############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:EBSeq.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings EBSeq_2.3.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/EBSeq.Rcheck’ * using R version 4.4.0 Patched (2024-04-24 r86482) * 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 13.6.6 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘EBSeq/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘EBSeq’ version ‘2.3.0’ * 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 ‘EBSeq’ can be installed ... WARNING Found the following significant warnings: /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/BH/include/boost/math/tools/config.hpp:23:6: warning: "The minimum language standard to use Boost.Math will be C++14 starting in July 2023 (Boost 1.82 release)" [-W#warnings] # warning "The minimum language standard to use Boost.Math will be C++14 starting in July 2023 (Boost 1.82 release)" See ‘/Users/biocbuild/bbs-3.20-bioc/meat/EBSeq.Rcheck/00install.out’ for details. * used C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.0.40.1)’ * used SDK: ‘MacOSX11.3.sdk’ * checking C++ specification ... NOTE Specified C++11: please drop specification unless essential * checking installed package size ... OK * checking package directory ... OK * checking DESCRIPTION meta-information ... NOTE 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 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 DenNHist: no visible global function definition for ‘hist’ DenNHist: no visible global function definition for ‘lines’ DenNHist: no visible global function definition for ‘dbeta’ DenNHist: no visible global function definition for ‘legend’ EBMultiTest : : no visible global function definition for ‘quantile’ EBMultiTest: no visible binding for global variable ‘var’ EBMultiTest: no visible binding for global variable ‘NumBin’ EBMultiTest: no visible global function definition for ‘quantile’ EBMultiTest: no visible binding for global variable ‘PoolLower’ EBMultiTest: no visible binding for global variable ‘PoolUpper’ EBMultiTest : : no visible binding for global variable ‘var’ EBMultiTest: no visible binding for global variable ‘Print’ EBTest : : no visible global function definition for ‘quantile’ EBTest: no visible binding for global variable ‘var’ EBTest: no visible global function definition for ‘quantile’ EBTest: no visible binding for global variable ‘PoolLower’ EBTest: no visible binding for global variable ‘PoolUpper’ EBTest: no visible binding for global variable ‘Print’ GetDEResults: no visible binding for global variable ‘median’ LogN: no visible global function definition for ‘optim’ LogNMulti: no visible global function definition for ‘optim’ MedianNorm : : no visible global function definition for ‘median’ MedianNorm : : : no visible global function definition for ‘median’ PlotPattern: no visible global function definition for ‘par’ PlotPattern: no visible global function definition for ‘rainbow’ PlotPattern: no visible global function definition for ‘heatmap’ PlotPostVsRawFC: no visible global function definition for ‘par’ PlotPostVsRawFC: no visible global function definition for ‘abline’ PlotPostVsRawFC: no visible global function definition for ‘rect’ PolyFitPlot: no visible global function definition for ‘lm’ PolyFitPlot: no visible global function definition for ‘smoothScatter’ PolyFitPlot: no visible global function definition for ‘axis’ PolyFitPlot: no visible global function definition for ‘lines’ QQP: no visible global function definition for ‘rbeta’ QQP: no visible global function definition for ‘qqplot’ QQP: no visible global function definition for ‘lm’ QQP: no visible global function definition for ‘abline’ QuantileNorm : : no visible global function definition for ‘quantile’ beta.mom: no visible global function definition for ‘var’ Undefined global functions or variables: NumBin PoolLower PoolUpper Print abline axis dbeta heatmap hist legend lines lm median optim par qqplot quantile rainbow rbeta rect smoothScatter var Consider adding importFrom("grDevices", "rainbow") importFrom("graphics", "abline", "axis", "hist", "legend", "lines", "par", "rect", "smoothScatter") importFrom("stats", "dbeta", "heatmap", "lm", "median", "optim", "qqplot", "quantile", "rbeta", "var") to your NAMESPACE file. * checking Rd files ... NOTE checkRd: (-1) EBTest.Rd:56: Lost braces; missing escapes or markup? 56 | X_{gis}|mu_{gi} ~ NB (r_{gi0} * l_s, q_{gi}) | ^ checkRd: (-1) EBTest.Rd:56: Lost braces; missing escapes or markup? 56 | X_{gis}|mu_{gi} ~ NB (r_{gi0} * l_s, q_{gi}) | ^ checkRd: (-1) EBTest.Rd:56: Lost braces; missing escapes or markup? 56 | X_{gis}|mu_{gi} ~ NB (r_{gi0} * l_s, q_{gi}) | ^ checkRd: (-1) EBTest.Rd:56: Lost braces; missing escapes or markup? 56 | X_{gis}|mu_{gi} ~ NB (r_{gi0} * l_s, q_{gi}) | ^ checkRd: (-1) EBTest.Rd:60: Lost braces; missing escapes or markup? 60 | The function will test "H0: q_{gi}^{C1} = q_{gi}^{C2}" and "H1: q_{gi}^{C1} != q_{gi}^{C2}." | ^ checkRd: (-1) EBTest.Rd:60: Lost braces; missing escapes or markup? 60 | The function will test "H0: q_{gi}^{C1} = q_{gi}^{C2}" and "H1: q_{gi}^{C1} != q_{gi}^{C2}." | ^ checkRd: (-1) EBTest.Rd:60: Lost braces; missing escapes or markup? 60 | The function will test "H0: q_{gi}^{C1} = q_{gi}^{C2}" and "H1: q_{gi}^{C1} != q_{gi}^{C2}." | ^ checkRd: (-1) EBTest.Rd:60: Lost braces; missing escapes or markup? 60 | The function will test "H0: q_{gi}^{C1} = q_{gi}^{C2}" and "H1: q_{gi}^{C1} != q_{gi}^{C2}." | ^ checkRd: (-1) EBTest.Rd:60: Lost braces; missing escapes or markup? 60 | The function will test "H0: q_{gi}^{C1} = q_{gi}^{C2}" and "H1: q_{gi}^{C1} != q_{gi}^{C2}." | ^ checkRd: (-1) EBTest.Rd:60: Lost braces; missing escapes or markup? 60 | The function will test "H0: q_{gi}^{C1} = q_{gi}^{C2}" and "H1: q_{gi}^{C1} != q_{gi}^{C2}." | ^ checkRd: (-1) EBTest.Rd:60: Lost braces; missing escapes or markup? 60 | The function will test "H0: q_{gi}^{C1} = q_{gi}^{C2}" and "H1: q_{gi}^{C1} != q_{gi}^{C2}." | ^ checkRd: (-1) EBTest.Rd:60: Lost braces; missing escapes or markup? 60 | The function will test "H0: q_{gi}^{C1} = q_{gi}^{C2}" and "H1: q_{gi}^{C1} != q_{gi}^{C2}." | ^ checkRd: (-1) MedianNorm.Rd:21: Lost braces 21 | hat{l_1} = median_g [ X_g1 / (X_g1*X_g2*...*X_gS)^{-S} ] (1) | ^ checkRd: (-1) MedianNorm.Rd:21: Lost braces; missing escapes or markup? 21 | hat{l_1} = median_g [ X_g1 / (X_g1*X_g2*...*X_gS)^{-S} ] (1) | ^ checkRd: (-1) MedianNorm.Rd:23: Lost braces; missing escapes or markup? 23 | which estimates l_1 / (l_1 * l_2 * ... * l_S)^{-S}. | ^ checkRd: (-1) MedianNorm.Rd:27: Lost braces 27 | hat{l_1} = median_g [ (X_g1/X_g1 * X_g1/X_g2 * .... * X_g1/X_gS)^{-S}] | ^ checkRd: (-1) MedianNorm.Rd:27: Lost braces; missing escapes or markup? 27 | hat{l_1} = median_g [ (X_g1/X_g1 * X_g1/X_g2 * .... * X_g1/X_gS)^{-S}] | ^ checkRd: (-1) MedianNorm.Rd:31: Lost braces; missing escapes or markup? 31 | Then estimate l_1 = l_1 / (l_1 * l_2 * ... * l_S)^{-S} by taking the | ^ checkRd: (-1) MedianNorm.Rd:34: Lost braces 34 | hat{l_1} = [ median_g(X_g1/X_g1) * median_g(X_g1/X_g2) * | ^ checkRd: (-1) MedianNorm.Rd:35: Lost braces; missing escapes or markup? 35 | median_g(X_g1/X_g3) * ... * median_g(X_g1/X_gS) ] ^{-S} | ^ * checking Rd metadata ... NOTE Invalid package aliases in Rd file 'EBSeq_NingLeng-package.Rd': ‘EBSeq_NingLeng-package’ * 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 data for ASCII and uncompressed saves ... 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 sizes of PDF files under ‘inst/doc’ ... OK * checking installed files from ‘inst/doc’ ... 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: 1 WARNING, 6 NOTEs See ‘/Users/biocbuild/bbs-3.20-bioc/meat/EBSeq.Rcheck/00check.log’ for details.