R Under development (unstable) (2024-08-17 r87027 ucrt) -- "Unsuffered Consequences" Copyright (C) 2024 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( Haplin ) > > test_check( "Haplin" ) Checking family and id variables... Provided arguments: --- rows chosen: 4, 5, 15, 16, 17, 18 ... 1531, 1532, 1536, 1537, 1556, 1557 INFO: Will select 176 rows and 740 columns. Saving data... ... saved to files: ./my_data_onlyDyads_gen.ffData, ./my_data_onlyDyads_gen.RData Checking family and id variables... Provided arguments: --- rows chosen: 1, 2, 3, 6, 7, 8 ... 1550, 1551, 1552, 1553, 1554, 1555 INFO: Will select 1362 rows and 740 columns. Saving data... ... saved to files: ./my_data_onlyTriads_gen.ffData, ./my_data_onlyTriads_gen.RData Read 864 items 'n.vars' was not given explicitly and will be set to 6 based on the format given. Reading the data in chunks... -- chunk 1 -- Read 1433376 items -- chunk 2 -- Read 0 items ... done reading. Reading the marker names... ...done Preparing data... ... done preparing Saving data... ... saved to files: ./ped_read_gen.ffData, ./ped_read_gen.RData Read 6 items Read 6 items Reading the data in chunks... -- chunk 1 -- Read 1494 items -- chunk 2 -- Read 0 items ... done reading. Reading the marker names... ...done Preparing data... ... done preparing Saving data... ... saved to files: ./haplin_read_no_cov_gen.ffData, ./haplin_read_no_cov_gen.RData Read 8 items The format of the file is 'haplin' with covariate data but no names of the covariate data is given. Will generate dummy names. Reading the data in chunks... -- chunk 1 -- Read 9112 items ----------------------- Something's wrong with the separator in the following data values: [1] "AA" "AB" "AG" "BB" "GG" Read 8 items The format of the file is 'haplin' with covariate data but no names of the covariate data is given. Will generate dummy names. Reading the data in chunks... -- chunk 1 -- Read 9112 items -- chunk 2 -- Read 0 items ... done reading. Reading the marker names... ...done Preparing data... ... done preparing Saving data... ... saved to files: ./haplin_read_cov_gen.ffData, ./haplin_read_cov_gen.RData The output file(s) exist! Read 864 items 'n.vars' was not given explicitly and will be set to 6 based on the format given. Reading the data in chunks... -- chunk 1 -- Read 1433376 items -- chunk 2 -- Read 0 items ... done reading. Reading the marker names... ...done Preparing data... ... done preparing Reading covariate file... 'cov.header' not given - assuming the first line is the header... ...done Saving data... ... saved to files: ./ped_read_gen.ffData, ./ped_read_gen.RData The output file(s) exist! Read 864 items 'n.vars' was not given explicitly and will be set to 6 based on the format given. Reading the data in chunks... -- chunk 1 -- Read 1433376 items -- chunk 2 -- Read 0 items ... done reading. Reading the marker names... ...done Preparing data... ... done preparing Saving data... ... saved to files: ./ped_read_gen.ffData, ./ped_read_gen.RData The output file(s) exist! Read 6 items Reading the data in chunks... -- chunk 1 -- Read 1494 items -- chunk 2 -- Read 0 items ... done reading. Reading the marker names... ...done Preparing data... ... done preparing Saving data... ... saved to files: ./haplin_read_no_cov_gen.ffData, ./haplin_read_no_cov_gen.RData The output file(s) exist! Read 8 items The format of the file is 'haplin' with covariate data but no names of the covariate data is given. Will generate dummy names. Reading the data in chunks... -- chunk 1 -- Read 9112 items -- chunk 2 -- Read 0 items ... done reading. Reading the marker names... ...done Preparing data... ... done preparing Saving data... ... saved to files: ./haplin_read_cov_gen.ffData, ./haplin_read_cov_gen.RData The output file(s) exist! Read 864 items 'n.vars' was not given explicitly and will be set to 6 based on the format given. Reading the data in chunks... -- chunk 1 -- Read 1433376 items -- chunk 2 -- Read 0 items ... done reading. Reading the marker names... ...done Preparing data... ... done preparing Saving data... ... saved to files: ./ped_read_gen.ffData, ./ped_read_gen.RData The output file(s) exist! Read 6 items Reading the data in chunks... -- chunk 1 -- Read 1494 items -- chunk 2 -- Read 0 items ... done reading. Reading the marker names... ...done Preparing data... ... done preparing Saving data... ... saved to files: ./haplin_read_no_cov_gen.ffData, ./haplin_read_no_cov_gen.RData Provided arguments: --- chosen markers: 31, 32, 33, 34, 35, 36, 37, 38, 39, 40 INFO: Will select 1659 rows and 20 columns. Saving data... ... saved to files: ./my_data_part_gen.ffData, ./my_data_part_gen.RData The output file(s) exist! Provided arguments: --- chosen markers: 425, 426, 427, 428, 429, 430 Provided arguments: --- individual IDs: 1 INFO: Will select 550 rows and 858 columns. Saving data... ... saved to files: ./my_data_part_gen.ffData, ./my_data_part_gen.RData The output file(s) exist! Provided arguments: --- individual IDs: 100 Provided arguments: --- rows chosen: 2, 3, 4, 5, 6, 7, 8, 9, 10 INFO: Will select 9 rows and 858 columns. Saving data... ... saved to files: ./my_data_part_gen.ffData, ./my_data_part_gen.RData The output file(s) exist! Provided arguments: --- argument: cc, chosen values: 1 INFO: Will select 815 rows and 858 columns. Saving data... ... saved to files: ./my_data_part_gen.ffData, ./my_data_part_gen.RData The output file(s) exist! Provided arguments: --- argument: cc, chosen values: 2 Provided arguments: --- argument: sex, chosen values: 1 INFO: Will select 794 rows and 858 columns. Saving data... ... saved to files: ./my_data_part_gen.ffData, ./my_data_part_gen.RData The output file(s) exist! Provided arguments: --- argument: sex, chosen values: 3 Provided arguments: --- argument: cc, chosen values: 1 --- argument: sex, chosen values: 1 INFO: Will select 384 rows and 858 columns. Saving data... ... saved to files: ./my_data_part_gen.ffData, ./my_data_part_gen.RData The output file(s) exist! Provided arguments: --- chosen markers: 54, 55, 56 --- argument: cc, chosen values: 1 --- argument: sex, chosen values: 1 INFO: Will select 384 rows and 6 columns. Saving data... ... saved to files: ./my_data_part_gen.ffData, ./my_data_part_gen.RData The output file(s) exist! Read 6 items Reading the data in chunks... -- chunk 1 -- Read 1494 items -- chunk 2 -- Read 0 items ... done reading. Reading the marker names... ...done Preparing data... ... done preparing Saving data... ... saved to files: ./haplin_read_no_cov_gen.ffData, ./haplin_read_no_cov_gen.RData The output file(s) exist! Read 8 items The format of the file is 'haplin' with covariate data but no names of the covariate data is given. Will generate dummy names. Reading the data in chunks... -- chunk 1 -- Read 9112 items -- chunk 2 -- Read 0 items ... done reading. Reading the marker names... ...done Preparing data... ... done preparing Saving data... ... saved to files: ./haplin_read_cov_gen.ffData, ./haplin_read_cov_gen.RData The output file(s) exist! Provided arguments: --- chosen markers: 2 INFO: Will select 1139 rows and 6 columns. Saving data... ... saved to files: ./my_data_part_gen.ffData, ./my_data_part_gen.RData The output file(s) exist! Provided arguments: --- chosen markers: 3, 4 Provided arguments: --- individual IDs: 1 Provided arguments: --- rows chosen: 2, 3, 4, 5, 6, 7, 8, 9, 10 INFO: Will select 9 rows and 12 columns. Saving data... ... saved to files: ./my_data_part_gen.ffData, ./my_data_part_gen.RData The output file(s) exist! Provided arguments: --- argument: cc, chosen values: 1 Provided arguments: --- argument: cov.1, chosen values: 1, 3 INFO: Will select 286 rows and 12 columns. Saving data... ... saved to files: ./my_data_part_gen.ffData, ./my_data_part_gen.RData The output file(s) exist! Provided arguments: --- argument: cov.2, chosen values: 1 INFO: Will select 377 rows and 12 columns. Saving data... ... saved to files: ./my_data_part_gen.ffData, ./my_data_part_gen.RData The output file(s) exist! Provided arguments: --- argument: cov.2, chosen values: 3 Provided arguments: --- argument: cov.1, chosen values: 1, 3 --- argument: cov.2, chosen values: 0 INFO: Will select 179 rows and 12 columns. Saving data... ... saved to files: ./my_data_part_gen.ffData, ./my_data_part_gen.RData The output file(s) exist! Provided arguments: --- chosen markers: 1 --- argument: cov.1, chosen values: 1, 3 --- argument: cov.2, chosen values: 0 INFO: Will select 179 rows and 6 columns. Saving data... ... saved to files: ./my_data_part_gen.ffData, ./my_data_part_gen.RData The output file(s) exist! Provided arguments: The output file(s) exist! Read 864 items 'n.vars' was not given explicitly and will be set to 6 based on the format given. Reading the data in chunks... -- chunk 1 -- Read 1433376 items -- chunk 2 -- Read 0 items ... done reading. Reading the marker names... ...done Preparing data... ... done preparing Saving data... ... saved to files: ./ped_read_gen.ffData, ./ped_read_gen.RData The output file(s) exist! Read 6 items Reading the data in chunks... -- chunk 1 -- Read 1494 items -- chunk 2 -- Read 0 items ... done reading. Reading the marker names... ...done Preparing data... ... done preparing Saving data... ... saved to files: ./haplin_read_no_cov_gen.ffData, ./haplin_read_no_cov_gen.RData The output file(s) exist! Read 8 items The format of the file is 'haplin' with covariate data but no names of the covariate data is given. Will generate dummy names. Reading the data in chunks... -- chunk 1 -- Read 9112 items -- chunk 2 -- Read 0 items ... done reading. Reading the marker names... ...done Preparing data... ... done preparing Saving data... ... saved to files: ./haplin_read_cov_gen.ffData, ./haplin_read_cov_gen.RData Reading the marker names... ...done Recoding covariate data... ...done Recoding genetic data (no. of loci: 2)... ...running on only one CPU core! This may take some time... ...checking alleles per SNP... ...done, all alleles: A G B ...recoding SNPs... ...done Saving data... ... saved to files: ./haplin_prep_cov_gen.ffData , ./haplin_prep_cov_gen.RData Provided arguments: --- chosen markers: 110, 111 INFO: Will select 1659 rows and 4 columns. Saving data... ... saved to files: ./my_data_part_gen.ffData, ./my_data_part_gen.RData Reading the marker names... ...done Converting PED format to internal haplin... Creating unique IDs for individuals... ...done. Checking family and id variables... Sorting and re-coding families... Recoding covariate data... ...done Recoding genetic data (no. of loci: 2)... ...running on only one CPU core! This may take some time... ...checking alleles per SNP... ...done, all alleles: A T G ...recoding SNPs... ...done Saving data... ... saved to files: ./ped_prep_gen.ffData , ./ped_prep_gen.RData Reading the marker names... ...done Recoding covariate data... ...done Recoding genetic data (no. of loci: 2)... ...running on only one CPU core! This may take some time... ...checking alleles per SNP... ...done, all alleles: A G B ...recoding SNPs... ...done Saving data... ... saved to files: ./data_preprocessed_gen.ffData , ./data_preprocessed_gen.RData The output file(s) exist! Provided arguments: --- chosen markers: 110, 111 INFO: Will select 1659 rows and 4 columns. Saving data... ... saved to files: ./my_data_part_gen.ffData, ./my_data_part_gen.RData Reading the marker names... ...done Converting PED format to internal haplin... Creating unique IDs for individuals... ...done. Checking family and id variables... Sorting and re-coding families... Recoding covariate data... ...done Recoding genetic data (no. of loci: 2)... ...running on only one CPU core! This may take some time... ...checking alleles per SNP... ...done, all alleles: A T G ...recoding SNPs... ...done Saving data... ... saved to files: ./ped_cc_prep_gen.ffData , ./ped_cc_prep_gen.RData The output file(s) exist! Provided arguments: --- chosen markers: 110, 111 INFO: Will select 1659 rows and 4 columns. Saving data... ... saved to files: ./my_data_part_gen.ffData, ./my_data_part_gen.RData Reading the marker names... ...done Converting PED format to internal haplin... Creating unique IDs for individuals... ...done. Checking family and id variables... Sorting and re-coding families... Recoding covariate data... ...done Recoding genetic data (no. of loci: 2)... ...running on only one CPU core! This may take some time... ...checking alleles per SNP... ...done, all alleles: A T G ...recoding SNPs... ...done Saving data... ... saved to files: ./ped_env_prep_gen.ffData , ./ped_env_prep_gen.RData Creating unique IDs for individuals... ...done. Checking family and id variables... Provided arguments: --- rows chosen: 1, 4, 7, 10, 13, 16 ... 1642, 1645, 1648, 1651, 1654, 1657 INFO: Will select 559 rows and 858 columns. Saving data... ... saved to files: ./my_data_onlyChildren_gen.ffData, ./my_data_onlyChildren_gen.RData Creating unique IDs for individuals... ...done. Checking family and id variables... Provided arguments: --- rows chosen: 2, 5, 8, 11, 14, 17 ... 1643, 1646, 1649, 1652, 1655, 1658 INFO: Will select 550 rows and 858 columns. Saving data... ... saved to files: ./my_data_onlyMothers_gen.ffData, ./my_data_onlyMothers_gen.RData Creating unique IDs for individuals... ...done. Checking family and id variables... Provided arguments: --- rows chosen: 3, 6, 9, 12, 15, 18 ... 1644, 1647, 1650, 1653, 1656, 1659 INFO: Will select 550 rows and 858 columns. Saving data... ... saved to files: ./my_data_onlyFathers_gen.ffData, ./my_data_onlyFathers_gen.RData Creating unique IDs for individuals... ...done. Checking family and id variables... The output file(s) exist! Provided arguments: --- rows chosen: 1, 2, 3, 7, 8, 9 ... 1651, 1652, 1653, 1654, 1655, 1656 INFO: Will select 1398 rows and 858 columns. Saving data... ... saved to files: ./my_data_onlyTriads_gen.ffData, ./my_data_onlyTriads_gen.RData Creating unique IDs for individuals... ...done. Checking family and id variables... The output file(s) exist! Provided arguments: --- rows chosen: 4, 5, 16, 17, 19, 20 ... 1630, 1632, 1636, 1637, 1657, 1658 INFO: Will select 168 rows and 858 columns. Saving data... ... saved to files: ./my_data_onlyDyads_gen.ffData, ./my_data_onlyDyads_gen.RData INFO: No parallel environment selected. Will run in sequential mode. Running Haplin on Window 'm1' (1/2)...: done Running Haplin on Window 'm2' (2/2)...: done --- haplinSlide has completed --- INFO: No parallel environment selected. Will run in sequential mode. Running Haplin on Window 'm1' (1/2)...: done Running Haplin on Window 'm2' (2/2)...: done --- haplinSlide has completed --- INFO: No parallel environment selected. Will run in sequential mode. Running Haplin on Window 'm1' (1/2)...: done Running Haplin on Window 'm2' (2/2)...: done --- haplinSlide has completed --- INFO: No parallel environment selected. Will run in sequential mode. Running Haplin on Window 'm1' (1/2)...: done Running Haplin on Window 'm2' (2/2)...: done --- haplinSlide has completed --- INFO: No parallel environment selected. Will run in sequential mode. Running Haplin on Window 'm1' (1/2)...: done Running Haplin on Window 'm2' (2/2)...: done --- haplinSlide has completed --- INFO: No parallel environment selected. Will run in sequential mode. Running Haplin on Window 'm1' (1/2)...: done Running Haplin on Window 'm2' (2/2)...: done --- haplinSlide has completed --- INFO: No parallel environment selected. Will run in sequential mode. Running Haplin on Window 'm1' (1/2)...: done Running Haplin on Window 'm2' (2/2)...: done --- haplinSlide has completed --- INFO: No parallel environment selected. Will run in sequential mode. Running Haplin on Window 'm1' (1/2)...: done Running Haplin on Window 'm2' (2/2)...: done --- haplinSlide has completed --- INFO: No parallel environment selected. Will run in sequential mode. Running Haplin on Window 'm1' (1/2)...: done Running Haplin on Window 'm2' (2/2)...: done --- haplinSlide has completed --- INFO: No parallel environment selected. Will run in sequential mode. Running Haplin on Window 'm1' (1/2)...: done Running Haplin on Window 'm2' (2/2)...: done --- haplinSlide has completed --- INFO: No parallel environment selected. Will run in sequential mode. Running Haplin on Window 'm1' (1/2)...: done Running Haplin on Window 'm2' (2/2)...: done --- haplinSlide has completed --- INFO: No parallel environment selected. Will run in sequential mode. Running Haplin on Window 'm1' (1/2)...: done Running Haplin on Window 'm2' (2/2)...: done --- haplinSlide has completed --- INFO: No parallel environment selected. Will run in sequential mode. Running Haplin on Window 'm1' (1/2)...: done Running Haplin on Window 'm2' (2/2)...: done --- haplinSlide has completed --- INFO: No parallel environment selected. Will run in sequential mode. Running Haplin on Window 'm1' (1/2)...: done Running Haplin on Window 'm2' (2/2)...: done --- haplinSlide has completed --- INFO: No parallel environment selected. Will run in sequential mode. Running Haplin on Window 'm1' (1/2)...: done Running Haplin on Window 'm2' (2/2)...: done --- haplinSlide has completed --- INFO: No parallel environment selected. Will run in sequential mode. Running Haplin on Window 'm1' (1/2)...: done Running Haplin on Window 'm2' (2/2)...: done --- haplinSlide has completed --- INFO: No parallel environment selected. Will run in sequential mode. Running Haplin on Window 'm1' (1/2)...: done Running Haplin on Window 'm2' (2/2)...: done --- haplinSlide has completed --- INFO: No parallel environment selected. Will run in sequential mode. Running Haplin on Window 'm1' (1/2)...: done Running Haplin on Window 'm2' (2/2)...: done --- haplinSlide has completed --- INFO: No parallel environment selected. Will run in sequential mode. Running Haplin on Window 'm1' (1/2)...: done Running Haplin on Window 'm2' (2/2)...: done --- haplinSlide has completed --- INFO: No parallel environment selected. Will run in sequential mode. Running Haplin on Window 'm1' (1/2)...: done Running Haplin on Window 'm2' (2/2)...: done --- haplinSlide has completed --- INFO: No parallel environment selected. Will run in sequential mode. Running Haplin on Window 'm1' (1/2)...: done Running Haplin on Window 'm2' (2/2)...: done --- haplinSlide has completed --- INFO: No parallel environment selected. Will run in sequential mode. Running Haplin on Window 'm1' (1/2)...: done Running Haplin on Window 'm2' (2/2)...: done --- haplinSlide has completed --- INFO: No parallel environment selected. Will run in sequential mode. Running Haplin on Window 'm1' (1/2)...: done Running Haplin on Window 'm2' (2/2)...: done --- haplinSlide has completed --- INFO: No parallel environment selected. Will run in sequential mode. Running Haplin on Window 'm1' (1/2)...: done Running Haplin on Window 'm2' (2/2)...: done --- haplinSlide has completed --- [ FAIL 0 | WARN 0 | SKIP 12 | PASS 184 ] ══ Skipped tests (12) ══════════════════════════════════════════════════════════ • On CRAN (12): 'test_6_haplinSlide.R:7:2', 'test_6_haplinSlide.R:29:2', 'test_6_haplinSlide.R:51:2', 'test_6_haplinSlide.R:73:2', 'test_7_haplinStrat.R:25:2', 'test_7_haplinStrat.R:56:2', 'test_7_haplinStrat.R:86:2', 'test_7_haplinStrat.R:118:2', 'test_9_plotting.R:31:2', 'test_9_plotting.R:46:2', 'test_9_plotting.R:62:2', 'test_9_plotting.R:90:2' [ FAIL 0 | WARN 0 | SKIP 12 | PASS 184 ] Warning message: In .Internal(paste(list(...), sep, collapse, recycle0)) : closing unused connection 4 (HAPLIN.trialdata2.txt) > > proc.time() user system elapsed 36.09 4.40 71.03