############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:Linnorm.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings Linnorm_2.28.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/Linnorm.Rcheck’ * using R version 4.4.0 (2024-04-24) * 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 ‘Linnorm/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘Linnorm’ version ‘2.28.0’ * 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 ‘Linnorm’ can be installed ... OK * used C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’ * used SDK: ‘MacOSX11.3.sdk’ * 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 Linnorm.HClust: no visible binding for global variable ‘y’ Linnorm.HClust: no visible binding for global variable ‘xend’ Linnorm.HClust: no visible binding for global variable ‘yend’ Linnorm.HClust: no visible binding for global variable ‘cluster’ Linnorm.HClust: no visible binding for global variable ‘X1’ Linnorm.HClust: no visible binding for global variable ‘X2’ Linnorm.HVar: no visible binding for global variable ‘SD’ Linnorm.HVar: no visible binding for global variable ‘group’ Undefined global functions or variables: SD X1 X2 cluster group xend y yend * checking Rd files ... NOTE checkRd: (-1) Linnorm.Cor.Rd:71: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) Linnorm.Cor.Rd:72: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) Linnorm.Cor.Rd:73: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) Linnorm.Cor.Rd:74: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) Linnorm.Cor.Rd:75: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) Linnorm.Cor.Rd:76: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) Linnorm.Cor.Rd:81: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) Linnorm.Cor.Rd:82: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) Linnorm.Cor.Rd:83: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) Linnorm.Cor.Rd:84: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) Linnorm.Cor.Rd:85: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) Linnorm.HClust.Rd:37: Lost braces; missing escapes or markup? 37 | \item{method_hclust}{Charcter. Method to be used in hierarchical clustering. (From hclust {fastcluster}: the agglomeration method to be used. This should be (an unambiguous abbreviation of) one of "ward.D", "ward.D2", "single", "complete", "average", "mcquitty", "median" or "centroid".) Defaults to "ward.D".} | ^ checkRd: (-1) Linnorm.HClust.Rd:39: Lost braces; missing escapes or markup? 39 | \item{method_dist}{Charcter. Method to be used in hierarchical clustering. (From Dist {amap}: the distance measure to be used. This must be one of "euclidean", "maximum", "manhattan", "canberra", "binary", "pearson", "correlation", "spearman" or "kendall". Any unambiguous substring can be given.) Defaults to "pearson".} | ^ checkRd: (-1) Linnorm.HClust.Rd:62: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) Linnorm.HClust.Rd:63: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) Linnorm.HClust.Rd:64: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) Linnorm.HVar.Rd:47: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) Linnorm.HVar.Rd:48: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) Linnorm.HVar.Rd:49: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) Linnorm.HVar.Rd:54: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) Linnorm.HVar.Rd:55: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) Linnorm.HVar.Rd:56: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) Linnorm.HVar.Rd:57: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) Linnorm.HVar.Rd:58: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) Linnorm.PCA.Rd:56: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) Linnorm.PCA.Rd:57: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) Linnorm.PCA.Rd:58: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) Linnorm.PCA.Rd:59: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) Linnorm.Rd:70: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) Linnorm.Rd:71: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) Linnorm.limma.Rd:38: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) Linnorm.limma.Rd:39: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) Linnorm.limma.Rd:40: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) Linnorm.limma.Rd:41: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) Linnorm.limma.Rd:42: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) Linnorm.limma.Rd:43: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) Linnorm.limma.Rd:48: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) Linnorm.limma.Rd:49: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) Linnorm.tSNE.Rd:50: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) Linnorm.tSNE.Rd:51: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) Linnorm.tSNE.Rd:52: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) Linnorm.tSNE.Rd:53: Lost braces in \itemize; \value handles \item{}{} directly * 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 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 files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed RnaXSim 88.670 2.138 91.701 Linnorm.Cor 60.323 0.934 62.020 Linnorm.Norm 23.515 1.083 24.855 Linnorm.limma 23.072 1.101 24.445 Linnorm 23.365 0.795 24.418 Linnorm.HClust 5.906 0.106 3.501 * 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: 4 NOTEs See ‘/Users/biocbuild/bbs-3.19-bioc/meat/Linnorm.Rcheck/00check.log’ for details.