############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:LinTInd.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings LinTInd_1.9.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/LinTInd.Rcheck’ * using R version 4.4.1 (2024-06-14) * using platform: aarch64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0 * running under: macOS Ventura 13.6.7 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘LinTInd/DESCRIPTION’ ... OK * this is package ‘LinTInd’ version ‘1.9.0’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib: cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES' 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 ‘LinTInd’ can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... NOTE License stub is invalid DCF. * 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 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 BuildTree: no visible global function definition for ‘write.csv’ FindIndel : find_barcode: no visible global function definition for ‘is’ FindIndel: no visible global function definition for ‘write.table’ IndelForm: no visible global function definition for ‘write.csv’ IndelIdents: no visible global function definition for ‘write.csv’ IndelIdents : max_reads_stat: no visible global function definition for ‘is’ IndelPlot: no visible binding for global variable ‘Site’ IndelPlot: no visible binding for global variable ‘Freq’ PlotTree: no visible binding for global variable ‘tags’ PlotTree: no visible binding for global variable ‘celltype’ PlotTree: no visible binding for global variable ‘Freq’ PlotTree : SortTree: no visible binding for global variable ‘tag_number’ PlotTree: no visible binding for global variable ‘y’ PlotTree: no visible binding for global variable ‘variable’ PlotTree: no visible binding for global variable ‘value’ ReadFasta: no visible global function definition for ‘read.table’ TagProcess: no visible binding for global variable ‘i’ change_form_stat : : no visible binding for global variable ‘scarref’ change_form_stat: no visible binding for global variable ‘scarref’ Undefined global functions or variables: Freq Site celltype i is read.table scarref tag_number tags value variable write.csv write.table y Consider adding importFrom("methods", "is") importFrom("utils", "read.table", "write.csv", "write.table") to your NAMESPACE file (and ensure that your DESCRIPTION Imports field contains 'methods'). * checking Rd files ... NOTE prepare_Rd: cellsinfo.Rd:10: Dropping empty section \source prepare_Rd: cellsinfo.Rd:11-12: Dropping empty section \references prepare_Rd: celltype.Rd:10: Dropping empty section \source prepare_Rd: celltype.Rd:11-12: Dropping empty section \references prepare_Rd: cutsite.Rd:10: Dropping empty section \source prepare_Rd: cutsite.Rd:11-12: Dropping empty section \references prepare_Rd: data.Rd:10: Dropping empty section \source prepare_Rd: data.Rd:11-12: Dropping empty section \references prepare_Rd: example_data.Rd:15-17: Dropping empty section \details prepare_Rd: example_data.Rd:18-20: Dropping empty section \source prepare_Rd: example_data.Rd:21-23: Dropping empty section \references prepare_Rd: ref.Rd:10: Dropping empty section \source prepare_Rd: ref.Rd:11-12: Dropping empty section \references prepare_Rd: scarform.Rd:10: Dropping empty section \source prepare_Rd: scarform.Rd:11-12: Dropping empty section \references prepare_Rd: scarinfo.Rd:10: Dropping empty section \source prepare_Rd: scarinfo.Rd:11-12: Dropping empty section \references prepare_Rd: scarref.Rd:10: Dropping empty section \source prepare_Rd: scarref.Rd:11-12: Dropping empty section \references prepare_Rd: scarref_all.Rd:10: Dropping empty section \source prepare_Rd: scarref_all.Rd:11-12: Dropping empty section \references prepare_Rd: tag.Rd:10: Dropping empty section \source prepare_Rd: tag.Rd:11-12: Dropping empty section \references prepare_Rd: treeinfo.Rd:10: Dropping empty section \source prepare_Rd: treeinfo.Rd:11-12: Dropping empty section \references * 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 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 ... 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: 3 NOTEs See ‘/Users/biocbuild/bbs-3.20-bioc/meat/LinTInd.Rcheck/00check.log’ for details.