Movatterモバイル変換

################################################################################################################################################################## Running command:######   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:Summix.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings Summix_2.16.0.tar.gz###############################################################################################################################################################* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/Summix.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 ‘Summix/DESCRIPTION’ ... OK* this is package ‘Summix’ version ‘2.16.0’* package encoding: UTF-8* 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 ‘Summix’ can be installed ... OK* 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 LazyData ... OK* checking data for ASCII and uncompressed saves ... OK* checking files in ‘vignettes’ ... OK* checking examples ... OK* 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* DONEStatus: OK

################################################################################################################################################################## Running command:######   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL Summix###############################################################################################################################################################* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library’* installing *source* package ‘Summix’ ...** this is package ‘Summix’ version ‘2.16.0’** using staged installation** R** data*** moving datasets to lazyload DB** inst** byte-compile and prepare package for lazy loading** help*** installing help indices*** copying figures** building package indices** installing vignettes** testing if installed package can be loaded from temporary location** testing if installed package can be loaded from final location** testing if installed package keeps a record of temporary installation path* DONE (Summix)

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.> # This file is part of the standard setup for testthat.> # It is recommended that you do not modify it.> #> # Where should you do additional test configuration?> # Learn more about the roles of various files in:> # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview> # * https://testthat.r-lib.org/articles/special-files.html> > library(testthat)> library(Summix)> > test_check("Summix")[1] "Note: In this AF adjustment, 0 SNPs (with adjusted AF > -.005 & < 0) were rounded to 0. 0 SNPs (with adjusted AF > 1) were rounded to 1, and 0 SNPs (with adjusted AF <= -.005) were removed from the final results."[1] $pi         ref.group pi.observed pi.target1 reference_AF_afr        0.85         12 reference_AF_eur        0.15         0[1] $observed.data[1] "observed AF data to update: 'gnomad_AF_afr'"[1] $Nsnps[1] 1000[1] $effective.sample.size[1] 18336[1] "use $adjusted.AF$adjustedAF to see adjusted AF data"[1] "Note: The accuracy of the AF adjustment is likely lower for rare variants (< .5%)."[1] "Done getting LA proportions"[ FAIL 0 | WARN 38 | SKIP 0 | PASS 3 ][ FAIL 0 | WARN 38 | SKIP 0 | PASS 3 ]> > proc.time()   user  system elapsed   5.228   0.336   7.853