Movatterモバイル変換

################################################################################################################################################################## Running command:######   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:GrafGen.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings GrafGen_1.6.0.tar.gz###############################################################################################################################################################* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/GrafGen.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 ‘GrafGen/DESCRIPTION’ ... OK* this is package ‘GrafGen’ version ‘1.6.0’* 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 ‘GrafGen’ can be installed ... WARNINGFound the following significant warnings:  ./GrafPop.h:1:17: warning: using directive refers to implicitly-defined namespace 'std'See ‘/Users/biocbuild/bbs-3.22-bioc/meat/GrafGen.Rcheck/00install.out’ for details.* used C compiler: ‘Apple clang version 15.0.0 (clang-1500.0.40.1)’* used C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.0.40.1)’* used SDK: ‘MacOSX11.3.1.sdk’* checking installed package size ... OK* checking package directory ... OK* checking ‘build’ directory ... OK* checking DESCRIPTION meta-information ... OK* 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 ... OK* checking Rd files ... OK* 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 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 elapsedgrafGen 4.605  0.171    6.54* checking for unstated dependencies in ‘tests’ ... OK* checking tests ...  Running ‘runTests.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: 1 WARNING, 1 NOTESee  ‘/Users/biocbuild/bbs-3.22-bioc/meat/GrafGen.Rcheck/00check.log’for details.

################################################################################################################################################################## Running command:######   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL GrafGen###############################################################################################################################################################* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library’* installing *source* package ‘GrafGen’ ...** this is package ‘GrafGen’ version ‘1.6.0’** using staged installation** libsusing C compiler: ‘Apple clang version 15.0.0 (clang-1500.0.40.1)’using 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/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c AncestrySnps.cpp -o AncestrySnps.oclang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c BedFileSnpGeno.cpp -o BedFileSnpGeno.oclang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c BimFileAncestrySnps.cpp -o BimFileAncestrySnps.oBimFileAncestrySnps.cpp:144:9: warning: variable 'numSwaps' set but not used [-Wunused-but-set-variable]    int numSwaps = 0;        ^1 warning generated.clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c FamFileSamples.cpp -o FamFileSamples.oFamFileSamples.cpp:65:9: warning: variable 'lineNo' set but not used [-Wunused-but-set-variable]    int lineNo = 0;        ^1 warning generated.clang -arch arm64 -std=gnu2x -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c GrafGenHp_init.c -o GrafGenHp_init.oclang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c GrafPop.cpp -o GrafPop.oIn file included from GrafPop.cpp:1:./GrafPop.h:1:17: warning: using directive refers to implicitly-defined namespace 'std'using namespace std;                ^1 warning generated.clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c SampleGenoAncestry.cpp -o SampleGenoAncestry.oclang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c SampleGenoDist.cpp -o SampleGenoDist.oclang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c Util.cpp -o Util.oclang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c VcfSampleAncestrySnpGeno.cpp -o VcfSampleAncestrySnpGeno.oVcfSampleAncestrySnpGeno.cpp:93:9: warning: variable 'buffNo' set but not used [-Wunused-but-set-variable]    int buffNo = 0;        ^VcfSampleAncestrySnpGeno.cpp:312:9: warning: variable 'ancSnpNo' set but not used [-Wunused-but-set-variable]    int ancSnpNo = 0;  // Final list of ancestry SNPs to be used for ancestry inference        ^2 warnings generated.clang++ -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 GrafGen.so AncestrySnps.o BedFileSnpGeno.o BimFileAncestrySnps.o FamFileSamples.o GrafGenHp_init.o GrafPop.o SampleGenoAncestry.o SampleGenoDist.o Util.o VcfSampleAncestrySnpGeno.o -F/Library/Frameworks/R.framework/.. -framework Rinstalling to /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/00LOCK-GrafGen/00new/GrafGen/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 (GrafGen)

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.> BiocGenerics:::testPackage("GrafGen")RUNIT TEST PROTOCOL -- Sat Dec 13 06:39:35 2025 *********************************************** Number of test functions: 2 Number of errors: 0 Number of failures: 0  1 Test Suite : GrafGen RUnit Tests - 2 test functions, 0 errors, 0 failuresNumber of test functions: 2 Number of errors: 0 Number of failures: 0 > > proc.time()   user  system elapsed   4.525   0.281   6.536