############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD check --install=check:scTreeViz.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings scTreeViz_1.13.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/scTreeViz.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 ‘scTreeViz/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘scTreeViz’ version ‘1.13.0’ * 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 ‘scTreeViz’ 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/scTreeViz.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 .generate_hierarchy_tree: no visible binding for global variable 'otu_index' .generate_leaf_of_table: no visible binding for global variable 'leaf' .generate_leaf_of_table: no visible binding for global variable 'otu_index' .generate_leaf_of_table: no visible binding for global variable 'id' .generate_node_ids : : no visible global function definition for '.' .generate_node_ids : : no visible binding for global variable 'otu_index' .generate_nodes_table: no visible binding for global variable 'id' .generate_nodes_table: no visible binding for global variable 'lineage' .generate_nodes_table: no visible binding for global variable 'node_label' .generate_nodes_table: no visible binding for global variable 'level' .preprocessAndCreateTreeViz: no visible global function definition for 'chracter' getNodes,TreeIndex: no visible binding for global variable 'level' getNodes,TreeIndex: no visible binding for global variable 'id' splitAt,TreeIndex: no visible binding for global variable 'level' splitAt,TreeIndex: no visible binding for global variable 'id' splitAt,TreeIndex: no visible binding for global variable 'lineage' splitAt,TreeIndex: no visible binding for global variable 'leaf' splitAt,TreeIndex: no visible binding for global variable 'otu_index' splitAt,TreeIndex: no visible global function definition for '.' splitAt,TreeIndex: no visible binding for global variable 'node_label' Undefined global functions or variables: . chracter id leaf level lineage node_label otu_index * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... OK * 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 files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed TreeIndex-methods 31.506 0.110 34.777 TreeIndex 13.373 0.060 14.164 TreeViz 13.230 0.044 14.133 createFromSCE 10.006 0.076 10.728 * 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, 5 NOTEs See ‘/home/biocbuild/bbs-3.21-bioc/meat/scTreeViz.Rcheck/00check.log’ for details.