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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/tests.html > # * https://testthat.r-lib.org/reference/test_package.html#special-files > > library(testthat) > library(kmeRtone) > > testthat::test_check("kmeRtone") ------------------------------------------------------------ Extraction of Case K-mers ------------------------------------------------------------ % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 0 70.3M 0 7892 0 0 11773 0 1:44:26 --:--:-- 1:44:26 11814 2 70.3M 2 1578k 0 0 951k 0 0:01:15 0:00:01 0:01:14 952k 24 70.3M 24 17.4M 0 0 7051k 0 0:00:10 0:00:02 0:00:08 7056k 56 70.3M 56 39.6M 0 0 11.0M 0 0:00:06 0:00:03 0:00:03 11.0M 88 70.3M 88 61.9M 0 0 13.3M 0 0:00:05 0:00:04 0:00:01 13.3M 100 70.3M 100 70.3M 0 0 14.0M 0 0:00:05 0:00:05 --:--:-- 16.1M % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 0 74.6M 0 7892 0 0 11793 0 1:50:34 --:--:-- 1:50:34 11814 2 74.6M 2 1578k 0 0 952k 0 0:01:20 0:00:01 0:01:19 953k 26 74.6M 26 19.4M 0 0 7804k 0 0:00:09 0:00:02 0:00:07 7809k 50 74.6M 50 37.9M 0 0 10.5M 0 0:00:07 0:00:03 0:00:04 10.5M 75 74.6M 75 56.5M 0 0 12.4M 0 0:00:06 0:00:04 0:00:02 12.4M 100 74.6M 100 74.6M 0 0 14.0M 0 0:00:05 0:00:05 --:--:-- 16.0M % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 0 61.0M 0 47892 0 0 57420 0 0:18:35 --:--:-- 0:18:35 57562 4 61.0M 4 2601k 0 0 1423k 0 0:00:43 0:00:01 0:00:42 1425k 31 61.0M 31 19.5M 0 0 7251k 0 0:00:08 0:00:02 0:00:06 7256k 65 61.0M 65 40.1M 0 0 10.5M 0 0:00:05 0:00:03 0:00:02 10.5M 100 61.0M 100 61.0M 0 0 12.9M 0 0:00:04 0:00:04 --:--:-- 12.9M % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 0 58.8M 0 374k 0 0 282k 0 0:03:33 0:00:01 0:03:32 282k 16 58.8M 16 9.9M 0 0 4692k 0 0:00:12 0:00:02 0:00:10 4695k 54 58.8M 54 31.7M 0 0 9.8M 0 0:00:05 0:00:03 0:00:02 9.8M 91 58.8M 91 53.9M 0 0 12.5M 0 0:00:04 0:00:04 --:--:-- 12.5M 100 58.8M 100 58.8M 0 0 13.1M 0 0:00:04 0:00:04 --:--:-- 13.6M % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 0 55.6M 0 187k 0 0 161k 0 0:05:54 0:00:01 0:05:53 161k 14 55.6M 14 8492k 0 0 3878k 0 0:00:14 0:00:02 0:00:12 3881k 48 55.6M 48 27.0M 0 0 8841k 0 0:00:06 0:00:03 0:00:03 8844k 81 55.6M 81 45.4M 0 0 11.1M 0 0:00:04 0:00:04 --:--:-- 11.1M 100 55.6M 100 55.6M 0 0 12.4M 0 0:00:04 0:00:04 --:--:-- 12.9M Extracting 2-mers from chr1.............DONE! -- 11.42 secs Extracting 2-mers from chr2.............DONE! -- 10.89 secs Extracting 2-mers from chr3.............DONE! -- 9.58 secs Extracting 2-mers from chr4.............DONE! -- 9.14 secs Extracting 2-mers from chr5.............DONE! -- 8.77 secs Downloading chr1.fa.gz from UCSC... Downloading chr2.fa.gz from UCSC... Downloading chr3.fa.gz from UCSC... Downloading chr4.fa.gz from UCSC... Downloading chr5.fa.gz from UCSC... Total time taken: 50.04 secs ------------------------------------------------------------ Extraction of Control K-mers ------------------------------------------------------------ Building control regions of chr1........DONE! -- 4.77 secs Building control regions of chr2........DONE! -- 4.39 secs Building control regions of chr3........DONE! -- 3.85 secs Building control regions of chr4........DONE! -- 3.63 secs Building control regions of chr5........DONE! -- 3.51 secs Total time taken: 20.23 secs Extracting 2-mers from chr1.............DONE! -- 5.03 secs Extracting 2-mers from chr2.............DONE! -- 3.96 secs Extracting 2-mers from chr3.............DONE! -- 3.99 secs Extracting 2-mers from chr4.............DONE! -- 3.94 secs Extracting 2-mers from chr5.............DONE! -- 3.45 secs Total time taken: 20.55 secs ------------------------------------------------------------ Calculation of K-mer Susceptibility ------------------------------------------------------------ The 2-mer scores are saved at D:\temp\Rtmp69HSIr/score_2-mer.csv FINISH! Total time taken: 1.51 mins [ FAIL 0 | WARN 0 | SKIP 0 | PASS 2 ] > > proc.time() user system elapsed 61.10 4.18 93.68