* using log directory ‘/srv/hornik/tmp/CRAN_pretest/AgeTopicModels.Rcheck’ * using R Under development (unstable) (2025-09-16 r88844) * using platform: x86_64-pc-linux-gnu * R was compiled by Debian clang version 19.1.7 (3+b1) Debian flang-new version 19.1.7 (3+b1) * running under: Debian GNU/Linux forky/sid * using session charset: UTF-8 * checking for file ‘AgeTopicModels/DESCRIPTION’ ... OK * this is package ‘AgeTopicModels’ version ‘0.1.0’ * package encoding: UTF-8 * checking CRAN incoming feasibility ... [4s/7s] NOTE Maintainer: ‘Xilin Jiang ’ New submission Size of tarball: 5025239 bytes * 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 executable files ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘AgeTopicModels’ can be installed ... [10s/10s] OK * checking package directory ... OK * checking for future file timestamps ... 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 ... [1s/1s] OK * checking whether the package can be loaded with stated dependencies ... [1s/1s] OK * checking whether the package can be unloaded cleanly ... [1s/1s] OK * checking whether the namespace can be loaded with stated dependencies ... [1s/1s] OK * checking whether the namespace can be unloaded cleanly ... [1s/1s] OK * checking loading without being on the library search path ... [1s/1s] OK * checking use of S3 registration ... 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 ... [8s/8s] OK * checking Rd files ... [0s/0s] OK * checking Rd metadata ... OK * checking Rd line widths ... 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 ... [1s/1s] OK * checking LazyData ... OK * checking data for ASCII and uncompressed saves ... OK * checking examples ... [20s/20s] OK * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... [90s/90s] ERROR Running ‘testthat.R’ [90s/90s] Running the tests in ‘tests/testthat.R’ failed. Complete output: > # 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(AgeTopicModels) > > test_check("AgeTopicModels") [1] "ATM RAM occupation: " 0 GB [1] "Disease code that have less than 5 entries will be removed." [1] "CVB inference number: 1" [1] "ATM RAM occupation: " 0 GB [1] "Interation: 1" [1] "Interation: 2" [1] "Interation: 3" [1] "Interation: 4" [1] "Interation: 5" [1] "Current Lower bound -22065.2523489598 at iteration: 5" [1] "Interation: 6" [1] "Interation: 7" [1] "Interation: 8" [1] "Interation: 9" [1] "Interation: 10" [1] "Current Lower bound -22045.1235988759 at iteration: 10" [1] "Interation: 11" [1] "Interation: 12" [1] "Interation: 13" [1] "Interation: 14" [1] "Interation: 15" [1] "Current Lower bound -22030.7394158993 at iteration: 15" [1] "Interation: 16" [1] "Interation: 17" [1] "Interation: 18" [1] "Interation: 19" [1] "Interation: 20" [1] "Current Lower bound -22017.2046833795 at iteration: 20" [1] "Interation: 21" [1] "Interation: 22" [1] "Interation: 23" [1] "Interation: 24" [1] "Interation: 25" [1] "Current Lower bound -22006.0480392512 at iteration: 25" [1] "Interation: 26" [1] "Interation: 27" [1] "Interation: 28" [1] "Interation: 29" [1] "Interation: 30" [1] "Current Lower bound -21999.9765364461 at iteration: 30" [1] "Interation: 31" [1] "Interation: 32" [1] "Interation: 33" [1] "Interation: 34" [1] "Interation: 35" [1] "Current Lower bound -21998.3267039331 at iteration: 35" [1] "Interation: 36" [1] "Interation: 37" [1] "Interation: 38" [1] "Interation: 39" [1] "Interation: 40" [1] "Current Lower bound -21997.7742021957 at iteration: 40" [1] "Interation: 41" [1] "Interation: 42" [1] "Interation: 43" [1] "Interation: 44" [1] "Interation: 45" [1] "Current Lower bound -22000.2498192226 at iteration: 45" [1] "Optimization converged at step 45" [1] "Number of diseases selected: 7" [1] "LFA RAM occupation: " 0.7 GB [1] "ATM RAM occupation: " 0 GB [1] "ATM RAM occupation: " 0 GB [1] "Interation: 1" [1] "Current Lower bound -6441.74549764809 at iteration: 1" [1] "Interation: 2" [1] "Current Lower bound -6441.74549764809 at iteration: 2" [1] "Optimization converged at step 2" [1] "ATM RAM occupation: " 0 GB [1] "Interation: 1" [1] "Current Lower bound -13069.6386416008 at iteration: 1" [1] "Interation: 2" [1] "Current Lower bound -13054.0460157405 at iteration: 2" [1] "Interation: 3" [1] "Current Lower bound -13054.0500274849 at iteration: 3" [1] "Optimization converged at step 3" [1] "ATM RAM occupation: " 0 GB [1] "Interation: 1" [1] "Current Lower bound -19722.8677347417 at iteration: 1" [1] "Interation: 2" [1] "Current Lower bound -19677.9397846554 at iteration: 2" [1] "Interation: 3" [1] "Current Lower bound -19677.5671341822 at iteration: 3" [1] "Interation: 4" [1] "Current Lower bound -19677.5238814901 at iteration: 4" [1] "Interation: 5" [1] "Current Lower bound -19677.519351279 at iteration: 5" [1] "Optimization converged at step 5" [1] "ATM RAM occupation: " 0 GB [1] "Interation: 1" [1] "Current Lower bound -26503.3247335579 at iteration: 1" [1] "Interation: 2" [1] "Current Lower bound -26421.1541716556 at iteration: 2" [1] "Interation: 3" [1] "Current Lower bound -26419.9252982012 at iteration: 3" [1] "Interation: 4" [1] "Current Lower bound -26419.7749537872 at iteration: 4" [1] "Interation: 5" [1] "Current Lower bound -26419.7515518041 at iteration: 5" [1] "Optimization converged at step 5" [1] "ATM RAM occupation: " 0 GB [1] "ATM RAM occupation: " 0 GB [1] "Interation: 1" [1] "Current Lower bound -6441.74549764809 at iteration: 1" [1] "Interation: 2" [1] "Current Lower bound -6441.74549764809 at iteration: 2" [1] "Optimization converged at step 2" [1] "ATM RAM occupation: " 0 GB [1] "ATM RAM occupation: " 0 GB [1] "Interation: 1" [1] "Current Lower bound -13069.713329535 at iteration: 1" [1] "Interation: 2" [1] "Current Lower bound -13054.0466040902 at iteration: 2" [1] "Interation: 3" [1] "Current Lower bound -13054.0499050412 at iteration: 3" [1] "Interation: 4" [1] "Current Lower bound -13054.0519788838 at iteration: 4" [1] "Interation: 5" [1] "Current Lower bound -13054.0531345281 at iteration: 5" [1] "Optimization converged at step 5" [1] "ATM RAM occupation: " 0 GB [1] "ATM RAM occupation: " 0 GB [1] "Interation: 1" [1] "Current Lower bound -19722.289912669 at iteration: 1" [1] "Interation: 2" [1] "Current Lower bound -19677.920987231 at iteration: 2" [1] "Interation: 3" [1] "Current Lower bound -19677.5616705449 at iteration: 3" [1] "Interation: 4" [1] "Current Lower bound -19677.5224504241 at iteration: 4" [1] "Interation: 5" [1] "Current Lower bound -19677.5189699113 at iteration: 5" [1] "Interation: 6" [1] "Current Lower bound -19677.517351052 at iteration: 6" [1] "Optimization converged at step 6" [1] "ATM RAM occupation: " 0 GB [1] "ATM RAM occupation: " 0 GB [1] "Interation: 1" [1] "Current Lower bound -26503.4763196834 at iteration: 1" [1] "Interation: 2" [1] "Current Lower bound -26421.1528415311 at iteration: 2" [1] "Interation: 3" [1] "Current Lower bound -26419.9221127337 at iteration: 3" [1] "Interation: 4" [1] "Current Lower bound -26419.7744791889 at iteration: 4" [1] "Interation: 5" [1] "Current Lower bound -26419.7513904143 at iteration: 5" [1] "Interation: 6" [1] "Current Lower bound -26419.7441428605 at iteration: 6" [1] "Interation: 7" [1] "Current Lower bound -26419.7421573661 at iteration: 7" [1] "Optimization converged at step 7" [1] "ATM RAM occupation: " 0 GB [1] "Interation: 1" [1] "Current Lower bound -6593.3340779008 at iteration: 1" [1] "Interation: 2" [1] "Current Lower bound -6593.3340779008 at iteration: 2" [1] "Optimization converged at step 2" [1] "ATM RAM occupation: " 0 GB [1] "Interation: 1" [1] "Current Lower bound -13403.5772291058 at iteration: 1" [1] "Interation: 2" [1] "Current Lower bound -13386.7053616365 at iteration: 2" [1] "Interation: 3" [1] "Current Lower bound -13386.7077626532 at iteration: 3" [1] "Optimization converged at step 3" [1] "ATM RAM occupation: " 0 GB [1] "Interation: 1" [1] "Current Lower bound -20253.8730069674 at iteration: 1" [1] "Interation: 2" [1] "Current Lower bound -20208.186270061 at iteration: 2" [1] "Interation: 3" [1] "Current Lower bound -20207.8593094506 at iteration: 3" [1] "Interation: 4" [1] "Current Lower bound -20207.8232202125 at iteration: 4" [1] "Interation: 5" [1] "Current Lower bound -20207.8199119111 at iteration: 5" [1] "Optimization converged at step 5" [1] "ATM RAM occupation: " 0 GB [1] "Interation: 1" [1] "Current Lower bound -27306.599179581 at iteration: 1" [1] "Interation: 2" [1] "Current Lower bound -27218.5547133527 at iteration: 2" [1] "Interation: 3" [1] "Current Lower bound -27217.2636510211 at iteration: 3" [1] "Interation: 4" [1] "Current Lower bound -27217.1058155457 at iteration: 4" [1] "Interation: 5" [1] "Current Lower bound -27217.080650976 at iteration: 5" [1] "Optimization converged at step 5" [1] "ATM RAM occupation: " 0 GB [1] "ATM RAM occupation: " 0 GB [1] "Interation: 1" [1] "Current Lower bound -6593.3340779008 at iteration: 1" [1] "Interation: 2" [1] "Current Lower bound -6593.3340779008 at iteration: 2" [1] "Optimization converged at step 2" [1] "ATM RAM occupation: " 0 GB [1] "ATM RAM occupation: " 0 GB [1] "Interation: 1" [1] "Current Lower bound -13402.1058028171 at iteration: 1" [1] "Interation: 2" [1] "Current Lower bound -13386.704036245 at iteration: 2" [1] "Interation: 3" [1] "Current Lower bound -13386.7075370014 at iteration: 3" [1] "Interation: 4" [1] "Current Lower bound -13386.7065961855 at iteration: 4" [1] "Optimization converged at step 4" [1] "ATM RAM occupation: " 0 GB [1] "ATM RAM occupation: " 0 GB [1] "Interation: 1" [1] "Current Lower bound -20250.0747774364 at iteration: 1" [1] "Interation: 2" [1] "Current Lower bound -20208.1710493718 at iteration: 2" [1] "Interation: 3" [1] "Current Lower bound -20207.8644995858 at iteration: 3" [1] "Interation: 4" [1] "Current Lower bound -20207.8244155642 at iteration: 4" [1] "Interation: 5" [1] "Current Lower bound -20207.8203058235 at iteration: 5" [1] "Interation: 6" [1] "Current Lower bound -20207.8185219795 at iteration: 6" [1] "Optimization converged at step 6" [1] "ATM RAM occupation: " 0 GB [1] "ATM RAM occupation: " 0 GB [1] "Interation: 1" [1] "Current Lower bound -27295.1889697687 at iteration: 1" [1] "Interation: 2" [1] "Current Lower bound -27218.4198663007 at iteration: 2" [1] "Interation: 3" [1] "Current Lower bound -27217.2554406248 at iteration: 3" [1] "Interation: 4" [1] "Current Lower bound -27217.1054557151 at iteration: 4" [1] "Interation: 5" [1] "Current Lower bound -27217.0806862614 at iteration: 5" [1] "Interation: 6" [1] "Current Lower bound -27217.0733276404 at iteration: 6" [1] "Interation: 7" [1] "Current Lower bound -27217.0713947053 at iteration: 7" [1] "Optimization converged at step 7" [1] "simulated alpha: 0.829773873739859" "simulated alpha: 0.88501810186966" [3] "simulated alpha: 1.11218076166064" [ FAIL 1 | WARN 15 | SKIP 1 | PASS 17 ] ══ Skipped tests (1) ═══════════════════════════════════════════════════════════ • empty test (1): 'test-lfa.R:14:1' ══ Failed tests ════════════════════════════════════════════════════════════════ ── Failure ('test-simulated_data.R:37:3'): Simulate genetic data ─────────────── sum(summary(md1)$coefficients[2:21, 4] < 0.05) is not strictly more than 5. Difference: 0 [ FAIL 1 | WARN 15 | SKIP 1 | PASS 17 ] Error: Test failures Execution halted * checking PDF version of manual ... [3s/3s] OK * checking HTML version of manual ... [0s/0s] OK * checking for non-standard things in the check directory ... OK * checking for detritus in the temp directory ... OK * DONE Status: 1 ERROR, 1 NOTE