Movatterモバイル変換

################################################################################################################################################################## Running command:######   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:Linnorm.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings Linnorm_2.34.0.tar.gz###############################################################################################################################################################* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/Linnorm.Rcheck’* using R version 4.5.2 (2025-10-31)* using platform: x86_64-pc-linux-gnu* R was compiled by    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0* running under: Ubuntu 24.04.3 LTS* using session charset: UTF-8* checking for file ‘Linnorm/DESCRIPTION’ ... OK* checking extension type ... Package* this is package ‘Linnorm’ version ‘2.34.0’* 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++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’* checking installed package size ... OK* checking package directory ... OK* checking ‘build’ directory ... OK* checking DESCRIPTION meta-information ... NOTELicense 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 ... NOTELinnorm.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 ... NOTEcheckRd: (-1) Linnorm.Cor.Rd:71: Lost braces in \itemize; \value handles \item{}{} directlycheckRd: (-1) Linnorm.Cor.Rd:72: Lost braces in \itemize; \value handles \item{}{} directlycheckRd: (-1) Linnorm.Cor.Rd:73: Lost braces in \itemize; \value handles \item{}{} directlycheckRd: (-1) Linnorm.Cor.Rd:74: Lost braces in \itemize; \value handles \item{}{} directlycheckRd: (-1) Linnorm.Cor.Rd:75: Lost braces in \itemize; \value handles \item{}{} directlycheckRd: (-1) Linnorm.Cor.Rd:76: Lost braces in \itemize; \value handles \item{}{} directlycheckRd: (-1) Linnorm.Cor.Rd:81: Lost braces in \itemize; \value handles \item{}{} directlycheckRd: (-1) Linnorm.Cor.Rd:82: Lost braces in \itemize; \value handles \item{}{} directlycheckRd: (-1) Linnorm.Cor.Rd:83: Lost braces in \itemize; \value handles \item{}{} directlycheckRd: (-1) Linnorm.Cor.Rd:84: Lost braces in \itemize; \value handles \item{}{} directlycheckRd: (-1) Linnorm.Cor.Rd:85: Lost braces in \itemize; \value handles \item{}{} directlycheckRd: (-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{}{} directlycheckRd: (-1) Linnorm.HClust.Rd:63: Lost braces in \itemize; \value handles \item{}{} directlycheckRd: (-1) Linnorm.HClust.Rd:64: Lost braces in \itemize; \value handles \item{}{} directlycheckRd: (-1) Linnorm.HVar.Rd:47: Lost braces in \itemize; \value handles \item{}{} directlycheckRd: (-1) Linnorm.HVar.Rd:48: Lost braces in \itemize; \value handles \item{}{} directlycheckRd: (-1) Linnorm.HVar.Rd:49: Lost braces in \itemize; \value handles \item{}{} directlycheckRd: (-1) Linnorm.HVar.Rd:54: Lost braces in \itemize; \value handles \item{}{} directlycheckRd: (-1) Linnorm.HVar.Rd:55: Lost braces in \itemize; \value handles \item{}{} directlycheckRd: (-1) Linnorm.HVar.Rd:56: Lost braces in \itemize; \value handles \item{}{} directlycheckRd: (-1) Linnorm.HVar.Rd:57: Lost braces in \itemize; \value handles \item{}{} directlycheckRd: (-1) Linnorm.HVar.Rd:58: Lost braces in \itemize; \value handles \item{}{} directlycheckRd: (-1) Linnorm.PCA.Rd:56: Lost braces in \itemize; \value handles \item{}{} directlycheckRd: (-1) Linnorm.PCA.Rd:57: Lost braces in \itemize; \value handles \item{}{} directlycheckRd: (-1) Linnorm.PCA.Rd:58: Lost braces in \itemize; \value handles \item{}{} directlycheckRd: (-1) Linnorm.PCA.Rd:59: Lost braces in \itemize; \value handles \item{}{} directlycheckRd: (-1) Linnorm.Rd:70: Lost braces in \itemize; \value handles \item{}{} directlycheckRd: (-1) Linnorm.Rd:71: Lost braces in \itemize; \value handles \item{}{} directlycheckRd: (-1) Linnorm.limma.Rd:38: Lost braces in \itemize; \value handles \item{}{} directlycheckRd: (-1) Linnorm.limma.Rd:39: Lost braces in \itemize; \value handles \item{}{} directlycheckRd: (-1) Linnorm.limma.Rd:40: Lost braces in \itemize; \value handles \item{}{} directlycheckRd: (-1) Linnorm.limma.Rd:41: Lost braces in \itemize; \value handles \item{}{} directlycheckRd: (-1) Linnorm.limma.Rd:42: Lost braces in \itemize; \value handles \item{}{} directlycheckRd: (-1) Linnorm.limma.Rd:43: Lost braces in \itemize; \value handles \item{}{} directlycheckRd: (-1) Linnorm.limma.Rd:48: Lost braces in \itemize; \value handles \item{}{} directlycheckRd: (-1) Linnorm.limma.Rd:49: Lost braces in \itemize; \value handles \item{}{} directlycheckRd: (-1) Linnorm.tSNE.Rd:50: Lost braces in \itemize; \value handles \item{}{} directlycheckRd: (-1) Linnorm.tSNE.Rd:51: Lost braces in \itemize; \value handles \item{}{} directlycheckRd: (-1) Linnorm.tSNE.Rd:52: Lost braces in \itemize; \value handles \item{}{} directlycheckRd: (-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 ... NOTENote: information on .o files is not available* checking files in ‘vignettes’ ... OK* checking examples ... OKExamples with CPU (user + system) or elapsed time > 5s                user system elapsedRnaXSim       67.295  0.074  67.373Linnorm.Cor   51.509  0.195  51.706Linnorm.limma 26.956  0.077  27.034Linnorm       26.570  0.073  26.643Linnorm.Norm  26.451  0.072  26.528* 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 re-building of vignette outputs ... OK* checking PDF version of manual ... OK* DONEStatus: 4 NOTEsSee  ‘/home/biocbuild/bbs-3.22-bioc/meat/Linnorm.Rcheck/00check.log’for details.

################################################################################################################################################################## Running command:######   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL Linnorm###############################################################################################################################################################* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’* installing *source* package ‘Linnorm’ ...** this is package ‘Linnorm’ version ‘2.34.0’** using staged installation** libsusing C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/RcppArmadillo/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c Misc.cpp -o Misc.og++ -std=gnu++17 -shared -L/home/biocbuild/bbs-3.22-bioc/R/lib -L/usr/local/lib -o Linnorm.so Misc.o -std=c++11 -llapack -L/home/biocbuild/bbs-3.22-bioc/R/lib -lRblas -lgfortran -lm -lquadmath -DARMA_64BIT_WORD=1 -L/home/biocbuild/bbs-3.22-bioc/R/lib -lRinstalling to /home/biocbuild/bbs-3.22-bioc/R/site-library/00LOCK-Linnorm/00new/Linnorm/libs** R** data** inst** byte-compile and prepare package for lazy loading** help*** installing help indices** building package indices** installing vignettes** testing if installed package can be loaded from temporary location** checking absolute paths in shared objects and dynamic libraries** testing if installed package can be loaded from final location** testing if installed package keeps a record of temporary installation path* DONE (Linnorm)

R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"Copyright (C) 2025 The R Foundation for Statistical ComputingPlatform: x86_64-pc-linux-gnuR is free software and comes with ABSOLUTELY NO WARRANTY.You are welcome to redistribute it under certain conditions.Type 'license()' or 'licence()' for distribution details.R is a collaborative project with many contributors.Type 'contributors()' for more information and'citation()' on how to cite R or R packages in publications.Type 'demo()' for some demos, 'help()' for on-line help, or'help.start()' for an HTML browser interface to help.Type 'q()' to quit R.> library(testthat)> library(Linnorm)> > test_check("Linnorm")[ FAIL 0 | WARN 0 | SKIP 0 | PASS 26 ]> > proc.time()   user  system elapsed  19.631   0.524  20.145