############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:iClusterPlus.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings iClusterPlus_1.43.1.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/iClusterPlus.Rcheck’ * using R Under development (unstable) (2024-10-21 r87258) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0 GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0 * running under: Ubuntu 24.04.1 LTS * using session charset: UTF-8 * checking for file ‘iClusterPlus/DESCRIPTION’ ... OK * this is package ‘iClusterPlus’ version ‘1.43.1’ * 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 ‘iClusterPlus’ can be installed ... OK * used C compiler: ‘gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0’ * used Fortran compiler: ‘GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0’ * checking installed package size ... INFO installed size is 17.1Mb sub-directories of 1Mb or more: data 12.4Mb doc 3.9Mb * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... NOTE Found a ‘configure.in’ file: ‘configure.ac’ has long been preferred. * 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 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 CNregions: no visible binding for global variable ‘chromosome’ CNregions: no visible binding for global variable ‘num.mark’ CNregions: no visible global function definition for ‘GRanges’ CNregions: no visible global function definition for ‘IRanges’ CNregions: no visible global function definition for ‘findOverlaps’ CNregions : get.medoid: no visible global function definition for ‘pam’ classError: no visible global function definition for ‘mapClass’ plotHMBayes: no visible global function definition for ‘bluered’ plotHMBayes : my.panel.levelplot: no visible global function definition for ‘panel.levelplot’ plotHMBayes : my.panel.levelplot: no visible global function definition for ‘panel.abline’ plotHMBayes : my.panel.levelplot.2: no visible global function definition for ‘panel.levelplot’ plotHMBayes : my.panel.levelplot.2: no visible global function definition for ‘panel.abline’ plotHMBayes: no visible global function definition for ‘levelplot’ plotHeatmap: no visible global function definition for ‘bluered’ plotHeatmap : my.panel.levelplot: no visible global function definition for ‘panel.levelplot’ plotHeatmap : my.panel.levelplot: no visible global function definition for ‘panel.abline’ plotHeatmap : my.panel.levelplot.2: no visible global function definition for ‘panel.levelplot’ plotHeatmap : my.panel.levelplot.2: no visible global function definition for ‘panel.abline’ plotHeatmap: no visible global function definition for ‘levelplot’ tune.iCluster2: no visible binding for global variable ‘glp’ tune.iClusterPlus: no visible binding for global variable ‘glp’ Undefined global functions or variables: GRanges IRanges bluered chromosome findOverlaps glp levelplot mapClass num.mark pam panel.abline panel.levelplot * 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 contents of ‘data’ directory ... OK * checking data for non-ASCII characters ... OK * checking LazyData ... OK * checking data for ASCII and uncompressed saves ... OK * checking line endings in shell scripts ... OK * checking line endings in C/C++/Fortran sources/headers ... OK * checking line endings in Makefiles ... OK * checking compilation flags in Makevars ... OK * checking for GNU extensions in Makefiles ... OK * checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK * checking use of PKG_*FLAGS in Makefiles ... OK * checking compiled code ... NOTE Note: information on .o files is not available * checking usage of KIND in Fortran files ... OK * checking installed files from ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed iCluster 10.641 0.051 10.693 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘runTests.R’ 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-3.21-bioc/meat/iClusterPlus.Rcheck/00check.log’ for details.