############################################################################## ############################################################################## ### ### Running command: ### ### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:scTreeViz.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings scTreeViz_1.1.1.tar.gz ### ############################################################################## ############################################################################## * using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/scTreeViz.Rcheck' * using R Under development (unstable) (2021-11-21 r81221) * using platform: x86_64-w64-mingw32 (64-bit) * using session charset: ISO8859-1 * using option '--no-vignettes' * checking for file 'scTreeViz/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'scTreeViz' version '1.1.1' * 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 whether package 'scTreeViz' 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 R 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 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 ... NOTE .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 ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * 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 18.11 1.69 19.75 TreeViz 9.19 0.35 9.53 TreeIndex 9.09 0.12 9.22 createFromSCE 8.28 0.12 8.45 * checking for unstated dependencies in 'tests' ... OK * checking tests ... Running 'testthat.R' OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes in 'inst/doc' ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 1 NOTE See 'D:/biocbuild/bbs-3.15-bioc/meat/scTreeViz.Rcheck/00check.log' for details.