############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:ctc.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings ctc_1.77.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/ctc.Rcheck’ * using R Under development (unstable) (2024-03-18 r86148) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 * running under: Ubuntu 22.04.4 LTS * using session charset: UTF-8 * checking for file ‘ctc/DESCRIPTION’ ... OK * this is package ‘ctc’ version ‘1.77.0’ * 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 ‘ctc’ can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... NOTE Malformed Title field: should not end in a period. 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 ... 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 loading without being on the library search path ... OK * checking whether startup messages can be suppressed ... OK * checking dependencies in R code ... NOTE 'library' or 'require' call to ‘amap’ which was already attached by Depends. Please remove these calls from your code. Package in Depends field not imported from: ‘amap’ These packages need to be imported from (in the NAMESPACE file) for when this namespace is loaded but not attached. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE .First.lib: warning in .packages(all = TRUE): partial argument match of 'all' to 'all.available' .onLoad: warning in .packages(all = TRUE): partial argument match of 'all' to 'all.available' hclust2treeview: warning in .packages(all = TRUE): partial argument match of 'all' to 'all.available' hclust2treeview: no visible global function definition for ‘hclust’ hclust2treeview: no visible global function definition for ‘dist’ r2atr: no visible global function definition for ‘write.table’ r2cdt: no visible global function definition for ‘write.table’ r2cluster: no visible global function definition for ‘write.table’ r2gtr: no visible global function definition for ‘write.table’ r2xcluster: no visible global function definition for ‘write.table’ read.eisen: no visible global function definition for ‘read.table’ xcluster2r: no visible global function definition for ‘read.table’ Undefined global functions or variables: dist hclust read.table write.table Consider adding importFrom("stats", "dist", "hclust") importFrom("utils", "read.table", "write.table") to your NAMESPACE file. * 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 * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 3 NOTEs See ‘/home/biocbuild/bbs-3.19-bioc/meat/ctc.Rcheck/00check.log’ for details.