Running command:######   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:POMA.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings POMA_1.20.0.tar.gz###############################################################################################################################################################* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/POMA.Rcheck’* using R version 4.5.2 Patched (2025-11-04 r88984)* using platform: aarch64-apple-darwin20* R was compiled by    Apple clang version 16.0.0 (clang-1600.0.26.6)    GNU Fortran (GCC) 14.2.0* running under: macOS Ventura 13.7.8* using session charset: UTF-8* using option ‘--no-vignettes’* checking for file ‘POMA/DESCRIPTION’ ... OK* this is package ‘POMA’ version ‘1.20.0’* package encoding: UTF-8* checking package namespace information ... OK* checking package dependencies ... INFOImports includes 31 non-default packages.Importing from so many packages makes the package vulnerable to any ofthem becoming unavailable.  Move as many as possible to Suggests anduse conditionally.* 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 ‘POMA’ 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 ... OK* 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 ... NOTE':::' call which should be '::': ‘purrr:::map_chr’  See the note in ?`:::` about the use of this operator.Unexported object imported by a ':::' call: ‘utils:::.getHelpFile’  See the note in ?`:::` about the use of this operator.* checking S3 generic/method consistency ... OK* checking replacement functions ... OK* checking foreign function calls ... OK* checking R code for possible problems ... NOTEPomaBatch: no visible global function definition for ‘is’PomaBatch: no visible global function definition for ‘validObject’PomaBoxplots: no visible global function definition for ‘is’PomaBoxplots: no visible binding for global variable ‘sample_id’PomaBoxplots: no visible binding for global variable ‘group_factor’PomaBoxplots: no visible binding for global variable ‘value’PomaBoxplots: no visible binding for global variable ‘name’PomaClust: no visible global function definition for ‘is’PomaClust: no visible binding for global variable ‘clust’PomaClust: no visible binding for global variable ‘V1’PomaClust: no visible binding for global variable ‘V2’PomaClust: no visible binding for global variable ‘Dim1’PomaClust: no visible binding for global variable ‘Dim2’PomaCorr: no visible global function definition for ‘is’PomaCorr: no visible global function definition for ‘cor’PomaCorr: no visible binding for global variable ‘column’PomaCorr: no visible binding for global variable ‘cor’PomaCorr: no visible binding for global variable ‘p’PomaCorr: no visible global function definition for ‘p.adjust’PomaCorr: no visible binding for global variable ‘pvalue’PomaCorr: no visible binding for global variable ‘corr’PomaCreateObject: no visible global function definition for  ‘validObject’PomaDESeq: no visible global function definition for ‘is’PomaDESeq: no visible global function definition for ‘formula’PomaDESeq: no visible binding for global variable ‘log2FoldChange’PomaDESeq: no visible binding for global variable ‘padj’PomaDESeq: no visible binding for global variable ‘adj_pvalue’PomaDensity: no visible global function definition for ‘is’PomaDensity: no visible binding for global variable ‘sample_id’PomaDensity: no visible binding for global variable ‘group_factor’PomaDensity: no visible binding for global variable ‘name’PomaDensity: no visible binding for global variable ‘value’PomaEnrichment: no visible binding for global variable ‘leadingEdge’PomaEnrichment: no visible binding for global variable ‘NES’PomaEnrichment: no visible binding for global variable ‘pathway’PomaEnrichment: no visible binding for global variable ‘pval’PomaEnrichment: no visible binding for global variable ‘padj’PomaEnrichment: no visible binding for global variable ‘direction’PomaEnrichment: no visible binding for global variable ‘size’PomaEnrichment: no visible binding for global variable ‘leading_edge’PomaEnrichment: no visible binding for global variable ‘adjPval’PomaEnrichment: no visible binding for global variable ‘overlapGenes’PomaEnrichment: no visible binding for global variable ‘overlap’PomaEnrichment: no visible binding for global variable ‘overlap_genes’PomaHeatmap: no visible global function definition for ‘is’PomaImpute: no visible global function definition for ‘is’PomaImpute: no visible global function definition for ‘aggregate’PomaImpute: no visible binding for global variable ‘group_factor’PomaImpute: no visible global function definition for ‘validObject’PomaLM: no visible global function definition for ‘is’PomaLM: no visible global function definition for ‘lm’PomaLM: no visible global function definition for ‘p.adjust’PomaLM: no visible binding for global variable ‘p.value’PomaLM: no visible binding for global variable ‘term’PomaLM: no visible binding for global variable ‘estimate’PomaLM: no visible binding for global variable ‘std.error’PomaLM: no visible binding for global variable ‘statistic’PomaLM: no visible binding for global variable ‘adj_pvalue’PomaLM: no visible binding for global variable ‘pvalue’PomaLM: no visible global function definition for ‘reorder’PomaLM: no visible binding for global variable ‘feature’PomaLM: no visible binding for global variable ‘std_err’PomaLMM: no visible global function definition for ‘is’PomaLMM : lmm_fun: no visible global function definition for ‘vcov’PomaLMM : lmm_fun: no visible binding for global variable ‘vcov’PomaLMM : lmm_fun: no visible binding for global variable ‘grp’PomaLMM : lmm_fun: no visible binding for global variable  ‘variance_percent’PomaLMM: no visible binding for global variable ‘feature’PomaLMM: no visible binding for global variable ‘name’PomaLMM: no visible binding for global variable ‘value’PomaLasso: no visible global function definition for ‘is’PomaLasso: no visible binding for global variable ‘estimate’PomaLasso: no visible binding for global variable ‘conf.low’PomaLasso: no visible binding for global variable ‘conf.high’PomaLasso: no visible global function definition for ‘predict’PomaLasso: no visible binding for global variable ‘term’PomaLimma: no visible global function definition for ‘is’PomaLimma: no visible global function definition for ‘as.formula’PomaLimma: no visible binding for global variable ‘logFC’PomaLimma: no visible binding for global variable ‘P.Value’PomaLimma: no visible binding for global variable ‘adj.P.Val’PomaNorm: no visible global function definition for ‘is’PomaNorm: no visible binding for global variable ‘var’PomaNorm : <anonymous>: no visible global function definition for ‘sd’PomaNorm: no visible global function definition for ‘validObject’PomaOddsRatio: no visible global function definition for ‘is’PomaOddsRatio: no visible binding for global variable ‘group’PomaOddsRatio: no visible binding for global variable ‘OddsRatio’PomaOddsRatio: no visible binding for global variable ‘feature’PomaOddsRatio: no visible binding for global variable ‘upr’PomaOddsRatio: no visible binding for global variable ‘lwr’PomaOutliers: no visible global function definition for ‘is’PomaOutliers: no visible binding for global variable ‘groups’PomaOutliers: no visible global function definition for ‘quantile’PomaOutliers: no visible global function definition for ‘IQR’PomaOutliers: no visible binding for global variable ‘limit’PomaOutliers: no visible binding for global variable ‘out’PomaOutliers : find_hull: no visible global function definition for  ‘chull’PomaOutliers: no visible binding for global variable ‘group’PomaOutliers: no visible binding for global variable ‘.’PomaOutliers: no visible binding for global variable ‘PCoA1’PomaOutliers: no visible binding for global variable ‘PCoA2’PomaOutliers: no visible global function definition for ‘validObject’PomaPCA: no visible global function definition for ‘is’PomaPCA: no visible global function definition for ‘prcomp’PomaPCA: no visible binding for global variable ‘PC1’PomaPCA: no visible binding for global variable ‘PC2’PomaPCA: no visible binding for global variable ‘group’PomaPCA: no visible binding for global variable ‘sample_id’PomaPCA: no visible global function definition for ‘reorder’PomaPCA: no visible binding for global variable ‘comp’PomaPCA: no visible binding for global variable ‘var_exp’PomaPCA: no visible binding for global variable ‘feature’PomaPCA: no visible binding for global variable ‘value’PomaPCA: no visible binding for global variable ‘name’PomaPCA: no visible binding for global variable ‘to_x’PomaPCA: no visible binding for global variable ‘to_y’PomaPCR: no visible global function definition for ‘is’PomaPCR: no visible binding for global variable ‘PC1’PomaPCR: no visible global function definition for ‘lm’PomaPCR: no visible global function definition for ‘p.adjust’PomaPCR: no visible binding for global variable ‘p.value’PomaPCR: no visible binding for global variable ‘term’PomaPCR: no visible binding for global variable ‘estimate’PomaPCR: no visible binding for global variable ‘std.error’PomaPCR: no visible binding for global variable ‘statistic’PomaPCR: no visible binding for global variable ‘adj_pvalue’PomaPCR: no visible binding for global variable ‘pvalue’PomaPLS: no visible global function definition for ‘is’PomaPLS: no visible binding for global variable ‘comp1’PomaPLS: no visible binding for global variable ‘comp2’PomaPLS: no visible binding for global variable ‘sample_id’PomaPLS: no visible binding for global variable ‘feature’PomaPLS: no visible global function definition for ‘reorder’PomaPLS: no visible binding for global variable ‘value’PomaPLS: no visible binding for global variable ‘name’PomaPLS: no visible binding for global variable ‘component’PomaPLS: no visible binding for global variable ‘error’PomaPLS: no visible binding for global variable ‘feature_sd’PomaPLS: no visible binding for global variable ‘sd’PomaRandForest: no visible global function definition for ‘is’PomaRandForest: no visible binding for global variable ‘OOB’PomaRandForest: no visible binding for global variable  ‘MeanDecreaseGini’PomaRandForest: no visible global function definition for ‘reorder’PomaRandForest: no visible binding for global variable ‘feature’PomaRankProd: no visible global function definition for ‘is’PomaRankProd: no visible global function definition for  ‘capture.output’PomaRankProd: no visible binding for global variable ‘P.value’PomaRankProd: no visible binding for global variable ‘gene.index’PomaUMAP: no visible global function definition for ‘is’PomaUMAP: no visible binding for global variable ‘clust’PomaUMAP: no visible binding for global variable ‘UMAP1’PomaUMAP: no visible binding for global variable ‘UMAP2’PomaUnivariate: no visible global function definition for ‘is’PomaUnivariate: no visible binding for global variable ‘group’PomaUnivariate : <anonymous>: no visible global function definition for  ‘t.test’PomaUnivariate: no visible global function definition for ‘p.adjust’PomaUnivariate: no visible binding for global variable ‘pvalue’PomaUnivariate: no visible binding for global variable ‘feature’PomaUnivariate: no visible binding for global variable ‘fold_change’PomaUnivariate: no visible binding for global variable ‘diff_means’PomaUnivariate: no visible binding for global variable ‘adj_pvalue’PomaUnivariate : <anonymous>: no visible global function definition for  ‘anova’PomaUnivariate : <anonymous>: no visible global function definition for  ‘aov’PomaUnivariate: no visible global function definition for ‘TukeyHSD’PomaUnivariate: no visible global function definition for ‘aov’PomaUnivariate: no visible binding for global variable ‘adj.p.value’PomaUnivariate: no visible global function definition for ‘as.formula’PomaUnivariate: no visible binding for global variable ‘term’PomaUnivariate: no visible binding for global variable ‘p.value’PomaUnivariate : <anonymous>: no visible global function definition for  ‘wilcox.test’PomaUnivariate : <anonymous>: no visible global function definition for  ‘kruskal.test’PomaUnivariate: no visible binding for global variable ‘kw_rank_sum’PomaUnivariate: no visible binding for global variable ‘Comparison’PomaUnivariate: no visible binding for global variable ‘P.adj’PomaUnivariate: no visible binding for global variable ‘contrast’PomaVolcano: no visible global function definition for ‘quantile’PomaVolcano: no visible binding for global variable ‘logFC’PomaVolcano: no visible binding for global variable ‘pvalue’PomaVolcano: no visible binding for global variable ‘feature’create_mock_data: no visible global function definition for ‘runif’create_mock_summarized_experiment: no visible global function  definition for ‘runif’help_extract: no visible global function definition for  ‘capture.output’make_legend: no visible binding for global variable ‘POMA’title_extract: no visible global function definition for  ‘capture.output’Undefined global functions or variables:  . Comparison Dim1 Dim2 IQR MeanDecreaseGini NES OOB OddsRatio P.Value  P.adj P.value PC1 PC2 PCoA1 PCoA2 POMA TukeyHSD UMAP1 UMAP2 V1 V2  adj.P.Val adj.p.value adjPval adj_pvalue aggregate anova aov  as.formula capture.output chull clust column comp comp1 comp2  component conf.high conf.low contrast cor corr diff_means direction  error estimate feature feature_sd fold_change formula gene.index  group group_factor groups grp is kruskal.test kw_rank_sum leadingEdge  leading_edge limit lm log2FoldChange logFC lwr name out overlap  overlapGenes overlap_genes p p.adjust p.value padj pathway prcomp  predict pval pvalue quantile reorder runif sample_id sd size  statistic std.error std_err t.test term to_x to_y upr validObject  value var var_exp variance_percent vcov wilcox.testConsider adding  importFrom("grDevices", "chull")  importFrom("methods", "is", "validObject")  importFrom("stats", "IQR", "TukeyHSD", "aggregate", "anova", "aov",             "as.formula", "cor", "formula", "kruskal.test", "lm",             "p.adjust", "prcomp", "predict", "quantile", "reorder",             "runif", "sd", "t.test", "var", "vcov", "wilcox.test")  importFrom("utils", "capture.output")to your NAMESPACE file (and ensure that your DESCRIPTION Imports fieldcontains 'methods').* checking Rd files ... OK* checking Rd metadata ... OK* checking Rd cross-references ... NOTENon-topic package-anchored link(s) in Rd file 'pipe.Rd':  ‘[magrittr:pipe]{%>%}’See section 'Cross-references' in the 'Writing R Extensions' manual.* 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 LazyData ... OK* checking data for ASCII and uncompressed saves ... OK* checking files in ‘vignettes’ ... OK* checking examples ... OKExamples with CPU (user + system) or elapsed time > 5s                 user system elapsedPomaEnrichment 64.805  1.098  92.112PomaPLS        49.515  0.753  70.893PomaUnivariate 33.441  0.313  45.822PomaBoxplots   26.103  0.935  37.283PomaBatch      13.944  0.411  20.203PomaLimma      11.092  0.109  15.844PomaHeatmap    10.213  0.254  14.722PomaUMAP        7.541  0.072  10.290PomaPCA         4.464  0.055   6.341PomaDensity     3.806  0.083   5.603* 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* DONEStatus: 3 NOTEsSee  ‘/Users/biocbuild/bbs-3.22-bioc/meat/POMA.Rcheck/00check.log’for details.

################################################################################################################################################################## Running command:######   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL POMA###############################################################################################################################################################* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library’* installing *source* package ‘POMA’ ...** this is package ‘POMA’ version ‘1.20.0’** using staged installation** R** data*** moving datasets to lazyload DB** inst** byte-compile and prepare package for lazy loading** help*** installing help indices*** copying figures** 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 (POMA)

R version 4.5.2 Patched (2025-11-04 r88984) -- "[Not] Part in a Rumble"Copyright (C) 2025 The R Foundation for Statistical ComputingPlatform: aarch64-apple-darwin20R 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)> library(POMA)Welcome to POMA!Version 1.20.0POMAShiny app: https://github.com/pcastellanoescuder/POMAShiny> > test_check("POMA")Warning: stack imbalance in '<-', 77 then 79Warning: stack imbalance in '{', 73 then 75[ FAIL 0 | WARN 53 | SKIP 6 | PASS 209 ]══ Skipped tests (6) ═══════════════════════════════════════════════════════════• This test is skipped. (6): 'test-PomaLMM.R:3:3', 'test-PomaLMM.R:12:3',  'test-PomaLMM.R:18:3', 'test-PomaLMM.R:27:3', 'test-PomaLMM.R:34:3',  'test-PomaLMM.R:40:3'[ FAIL 0 | WARN 53 | SKIP 6 | PASS 209 ]> > proc.time()   user  system elapsed  90.634   1.668 116.297