Movatterモバイル変換

################################################################################################################################################################## Running command:######   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:cola.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings cola_2.16.0.tar.gz###############################################################################################################################################################* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/cola.Rcheck’* using R version 4.5.2 Patched (2025-11-04 r88984)* using platform: aarch64-apple-darwin20* R was compiled by    Apple clang version 16.0.0 (clang-1600.0.26.6)    GNU Fortran (GCC) 14.2.0* running under: macOS Ventura 13.7.8* using session charset: UTF-8* using option ‘--no-vignettes’* checking for file ‘cola/DESCRIPTION’ ... OK* checking extension type ... Package* this is package ‘cola’ version ‘2.16.0’* checking package namespace information ... OK* checking package dependencies ... INFOImports includes 27 non-default packages.Importing from so many packages makes the package vulnerable to any ofthem becoming unavailable.  Move as many as possible to Suggests anduse conditionally.* 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 ‘cola’ can be installed ... OK* used C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.0.40.1)’* used SDK: ‘MacOSX11.3.1.sdk’* checking installed package size ... INFO  installed size is  5.8Mb  sub-directories of 1Mb or more:    data      3.2Mb    extdata   1.0Mb* 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 whether startup messages can be suppressed ... 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 ... OK* checking Rd files ... OK* checking Rd metadata ... OK* checking Rd cross-references ... NOTENon-topic package-anchored link(s) in Rd file 'collect_classes-ConsensusPartitionList-method.Rd':  ‘[ComplexHeatmap:draw-HeatmapList-method]{draw,HeatmapList-method}’See section 'Cross-references' in the 'Writing R Extensions' manual.Found the following Rd file(s) with Rd \link{} targets missing packageanchors:  predict_classes-ConsensusPartition-method.Rd: colorRamp2  predict_classes-matrix-method.Rd: colorRamp2Please provide package anchors for all Rd \link{} targets not in thepackage itself and the base packages.* 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 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 elapsedconsensus_partition                             18.496  0.275  29.098get_signatures-ConsensusPartition-method         5.460  0.179   8.701compare_signatures-HierarchicalPartition-method  4.971  0.190   8.147top_rows_heatmap-matrix-method                   4.296  0.228   6.954collect_classes-ConsensusPartitionList-method    3.389  0.040   5.290* checking for unstated dependencies in ‘tests’ ... OK* checking tests ...  Running ‘test-all.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* DONEStatus: 3 NOTEsSee  ‘/Users/biocbuild/bbs-3.22-bioc/meat/cola.Rcheck/00check.log’for details.

################################################################################################################################################################## Running command:######   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL cola###############################################################################################################################################################* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library’* installing *source* package ‘cola’ ...** this is package ‘cola’ version ‘2.16.0’** using staged installation** libsusing C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.0.40.1)’using SDK: ‘MacOSX11.3.1.sdk’clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c RcppExports.cpp -o RcppExports.oclang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c atc.cpp -o atc.oclang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c cal_consensus_mat.cpp -o cal_consensus_mat.oclang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c pdist.cpp -o pdist.oclang++ -arch arm64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o cola.so RcppExports.o atc.o cal_consensus_mat.o pdist.o -F/Library/Frameworks/R.framework/.. -framework Rinstalling to /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/00LOCK-cola/00new/cola/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 (cola)

R version 4.5.2 Patched (2025-11-04 r88984) -- "[Not] Part in a Rumble"Copyright (C) 2025 The R Foundation for Statistical ComputingPlatform: aarch64-apple-darwin20R 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)> suppressWarnings(suppressPackageStartupMessages(library(cola)))> > test_check("cola")[ FAIL 0 | WARN 0 | SKIP 0 | PASS 18 ]> > > proc.time()   user  system elapsed   5.191   0.330   8.267