R Under development (unstable) (2023-12-04 r85659 ucrt) -- "Unsuffered Consequences" Copyright (C) 2023 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 R 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("vcfR") > # > # > test_check("vcfR") Loading required package: vcfR ***** *** vcfR *** ***** This is vcfR 1.15.0 browseVignettes('vcfR') # Documentation citation('vcfR') # Citation ***** ***** ***** ***** [ FAIL 0 | WARN 0 | SKIP 0 | PASS 495 ] > > > #test_file("testthat/test_10_write_vcf.R") > #test_file("testthat/test_1_vcf.R") > #test_file("testthat/test_2_chromR.R") > #test_file("testthat/test_3_extract_gt.R") > #test_file("testthat/test_4_vcfR2DNAbin.R") > #test_file("testthat/test_io.R") > #test_file("testthat/test_proc_chromR.R") > #test_file("testthat/test_conversion.R") > #test_file("testthat/test_vcfR_methods.R") > #test_file("testthat/test_chromR_method.R") > #test_file("testthat/test_addID.R") > #test_file("testthat/test_maf.R") > #test_file("testthat/test_genotype_matrix_functions.R") > #test_file("testthat/test_vcfRtidy.R") > #test_file("testthat/test_ad_frequency.R") > #test_file("testthat/test_freq_peak.R") > #test_file("testthat/test_is_het.R") > #test_file("testthat/test_get.R") > #test_file("testthat/test_genetic_diff.R") > #test_file("testthat/test_INFO2df.R") > #test_file("testthat/test_query_gt.R") > #test_file("testthat/test_queryMETA.R") > #test_file("testthat/test_summary_tables.R") > #test_file("testthat/test_heatmapbp.R") > #test_file("testthat/test_vcfR2migrate.R") > > > # This test will write the plots to a file on the filesystem. > # This should cause CRAN to complain. > # Comment out this test prior to CRAN submission. > # > #test_file("testthat/test_chromo_plot.R") > #test_file("testthat/test_drplot.R") > > > > ##### ##### ##### ##### ##### > > > #test_file("testthat/test_rank_variants.R") > > #test_file("testthat/test_var_window.R") > > > > ##### ##### ##### ##### ##### > # Notes on debugging compiled code. > > # lldg gdb > # http://kevinushey.github.io/blog/2015/04/13/debugging-with-lldb/ > > # R -d gdb > # run > # q() > # quit > > # Also control-c returns to gdb. > # continue returns from gdb to R (plus a second return) > > # in gdb > # b rcppMean > # sets a breakpoint at the function rcppMean > > # b read_body_gz > # c > > # breakpoint set --line 46 > > > > # valgrind > # http://kevinushey.github.io/blog/2015/04/05/debugging-with-valgrind/ > > # R -d "valgrind --db-attach=yes" -f test_1_vcf.R > # R -d "valgrind --track-origins=yes" -f test_1_vcf.R > > # R -d "valgrind --track-origins=yes" -f testthat/test_conversion.R > # R -d "valgrind --track-origins=yes" -f testthat/test_windowing.R > > > # 2016-08-05 > > # R -d "valgrind --leak-check=full --vgdb-error=1" -f tests/testthat/test_1_vcf.R > # R -d "valgrind --leak-check=full --vgdb-error=1" -f tests/testthat/test_10_write_vcf.R > # R -d "valgrind --leak-check=full --vgdb-error=1" -f tests/testthat/test_freq_peak.R > > # R -d "valgrind --leak-check=full --vgdb-error=1" -f tests/testthat/test_3_extract_gt.R > > > # R -d "valgrind --leak-check=full --vgdb-error=1" -f tests/testthat/test_conversion.R > # R -d "valgrind --leak-check=full --vgdb-error=1" -f tests/testthat/test_conversion.R > > # R -d "valgrind --leak-check=full --vgdb-error=1" -f tests/testthat.R > > # R -d "valgrind --leak-check=full --vgdb-error=1" -f tests/testthat.R --restore --save --no-readline --vanilla > log.txt 2>&1 > > > ##### ##### ##### ##### ##### > # g++ > > # g++ -std=c++0x -I"C:/PROGRA~1/R/R-33~1.2/include" -DNDEBUG -I"C:/Users/USERtqITJhLcoQ/R/Rcpp/include" -I"d:/Compiler/gcc-4.9.3/local330/include" -O2 -Wall -mtune=core2 -c gt_to_popsum.cpp -o gt_to_popsum.o > # g++ -std=c++11 -I/usr/share/R/include -DNDEBUG -I"/home/knausb/R/x86_64-pc-linux-gnu-library/3.3/Rcpp/include" -fpic -g -O2 -fstack-protector-strong -Wsign-compare -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c gt_to_popsum.cpp -o gt_to_popsum.o > > > # g++ -std=c++11 -fsanitize=address -fno-omit-frame-pointer -I/usr/share/R/include -DNDEBUG -I"/home/local/USDA-ARS/knausb/R/x86_64-pc-linux-gnu-library/3.3/Rcpp/include" -fpic -g -O2 -fstack-protector-strong -Wsign-compare -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c extractGT2NM.cpp -o extractGT2NM.o > > > > > > ##### ##### ##### ##### ##### > # EOF. > > proc.time() user system elapsed 34.51 1.32 35.84