Movatterモバイル変換

################################################################################################################################################################## Running command:######   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:ASAFE.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings ASAFE_1.36.0.tar.gz###############################################################################################################################################################* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/ASAFE.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 ‘ASAFE/DESCRIPTION’ ... OK* checking extension type ... Package* this is package ‘ASAFE’ version ‘1.36.0’* 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 ‘ASAFE’ 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 sizes of PDF files under ‘inst/doc’ ... 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 ASAFE###############################################################################################################################################################* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library’* installing *source* package ‘ASAFE’ ...** this is package ‘ASAFE’ version ‘1.36.0’** using staged installation** R** data*** moving datasets to lazyload DB** 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** testing if installed package can be loaded from final location** testing if installed package keeps a record of temporary installation path* DONE (ASAFE)

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.> # The line you need to have R CMD check work,> # and avoid some weird error I got from R CMD check.> > Sys.setenv("R_TESTS" = "")> > # The following commands model off of > # https://github.com/hadley/testthat> > library(testthat)> library(ASAFE)> > test_check("ASAFE")[1] "alleles_1 and ancestries_1 have been defined so that\n          n is an 18-long vector of 1's,\n          algorithm_1snp(alleles_1, ancestries_1) =\n          em(n = replicate(n = 18, expr = 1), epsilon = 10^-8, iteration_cap = 1000).\n          algorithm_1snp(alleles_1, ancestries_1) = "[1] 0.5 0.5 0.5[1] "alleles are: "      rs1 rs2 [1,]   0   0 [2,]   0   0 [3,]   0   0 [4,]   0   0 [5,]   0   0 [6,]   0   0 [7,]   0   0 [8,]   0   0 [9,]   0   0[10,]   0   0[11,]   0   0[12,]   0   0[13,]   0   0[14,]   1   1[15,]   0   0[16,]   1   1[17,]   0   0[18,]   1   1[19,]   0   0[20,]   1   1[21,]   0   0[22,]   1   1[23,]   0   0[24,]   1   1[25,]   1   1[26,]   1   1[27,]   1   1[28,]   1   1[29,]   1   1[30,]   1   1[31,]   1   1[32,]   1   1[33,]   1   1[34,]   1   1[35,]   1   1[36,]   1   1[1] "ancestries are: "             [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11] [,12]ancestries_1    0    0    0    1    0    2    1    1    1     2     2     2ancestries_1    0    0    0    1    0    2    1    1    1     2     2     2             [,13] [,14] [,15] [,16] [,17] [,18] [,19] [,20] [,21] [,22] [,23]ancestries_1     0     0     0     1     0     2     1     1     1     2     2ancestries_1     0     0     0     1     0     2     1     1     1     2     2             [,24] [,25] [,26] [,27] [,28] [,29] [,30] [,31] [,32] [,33] [,34]ancestries_1     2     0     0     0     1     0     2     1     1     1     2ancestries_1     2     0     0     0     1     0     2     1     1     1     2             [,35] [,36]ancestries_1     2     2ancestries_1     2     2[1] "algorithm_1snp_wrapper(i = 1,\n                                  alleles = alleles,\n                                  ancestries = ancestries)"[1] "rs1" "0.5" "0.5" "0.5"[1] "algorithm_1snp_wrapper(i = 2,\n                                  alleles = alleles,\n                                  ancestries = ancestries)"[1] "rs2" "0.5" "0.5" "0.5"[1] "change_ancestry(anc = 0, error_rate = 1) should be 1 or 2"[1] 1[1] "change_ancestry(anc = 1, error_rate = 1) should be 0 or 2"[1] 0[1] "change_ancestry(anc = 2, error_rate = 1) should be 0 or 1"[1] 1[1] "draw_allele_given_anc(anc = 0, freqs = c(1, 0, 0)) should return 1"[1] "draw_allele_given_anc(anc = 0, freqs = c(0, 0, 0)) should return 0"[1] "draw_allele_given_anc(anc = 1, freqs = c(0, 1, 0)) should return 1"[1] "draw_allele_given_anc(anc = 1, freqs = c(0, 0, 0)) should return 0"[1] "draw_allele_given_anc(anc = 2, freqs = c(0, 0, 1)) should return 1"[1] "draw_allele_given_anc(anc = 2, freqs = c(0, 0, 0)) should return 0"[1] "draw_allele_given_anc(anc = 3, freqs = c(0, 0, 0)) should return error"[1] "em(n = replicate(n = 18, expr = 1),\n       epsilon = 10^-8, iteration_cap = 1000) = "[1] 0.5 0.5 0.5[1] "The following should run: "[1] "n_ind =  3"[1] "n_markers =  2"[1] "ancestries_matrix = "     [,1] [,2][1,]    0    0[2,]    0    0[3,]    1    1[4,]    1    1[5,]    2    2[6,]    2    2[1] "get_errors_1_scenario(p0 = 1, p1 = 1, p2 = 1,\n                                                ancestries_matrix_true = ancestries_matrix,\n                                                ancestries_matrix_estimated = ancestries_matrix)"       [,1]   [,2][1,] -3e-08 -3e-08[2,] -3e-08 -3e-08[3,] -3e-08 -3e-08[1] "The following should run: "[1] "n_ind =  3"[1] "n_markers =  2"[1] "ancestries_matrix = "     [,1] [,2][1,]    0    0[2,]    0    0[3,]    1    1[4,]    1    1[5,]    2    2[6,]    2    2[1] "get_errors_1_scenario(p0 = 1, p1 = 1, p2 = 1,\n                                                ancestries_matrix_true = ancestries_matrix,\n                                                ancestries_matrix_estimated = ancestries_matrix)"       [,1]   [,2][1,] -3e-08 -3e-08[2,] -3e-08 -3e-08[3,] -3e-08 -3e-08[1] "get_errors_summary_stats_1_scenario(p0 = 1, p1 = 1, p2 = 1,\n                                        ancestries_matrix_true = ancestries_matrix,\n                                        ancestries_matrix_estimated = ancestries_matrix)\n          takes mean error over snp columns, and errors across snps should be identical,\n          so mean errors should be the same as a column from the output of\n          the get_errors_1_scenario() call"     mean_errors sd_errors[1,]      -3e-08         0[2,]      -3e-08         0[3,]      -3e-08         0[1] "Constructing an example where I know what to expect\n          from this function."[1] "Say estimates are: "     rsid Freq1_Anc0 Freq1_Anc1 Freq1_Anc2[1,]    1       0.15       0.15       0.15[2,]    2       0.36       0.36       0.36[3,]    3       0.57       0.57       0.57[4,]    4       0.78       0.78       0.78[5,]    5       0.99       0.99       0.99[1] "Say truth is: "     rsid Freq1_Anc0 Freq1_Anc1 Freq1_Anc2[1,]    1        0.1        0.1        0.1[2,]    2        0.3        0.3        0.3[3,]    3        0.5        0.5        0.5[4,]    4        0.7        0.7        0.7[5,]    5        0.9        0.9        0.9[1] "Constructing an example where I know what to expect\n          from this function."[1] "Say estimates are: "     rsid Freq1_Anc0 Freq1_Anc1 Freq1_Anc2[1,]    1        0.1        0.1        0.1[2,]    2        0.1        0.1        0.1[3,]    3        0.1        0.1        0.1[4,]    4        0.9        0.9        0.9[5,]    5        0.9        0.9        0.9[6,]    6        0.9        0.9        0.9[1] "Say truth is: "     rsid Freq1_Anc0 Freq1_Anc1 Freq1_Anc2[1,]    1        0.2        0.2        0.2[2,]    2        0.2        0.2        0.2[3,]    3        0.5        0.5        0.5[4,]    4        0.5        0.5        0.5[5,]    5        0.8        0.8        0.8[6,]    6        0.8        0.8        0.8[1] "n_ind =  3"[1] "n_markers =  2"[1] "anc_spec_freqs = "     [,1] [,2] [,3][1,]  1.0  1.0  1.0[2,]  0.0  0.0  0.0[3,]  0.5  0.5  0.5[1] "ancestries_matrix = "     [,1] [,2][1,]    0    0[2,]    0    0[3,]    1    1[4,]    1    1[5,]    2    2[6,]    2    2[1] "get_results_error(error_rate = 0,\n           anc_spec_freqs, ancestries_matrix_true) = "                    p0  p1  p2     Mean          SDAbs_Error_Afr_Freq 1.0 1.0 1.0 -3.0e-08 0.00000e+00Abs_Error_Eur_Freq 1.0 1.0 1.0 -3.0e-08 0.00000e+00Abs_Error_NA_Freq  1.0 1.0 1.0 -3.0e-08 0.00000e+00Abs_Error_Afr_Freq 0.0 0.0 0.0  3.0e-08 0.00000e+00Abs_Error_Eur_Freq 0.0 0.0 0.0  3.0e-08 0.00000e+00Abs_Error_NA_Freq  0.0 0.0 0.0  3.0e-08 0.00000e+00Abs_Error_Afr_Freq 0.5 0.5 0.5  1.5e-08 2.12132e-08Abs_Error_Eur_Freq 0.5 0.5 0.5  0.0e+00 0.00000e+00Abs_Error_NA_Freq  0.5 0.5 0.5  1.5e-08 2.12132e-08[1] "get_results_error(error_rate = 1,\n           anc_spec_freqs, ancestries_matrix_true) = "                    p0  p1  p2         Mean           SDAbs_Error_Afr_Freq 1.0 1.0 1.0 -0.000000045 2.121320e-08Abs_Error_Eur_Freq 1.0 1.0 1.0 -0.000000025 7.071067e-09Abs_Error_NA_Freq  1.0 1.0 1.0 -0.000000030 0.000000e+00Abs_Error_Afr_Freq 0.0 0.0 0.0  0.000000045 2.121320e-08Abs_Error_Eur_Freq 0.0 0.0 0.0  0.000000025 7.071067e-09Abs_Error_NA_Freq  0.0 0.0 0.0  0.000000030 0.000000e+00Abs_Error_Afr_Freq 0.5 0.5 0.5 -0.499999970 7.071067e-01Abs_Error_Eur_Freq 0.5 0.5 0.5  0.333333333 4.714045e-01Abs_Error_NA_Freq  0.5 0.5 0.5  0.000000000 0.000000e+00[1] "anc_spec_freqs = "     [,1] [,2] [,3][1,]  1.0  1.0  1.0[2,]  0.0  0.0  0.0[3,]  0.5  0.5  0.5[1] "ancestries_matrix = "     [,1] [,2][1,]    0    0[2,]    0    0[3,]    1    1[4,]    1    1[5,]    2    2[6,]    2    2[1] "get_scenario_errors(row = 1, anc_spec_freqs = anc_spec_freqs,\n                        ancestries_matrix_true = ancestries_matrix,\n                        ancestries_matrix_estimated = ancestries_matrix)"     p0 p1 p2 mean_errors sd_errors[1,]  1  1  1      -3e-08         0[2,]  1  1  1      -3e-08         0[3,]  1  1  1      -3e-08         0[1] "get_scenario_errors(row = 2, anc_spec_freqs = anc_spec_freqs,\n                        ancestries_matrix_true = ancestries_matrix,\n                        ancestries_matrix_estimated = ancestries_matrix)"     p0 p1 p2 mean_errors sd_errors[1,]  0  0  0       3e-08         0[2,]  0  0  0       3e-08         0[3,]  0  0  0       3e-08         0[1] "get_scenario_errors(row = 3, anc_spec_freqs = anc_spec_freqs,\n                        ancestries_matrix_true = ancestries_matrix,\n                        ancestries_matrix_estimated = ancestries_matrix)"      p0  p1  p2   mean_errors    sd_errors[1,] 0.5 0.5 0.5 -3.000000e-08 0.000000e+00[2,] 0.5 0.5 0.5  0.000000e+00 0.000000e+00[3,] 0.5 0.5 0.5  2.974014e-17 4.242641e-08[1] "get_true_freqs_1snp(alleles_1 = c(0, 0, 1, 0, 1, 1),\n           ancestries_1 = c(0, 1, 0, 2, 1, 2))\n           should return [0.5, 0.5, 0.5]"[1] "sample_ancestry(0) = Should be something other than 0"[1] 2[1] "sample_ancestry(1) = Should be something other than 1"[1] 2[1] "sample_ancestry(2) = Should be something other than 2"[1] 1[ FAIL 0 | WARN 0 | SKIP 5 | PASS 63 ]══ Skipped tests (5) ═══════════════════════════════════════════════════════════• empty test (5): 'test_algorithm_1snp_wrapper.R:1:1',  'test_get_errors_1_scenario.R:1:1', 'test_get_results_error.R:1:1',  'test_get_scenario_errors.R:1:1', 'test_sample_ancestry.R:1:1'[ FAIL 0 | WARN 0 | SKIP 5 | PASS 63 ]> > # Note that in the directory tests/testthat,> # there's 1 test file per function. I like that format,> # because I don't have to scroll through a long file.> # Hadley does the same thing here: > # https://github.com/hadley/testthat/tree/master/tests/testthat.> > proc.time()   user  system elapsed   1.151   0.157   2.050