############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD check --install=check:scone.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings scone_1.31.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/scone.Rcheck’ * using R Under development (unstable) (2024-11-24 r87369) * using platform: aarch64-unknown-linux-gnu * R was compiled by aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0 GNU Fortran (GCC) 14.2.0 * running under: openEuler 24.03 (LTS) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘scone/DESCRIPTION’ ... OK * this is package ‘scone’ version ‘1.31.0’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... INFO Imports includes 22 non-default packages. Importing from so many packages makes the package vulnerable to any of them becoming unavailable. Move as many as possible to Suggests and use 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 ‘scone’ can be installed ... WARNING Found the following significant warnings: Warning: program compiled against libxml 212 using older 211 See ‘/home/biocbuild/bbs-3.21-bioc/meat/scone.Rcheck/00install.out’ for details. * 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 ... NOTE Warning: program compiled against libxml 212 using older 211 A namespace must be able to be loaded with just the base namespace loaded: otherwise if the namespace gets loaded by a saved object, the session will be unable to start. Probably some imports need to be declared in the NAMESPACE file. * checking whether the namespace can be unloaded cleanly ... OK * checking loading without being on the library search path ... OK * checking dependencies in R code ... NOTE Warning: program compiled against libxml 212 using older 211 * checking S3 generic/method consistency ... WARNING Warning: program compiled against libxml 212 using older 211 See section ‘Generic functions and methods’ in the ‘Writing R Extensions’ manual. * checking replacement functions ... WARNING Warning: program compiled against libxml 212 using older 211 The argument of a replacement function which corresponds to the right hand side must be named ‘value’. * checking foreign function calls ... NOTE Warning: program compiled against libxml 212 using older 211 See chapter ‘System and foreign language interfaces’ in the ‘Writing R Extensions’ manual. * checking R code for possible problems ... NOTE Warning: program compiled against libxml 212 using older 211 sconeReport: no visible global function definition for ‘visNetworkOutput’ sconeReport: no visible global function definition for ‘plotlyOutput’ sconeReport : server: no visible global function definition for ‘renderVisNetwork’ sconeReport : server: no visible global function definition for ‘%>%’ sconeReport : server: no visible global function definition for ‘visNetwork’ sconeReport : server: no visible global function definition for ‘visHierarchicalLayout’ sconeReport : server: no visible global function definition for ‘visGroups’ sconeReport : server: no visible global function definition for ‘visEdges’ sconeReport : server: no visible global function definition for ‘visOptions’ sconeReport : server: no visible global function definition for ‘visLegend’ sconeReport : server: no visible global function definition for ‘visNetworkProxy’ sconeReport : server: no visible global function definition for ‘visSelectNodes’ sconeReport : server: no visible global function definition for ‘plot_ly’ sconeReport : server: no visible global function definition for ‘ggplot’ sconeReport : server: no visible global function definition for ‘aes’ sconeReport : server: no visible global function definition for ‘geom_bar’ sconeReport : server: no visible global function definition for ‘ylim’ sconeReport : server: no visible global function definition for ‘labs’ sconeReport : server: no visible global function definition for ‘theme’ sconeReport : server: no visible global function definition for ‘element_blank’ sconeReport : server: no visible global function definition for ‘ggplotly’ sconeReport : server: no visible global function definition for ‘geom_violin’ sconeReport : server: no visible global function definition for ‘coord_cartesian’ sconeReport : server: no visible global function definition for ‘scale_fill_manual’ sconeReport : server: no visible global function definition for ‘geom_point’ sconeReport : server: no visible global function definition for ‘guides’ Undefined global functions or variables: %>% aes coord_cartesian element_blank geom_bar geom_point geom_violin ggplot ggplotly guides labs plot_ly plotlyOutput renderVisNetwork scale_fill_manual theme visEdges visGroups visHierarchicalLayout visLegend visNetwork visNetworkOutput visNetworkProxy visOptions visSelectNodes ylim * checking Rd files ... NOTE checkRd: (-1) estimate_ziber.Rd:57: Lost braces; missing escapes or markup? 57 | expression rate (Z in {0,1}). Detection conditioned on expression is a | ^ checkRd: (-1) estimate_ziber.Rd:42-43: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) estimate_ziber.Rd:43-44: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) estimate_ziber.Rd:44: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) estimate_ziber.Rd:44-45: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) estimate_ziber.Rd:46: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) estimate_ziber.Rd:47-48: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) estimate_ziber.Rd:48-49: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) estimate_ziber.Rd:49: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) estimate_ziber.Rd:50-51: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) fast_estimate_ziber.Rd:59: Lost braces; missing escapes or markup? 59 | expression rate (Z in {0,1}). Detection conditioned on expression is a | ^ checkRd: (-1) fast_estimate_ziber.Rd:43-44: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) fast_estimate_ziber.Rd:44-45: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) fast_estimate_ziber.Rd:45: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) fast_estimate_ziber.Rd:45-46: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) fast_estimate_ziber.Rd:47: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) fast_estimate_ziber.Rd:48-49: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) fast_estimate_ziber.Rd:49-50: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) fast_estimate_ziber.Rd:50: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) fast_estimate_ziber.Rd:51-52: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) impute_expectation.Rd:23: Lost braces; missing escapes or markup? 23 | y_{ij}* = y_{ij} * Pr( No Drop | y_{ij}) + mu_{i} * Pr( Drop | y_{ij}). | ^ checkRd: (-1) impute_expectation.Rd:23: Lost braces; missing escapes or markup? 23 | y_{ij}* = y_{ij} * Pr( No Drop | y_{ij}) + mu_{i} * Pr( Drop | y_{ij}). | ^ checkRd: (-1) impute_expectation.Rd:23: Lost braces; missing escapes or markup? 23 | y_{ij}* = y_{ij} * Pr( No Drop | y_{ij}) + mu_{i} * Pr( Drop | y_{ij}). | ^ checkRd: (-1) impute_expectation.Rd:23: Lost braces; missing escapes or markup? 23 | y_{ij}* = y_{ij} * Pr( No Drop | y_{ij}) + mu_{i} * Pr( Drop | y_{ij}). | ^ checkRd: (-1) impute_expectation.Rd:23: Lost braces; missing escapes or markup? 23 | y_{ij}* = y_{ij} * Pr( No Drop | y_{ij}) + mu_{i} * Pr( Drop | y_{ij}). | ^ checkRd: (-1) metric_sample_filter.Rd:104-105: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) metric_sample_filter.Rd:105-106: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) metric_sample_filter.Rd:106-107: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) metric_sample_filter.Rd:107-108: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) scone.Rd:126-127: Lost braces in \itemize; meant \describe ? checkRd: (-1) scone.Rd:128: Lost braces in \itemize; meant \describe ? checkRd: (-1) scone.Rd:129: Lost braces in \itemize; meant \describe ? checkRd: (-1) scone.Rd:144: Lost braces in \itemize; meant \describe ? checkRd: (-1) scone.Rd:145-146: Lost braces in \itemize; meant \describe ? checkRd: (-1) scone.Rd:147-148: Lost braces in \itemize; meant \describe ? checkRd: (-1) scone.Rd:149: Lost braces in \itemize; meant \describe ? checkRd: (-1) score_matrix.Rd:98-99: Lost braces in \itemize; meant \describe ? checkRd: (-1) score_matrix.Rd:100-101: Lost braces in \itemize; meant \describe ? checkRd: (-1) score_matrix.Rd:76-77: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) score_matrix.Rd:77-78: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) score_matrix.Rd:78-79: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) score_matrix.Rd:80-81: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) score_matrix.Rd:81-83: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) score_matrix.Rd:83-85: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) score_matrix.Rd:85-87: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) score_matrix.Rd:87-88: Lost braces in \itemize; \value handles \item{}{} directly * checking Rd metadata ... OK * checking Rd cross-references ... NOTE Found the following Rd file(s) with Rd \link{} targets missing package anchors: SconeExperiment-class.Rd: SummarizedExperiment-class, SummarizedExperiment Please provide package anchors for all Rd \link{} targets not in the package itself and the base packages. * checking for missing documentation entries ... WARNING Warning: program compiled against libxml 212 using older 211 All user-level objects in a package should have documentation entries. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. * checking for code/documentation mismatches ... WARNING Warning: program compiled against libxml 212 using older 211 Warning: program compiled against libxml 212 using older 211 Warning: program compiled against libxml 212 using older 211 * checking Rd \usage sections ... NOTE Warning: program compiled against libxml 212 using older 211 The \usage entries for S3 methods should use the \method markup and not their full name. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. * 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 * 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: 5 WARNINGs, 7 NOTEs See ‘/home/biocbuild/bbs-3.21-bioc/meat/scone.Rcheck/00check.log’ for details.