R Under development (unstable) (2025-06-03 r88266 ucrt) -- "Unsuffered Consequences" Copyright (C) 2025 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. > # 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/testing-design.html#sec-tests-files-overview > # * https://testthat.r-lib.org/articles/special-files.html > > library(testthat) > library(LBDiscover) Loading LBDiscover package > > test_check("LBDiscover") Filtered 2 B terms (100%) that weren't valid biomedical entities No suitable B terms found with association score > 0.1 after filtering Filtered 2 B terms (100%) that weren't valid biomedical entities No suitable B terms found with association score > 0.1 after filtering Filtered 2 B terms (100%) that weren't valid biomedical entities No suitable B terms found with association score > 0.1 after filtering Filtered 2 B terms (100%) that weren't valid biomedical entities No suitable B terms found with association score > 0.1 after filtering Filtered 2 B terms (100%) that weren't valid biomedical entities No suitable B terms found with association score > 0.1 after filtering No suitable B terms found with association score > 0.9 after filtering Using optimized approach for large matrix validation... Estimated document count: 1 Calculating statistical significance using hypergeometric test... 0.0% of connections are statistically significant (p < 0.05) Validating biomedical relevance of B terms... Retained 6 biomedically relevant B terms after filtering Validating biomedical relevance of C terms... Retained 16 biomedically relevant C terms after filtering Analyzing 16 potential C terms... | | | 0% | |==== | 6% | |========= | 12% | |============= | 19% | |================== | 25% | |====================== | 31% | |========================== | 38% | |=============================== | 44% | |=================================== | 50% | |======================================= | 56% | |============================================ | 62% | |================================================ | 69% | |==================================================== | 75% | |========================================================= | 81% | |============================================================= | 88% | |================================================================== | 94% | |======================================================================| 100% Validating biomedical relevance of B terms... Retained 6 biomedically relevant B terms after filtering Validating biomedical relevance of C terms... Retained 4 biomedically relevant C terms after filtering Analyzing 4 potential C terms... | | | 0% | |================== | 25% | |=================================== | 50% | |==================================================== | 75% | |======================================================================| 100% No AnC connections found Analyzing 26 potential C terms... | | | 0% | |=== | 4% | |===== | 8% | |======== | 12% | |=========== | 15% | |============= | 19% | |================ | 23% | |=================== | 27% | |====================== | 31% | |======================== | 35% | |=========================== | 38% | |============================== | 42% | |================================ | 46% | |=================================== | 50% | |====================================== | 54% | |======================================== | 58% | |=========================================== | 62% | |============================================== | 65% | |================================================ | 69% | |=================================================== | 73% | |====================================================== | 77% | |========================================================= | 81% | |=========================================================== | 85% | |============================================================== | 88% | |================================================================= | 92% | |=================================================================== | 96% | |======================================================================| 100% Analyzing 10 B terms... | | | 0% | |======= | 10% | |============== | 20% | |===================== | 30% | |============================ | 40% | |=================================== | 50% | |========================================== | 60% | |================================================= | 70% | |======================================================== | 80% | |=============================================================== | 90% | |======================================================================| 100% Performing SVD with 10 factors... Validating biomedical relevance of terms... Retained 7 biomedically relevant terms after validation Performing SVD with 10 factors... Number of unique terms: 20 First few terms: A_Term_1, A_Term_2, B_Term_2, B_Term_6, B_Term_9 Role assignments: A=2, B=10, C=8 Number of unique terms: 16 First few terms: A_Term_1, A_Term_2, B_Term_2, B_Term_6, B_Term_9 Role assignments: A=2, B=8, C=6 Number of unique terms: 20 First few terms: A_Term_1, A_Term_2, B_Term_2, B_Term_6, B_Term_9 Role assignments: A=2, B=10, C=8 Number of unique terms: 15 First few terms: A_Term_2, A_Term_1, B_Term_9, B_Term_8, B_Term_10 Role assignments: A=2, B=7, C=6 Number of unique terms: 15 First few terms: A_Term_2, A_Term_1, B_Term_9, B_Term_8, B_Term_10 Role assignments: A=2, B=7, C=6 Number of unique terms: 11 First few terms: A_Term_1, A_Term_2, B_Term_9, B_Term_6, B_Term_3 Role assignments: A=2, B=4, C=5 Number of unique terms: 13 First few terms: A_Term_1, A_Term_2, B_Term_9, Term with backslash, B_Term_5 Role assignments: A=2, B=5, C=6 Processing text in 1 chunks... | | | 0% | |======================================================================| 100% Processing text in 1 chunks... | | | 0% | |======================================================================| 100% Processing text in 1 chunks... | | | 0% | |======================================================================| 100% Processing text in 1 chunks... | | | 0% | |======================================================================| 100% Processing text in 1 chunks... | | | 0% | |======================================================================| 100% Processing text in 1 chunks... | | | 0% | |======================================================================| 100% Processing text in 1 chunks... | | | 0% | |======================================================================| 100% Processing text in 1 chunks... | | | 0% | |======================================================================| 100% Processing text in 1 chunks... | | | 0% | |======================================================================| 100% Enhancing 8 unique terms with umls information... | | | 0% | |========= | 12% | |================== | 25% | |========================== | 38% | |=================================== | 50% | |============================================ | 62% | |==================================================== | 75% | |============================================================= | 88% | |======================================================================| 100% Enhancing 8 unique terms with mesh information... | | | 0% | |========= | 12% | |================== | 25% | |========================== | 38% | |=================================== | 50% | |============================================ | 62% | |==================================================== | 75% | |============================================================= | 88% | |======================================================================| 100% ABC results are empty Generated comprehensive report: D:\temp\2025_06_04_06_30_16_7444\RtmpABQQ0d\filed65c22fa7671.html [ FAIL 0 | WARN 0 | SKIP 11 | PASS 202 ] ══ Skipped tests (11) ══════════════════════════════════════════════════════════ • On CRAN (1): 'test-network.R:179:3' • Skipping visualization tests in non-interactive mode (5): 'test-heatmap.R:45:3', 'test-heatmap.R:67:3', 'test-heatmap.R:112:3', 'test-network.R:45:3', 'test-network.R:66:3' • empty test (2): 'test-abc_model.R:60:1', 'test-abc_model.R:91:1' • igraph package is available (1): 'test-network.R:165:3' • interactive() && requireNamespace("rentrez", quietly = TRUE) is not TRUE (1): 'test-queries.R:138:3' • interactive() is not TRUE (1): 'test-queries.R:31:3' [ FAIL 0 | WARN 0 | SKIP 11 | PASS 202 ] > > proc.time() user system elapsed 4.31 0.85 8.71