############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:HiCcompare.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings HiCcompare_1.25.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/HiCcompare.Rcheck’ * using R Under development (unstable) (2024-03-18 r86148) * using platform: x86_64-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 Monterey 12.7.1 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘HiCcompare/DESCRIPTION’ ... OK * this is package ‘HiCcompare’ version ‘1.25.0’ * 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 ‘HiCcompare’ 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 .adjust_pval : : no visible binding for global variable ‘p.adj’ .adjust_pval : : no visible binding for global variable ‘p.value’ .adjust_pval: no visible binding for global variable ‘p.value’ .adjust_pval: no visible binding for global variable ‘p.adj’ .calc.diff.thresh: no visible global function definition for ‘sd’ .calc.pval: no visible binding for global variable ‘D’ .calc.pval: no visible binding for global variable ‘p.value’ .calc.pval: no visible binding for global variable ‘p.adj’ .calc.pval: no visible binding for global variable ‘adj.M’ .calc.pval: no visible binding for global variable ‘fold.change’ .calc.pval: no visible binding for global variable ‘adj.IF2’ .calc.pval: no visible binding for global variable ‘adj.IF1’ .calc_z2: no visible global function definition for ‘sd’ .calc_z2: no visible binding for global variable ‘Z’ .calc_z2: no visible global function definition for ‘pnorm’ .calc_z2: no visible binding for global variable ‘p.value’ .loess.matrix: no visible binding for global variable ‘adj.IF1’ .loess.matrix: no visible binding for global variable ‘IF1’ .loess.matrix: no visible binding for global variable ‘adj.IF2’ .loess.matrix: no visible binding for global variable ‘IF2’ .loess.matrix: no visible binding for global variable ‘adj.M’ .loess.matrix: no visible binding for global variable ‘A’ .sim.mat: no visible global function definition for ‘head’ .split_cent: no visible binding for global variable ‘centromere_locations’ .split_cent: no visible binding for global variable ‘start1’ .split_cent: no visible binding for global variable ‘start2’ .split_cent: no visible binding for global variable ‘chr1’ .split_cent: no visible binding for global variable ‘chr2’ MA_norm: no visible binding for global variable ‘D’ MA_norm: no visible binding for global variable ‘M’ MA_norm: no visible binding for global variable ‘adj.IF1’ MA_norm: no visible binding for global variable ‘IF1’ MA_norm: no visible binding for global variable ‘adj.IF2’ MA_norm: no visible binding for global variable ‘IF2’ MA_norm: no visible binding for global variable ‘adj.M’ cooler2sparse: no visible binding for global variable ‘chr1’ cooler2sparse: no visible binding for global variable ‘chr2’ cooler2sparse: no visible binding for global variable ‘IF’ create.hic.table: no visible binding for global variable ‘D’ create.hic.table: no visible binding for global variable ‘region2’ create.hic.table: no visible binding for global variable ‘region1’ create.hic.table: no visible binding for global variable ‘IF2’ create.hic.table: no visible binding for global variable ‘M’ create.hic.table: no visible binding for global variable ‘IF1’ create.hic.table: no visible binding for global variable ‘i’ create.hic.table: no visible binding for global variable ‘j’ filter_params: no visible binding for global variable ‘M’ filter_params: no visible binding for global variable ‘IF1’ filter_params: no visible binding for global variable ‘IF2’ filter_params: no visible global function definition for ‘axis’ full2sparse: no visible binding for global variable ‘IF’ hic_compare : : no visible binding for global variable ‘p.adj’ hic_simulate: no visible binding for global variable ‘bias.slope’ hic_simulate: no visible global function definition for ‘na.omit’ hicpro2bedpe: no visible binding for global variable ‘chr1’ hicpro2bedpe: no visible binding for global variable ‘chr2’ manhattan_plot: no visible binding for global variable ‘bp’ manhattan_plot: no visible binding for global variable ‘count’ sim.other.methods: no visible binding for global variable ‘adj.IF1’ sim.other.methods: no visible binding for global variable ‘IF1’ sim.other.methods: no visible binding for global variable ‘adj.IF2’ sim.other.methods: no visible binding for global variable ‘IF2’ sim.other.methods: no visible binding for global variable ‘adj.M’ sim.other.methods: no visible binding for global variable ‘M’ sim.other.methods: no visible global function definition for ‘na.omit’ sim_matrix: no visible binding for global variable ‘bias.slope’ total_sum: no visible binding for global variable ‘IF2’ total_sum: no visible binding for global variable ‘M’ total_sum: no visible binding for global variable ‘IF1’ total_sum: no visible binding for global variable ‘chr1’ volcano: no visible binding for global variable ‘A’ volcano: no visible binding for global variable ‘adj.IF1’ volcano: no visible binding for global variable ‘adj.IF2’ volcano: no visible binding for global variable ‘p.value’ volcano: no visible binding for global variable ‘D’ Undefined global functions or variables: A D IF IF1 IF2 M Z adj.IF1 adj.IF2 adj.M axis bias.slope bp centromere_locations chr1 chr2 count fold.change head i j na.omit p.adj p.value pnorm region1 region2 sd start1 start2 Consider adding importFrom("graphics", "axis") importFrom("stats", "D", "na.omit", "pnorm", "sd") importFrom("utils", "head") 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 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 ‘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: 2 NOTEs See ‘/Users/biocbuild/bbs-3.19-bioc/meat/HiCcompare.Rcheck/00check.log’ for details.