* using log directory ‘/srv/hornik/tmp/CRAN/simbaR.Rcheck’ * using R Under development (unstable) (2024-07-31 r86945) * using platform: x86_64-pc-linux-gnu * R was compiled by Debian clang version 18.1.8 (3) Debian flang-new version 18.1.8 (3) * running under: Debian GNU/Linux trixie/sid * using session charset: UTF-8 * checking for file ‘simbaR/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘simbaR’ version ‘0.5.2’ * package encoding: UTF-8 * checking CRAN incoming feasibility ... [4s/6s] NOTE Maintainer: ‘Jakob Wirbel ’ New submission Possibly misspelled words in DESCRIPTION: Microbiome (3:22) Wirbel (23:9) al (23:27) benchmarking (20:16, 23:55) et (23:24) metagenomic (16:5) microbiome (15:28) The Description field contains methods Please write DOIs as . * 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 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 ‘simbaR’ can be installed ... [7s/8s] OK * checking package directory ... OK * checking for future file timestamps ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... NOTE Malformed Description field: should contain one or more complete sentences. * 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 ... [2s/2s] 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 use of S3 registration ... OK * checking dependencies in R code ... WARNING '::' or ':::' import not declared from: ‘sparseDOSSA’ Unavailable namespace imported from by a ':::' call: ‘sparseDOSSA’ 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 ... [13s/13s] NOTE ANCOM: no visible global function definition for ‘%>%’ ANCOM: no visible global function definition for ‘pull’ ANCOM: no visible global function definition for ‘mutate’ confounder.check: no visible global function definition for ‘ggplot’ confounder.check: no visible global function definition for ‘aes’ confounder.check: no visible binding for global variable ‘effect.size’ confounder.check: no visible binding for global variable ‘p.val’ confounder.check: no visible global function definition for ‘geom_point’ confounder.check: no visible global function definition for ‘facet_grid’ microbesim: no visible global function definition for ‘taxa_sums’ microbesim: no visible global function definition for ‘phyloseq’ pcoa.plot: no visible global function definition for ‘ggplot’ pcoa.plot: no visible global function definition for ‘aes’ pcoa.plot: no visible binding for global variable ‘V1’ pcoa.plot: no visible binding for global variable ‘V2’ pcoa.plot: no visible global function definition for ‘theme_classic’ pcoa.plot: no visible global function definition for ‘scale_colour_manual’ pcoa.plot: no visible global function definition for ‘xlab’ pcoa.plot: no visible global function definition for ‘ylab’ pcoa.plot: no visible global function definition for ‘str_detect’ pcoa.plot: no visible global function definition for ‘geom_point’ pcoa.plot: no visible binding for global variable ‘confounder’ pcoa.plot: no visible global function definition for ‘scale_shape_manual’ qbetabin: no visible global function definition for ‘dbb’ reality.check: no visible global function definition for ‘siamcat’ reality.check: no visible global function definition for ‘normalize.features’ reality.check: no visible global function definition for ‘get.norm_feat.matrix’ reality.check: no visible global function definition for ‘label’ reality.check: no visible global function definition for ‘resample’ rmvbetabin: no visible global function definition for ‘rmvnorm’ rmvnegbin : : no visible global function definition for ‘.negbin_getK’ rmvnegbin: no visible global function definition for ‘rmvnorm’ simulate.MMH: no visible global function definition for ‘otu_table’ simulate.MMH: no visible global function definition for ‘sample_sums’ simulate.SimMSeq: no visible global function definition for ‘SimulateMSeq’ simulate.W: no visible global function definition for ‘otu_table’ simulate.W: no visible global function definition for ‘sample_sums’ simulate.betabin: no visible global function definition for ‘spiec.easi’ simulate.betabin: no visible global function definition for ‘getOptCov’ simulate.markers.MMH: no visible global function definition for ‘taxa_names’ simulate.markers.MMH: no visible global function definition for ‘otu_table’ simulate.markers.MMH: no visible global function definition for ‘otu_table<-’ simulate.markers.W: no visible global function definition for ‘otu_table<-’ simulate.markers.W: no visible global function definition for ‘otu_table’ simulate.markers.W: no visible global function definition for ‘taxa_names’ simulate.markers.W: no visible global function definition for ‘sample_sums’ simulate.negbin: no visible global function definition for ‘spiec.easi’ simulate.negbin: no visible global function definition for ‘getOptCov’ test.ANCOMBC: no visible global function definition for ‘phyloseq’ test.ANCOMBC: no visible global function definition for ‘otu_table’ test.ANCOMBC: no visible global function definition for ‘sample_data’ test.ANCOMBC: no visible global function definition for ‘ancombc’ test.DESeq: no visible global function definition for ‘otu_table’ test.DESeq: no visible global function definition for ‘phyloseq’ test.DESeq: no visible global function definition for ‘sample_data’ test.DESeq: no visible global function definition for ‘phyloseq_to_deseq2’ test.DESeq: no visible global function definition for ‘counts’ test.DESeq: no visible global function definition for ‘estimateSizeFactors’ test.DESeq: no visible global function definition for ‘DESeq’ test.DESeq: no visible global function definition for ‘results’ test.LDM: no visible global function definition for ‘ldm’ test.MAST: no visible global function definition for ‘FromMatrix’ test.MAST: no visible global function definition for ‘zlm’ test.MGS: no visible global function definition for ‘newMRexperiment’ test.MGS: no visible global function definition for ‘cumNormStat’ test.MGS: no visible global function definition for ‘cumNorm’ test.MGS: no visible global function definition for ‘zigControl’ test.MGS: no visible global function definition for ‘fitZig’ test.MGS: no visible global function definition for ‘fitFeatureModel’ test.MGS: no visible global function definition for ‘MRcoefs’ test.ZIBseq : .f_test: no visible global function definition for ‘gamlss’ test.ZIBseq : .f_test: no visible global function definition for ‘BEZI’ test.ZIBseq : .f_test: no visible global function definition for ‘gamlss.control’ test.ZINQ: no visible global function definition for ‘ZINQ_tests’ test.ZINQ: no visible global function definition for ‘ZINQ_combination’ test.ZicoSeq: no visible global function definition for ‘ZicoSeq’ test.aldex2: no visible global function definition for ‘aldex’ test.aldex2: no visible global function definition for ‘aldex.clr’ test.aldex2: no visible global function definition for ‘aldex.glm’ test.aldex2: no visible global function definition for ‘aldex.glm.effect’ test.corncob: no visible global function definition for ‘phyloseq’ test.corncob: no visible global function definition for ‘otu_table’ test.corncob: no visible global function definition for ‘sample_data’ test.corncob: no visible global function definition for ‘differentialTest’ test.distinct: no visible global function definition for ‘SingleCellExperiment’ test.distinct: no visible global function definition for ‘colData’ test.distinct: no visible global function definition for ‘colData<-’ test.distinct: no visible global function definition for ‘distinct_test’ test.edgeR: no visible global function definition for ‘DGEList’ test.edgeR: no visible global function definition for ‘estimateCommonDisp’ test.edgeR: no visible global function definition for ‘estimateTagwiseDisp’ test.edgeR: no visible global function definition for ‘exactTest’ test.edgeR: no visible global function definition for ‘topTags’ test.fastANCOM: no visible global function definition for ‘fastANCOM’ test.linda: no visible global function definition for ‘linda’ test.lm : : no visible global function definition for ‘Anova’ test.lme : : no visible global function definition for ‘lmer’ test.lminter : : no visible global function definition for ‘Anova’ test.mixMC: no visible global function definition for ‘tune.splsda’ test.mixMC: no visible global function definition for ‘splsda’ test.mixMC: no visible global function definition for ‘selectVar’ test.scde: no visible global function definition for ‘clean.counts’ test.scde: no visible global function definition for ‘scde.error.models’ test.scde: no visible global function definition for ‘scde.expression.prior’ test.scde: no visible global function definition for ‘scde.expression.difference’ test.via.limma: no visible global function definition for ‘eBayes’ test.wilcoxon: no visible global function definition for ‘wilcox_test’ test.wilcoxon: no visible global function definition for ‘pvalue’ validate.original.data: no visible global function definition for ‘reduce’ Undefined global functions or variables: %>% .negbin_getK Anova BEZI DESeq DGEList FromMatrix MRcoefs SimulateMSeq SingleCellExperiment V1 V2 ZINQ_combination ZINQ_tests ZicoSeq aes aldex aldex.clr aldex.glm aldex.glm.effect ancombc clean.counts colData colData<- confounder counts cumNorm cumNormStat dbb differentialTest distinct_test eBayes effect.size estimateCommonDisp estimateSizeFactors estimateTagwiseDisp exactTest facet_grid fastANCOM fitFeatureModel fitZig gamlss gamlss.control geom_point get.norm_feat.matrix getOptCov ggplot label ldm linda lmer mutate newMRexperiment normalize.features otu_table otu_table<- p.val phyloseq phyloseq_to_deseq2 pull pvalue reduce resample results rmvnorm sample_data sample_sums scale_colour_manual scale_shape_manual scde.error.models scde.expression.difference scde.expression.prior selectVar siamcat spiec.easi splsda str_detect taxa_names taxa_sums theme_classic topTags tune.splsda wilcox_test xlab ylab zigControl zlm * checking Rd files ... [0s/0s] OK * checking Rd metadata ... OK * checking Rd line widths ... OK * checking Rd cross-references ... NOTE Package unavailable to check Rd xrefs: ‘SIAMCAT’ * 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 ... [0s/0s] 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 ... NONE * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... [65s/65s] OK * checking PDF version of manual ... [3s/3s] OK * checking HTML version of manual ... [0s/0s] OK * checking for non-standard things in the check directory ... OK * checking for detritus in the temp directory ... OK * DONE Status: 1 WARNING, 4 NOTEs