Running 'testthat.R' [65s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > 
  > library("testthat")
  > #library("vcfR")
  > #
  > #
  > test_check("vcfR")
  Loading required package: vcfR
  
     *****       ***   vcfR   ***       *****
     This is vcfR 1.8.0 
       browseVignettes('vcfR') # Documentation
       citation('vcfR') # Citation
     *****       *****      *****       *****
  
  == testthat results  ===========================================================
  [ OK: 474 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
  > 
  > 
  > #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 
    60.60    2.99   65.17 
  Error: failed to load sRGB colorspace file
  Execution halted