############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD check --install=check:Linnorm.install-out.txt --library=/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library --no-vignettes --timings Linnorm_2.28.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/Linnorm.Rcheck’ * using R version 4.4.0 beta (2024-04-15 r86425) * using platform: aarch64-unknown-linux-gnu * R was compiled by gcc (GCC) 10.3.1 GNU Fortran (GCC) 10.3.1 * running under: openEuler 22.03 (LTS-SP1) * 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: ‘g++ (GCC) 10.3.1’ * 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 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 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 files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed RnaXSim 107.841 0.092 108.176 Linnorm.Cor 63.706 0.148 63.954 Linnorm.limma 48.381 0.031 48.534 Linnorm 47.926 0.032 48.063 Linnorm.Norm 47.755 0.056 47.855 Linnorm.HClust 6.952 0.012 4.191 Linnorm.tSNE 5.349 0.024 5.385 * 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 ‘/home/biocbuild/bbs-3.19-bioc/meat/Linnorm.Rcheck/00check.log’ for details.