* using log directory ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/pvEBayes.Rcheck’ * using R Under development (unstable) (2025-07-13 r88407) * 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 13 (trixie) * using session charset: UTF-8 * checking for file ‘pvEBayes/DESCRIPTION’ ... OK * this is package ‘pvEBayes’ version ‘0.1.1’ * package encoding: UTF-8 * checking CRAN incoming feasibility ... [1s/1s] OK * 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 ‘pvEBayes’ can be installed ... OK See 'https://www.r-project.org/nosvn/R.check/r-devel-linux-x86_64-debian-clang/pvEBayes-00install.html' for details. * used C++ compiler: ‘Debian clang version 19.1.7 (3+b1)’ * 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 ... [0s/1s] OK * checking whether the package can be unloaded cleanly ... [0s/1s] OK * checking whether the namespace can be loaded with stated dependencies ... [0s/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/12s] OK * checking Rd files ... [0s/1s] 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 ... [0s/0s] OK * checking LazyData ... OK * checking data for ASCII and uncompressed saves ... OK * checking line endings in C/C++/Fortran sources/headers ... OK * checking pragmas in C/C++ headers and code ... OK * checking compilation flags used ... OK * checking compiled code ... OK * checking examples ... [26s/33s] OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed eyeplot_pvEBayes 7.155 0.116 8.108 plot.pvEBayes 6.505 0.093 8.458 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... [17s/22s] ERROR Running ‘testthat.R’ [17s/22s] 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/testing-design.html#sec-tests-files-overview > # * https://testthat.r-lib.org/articles/special-files.html > > library(testthat) > library(pvEBayes) > > test_check("pvEBayes") The alpha value selected under AIC is 0, The alpha value selected under BIC is 0. alpha AIC BIC num_mixture 1 0.0 1226.166 1273.831 200 2 0.1 1226.166 1273.831 200 3 0.3 1226.166 1273.831 200 4 0.5 1226.166 1273.831 200 5 0.7 1226.166 1273.831 200 6 0.9 1226.166 1273.831 200 The hyperparameters selected under AIC is (p = 120, c0 = 0.01), The hyperparameters selected under BIC is (p = 120, c0 = 0.01)., p c0 AIC BIC 1 40 1e-05 34.10699 34.42255 2 60 1e-05 34.90759 35.25496 3 80 1e-05 35.72419 36.10400 4 100 1e-05 37.80020 38.26246 5 120 1e-05 38.73868 39.23823 6 40 1e-04 29.66394 29.80296 7 60 1e-04 32.01391 32.24629 8 80 1e-04 33.63691 33.93376 9 100 1e-04 34.71119 35.05072 10 120 1e-04 35.61688 35.99239 11 40 1e-03 22.79611 22.66169 12 60 1e-03 26.97632 27.00808 13 80 1e-03 29.51066 29.64316 14 100 1e-03 30.55376 30.72775 15 120 1e-03 31.16307 31.36130 16 40 1e-02 24.28846 24.19956 17 60 1e-02 23.20719 23.07582 18 80 1e-02 21.68559 21.49393 19 100 1e-02 20.64329 20.41039 20 120 1e-02 19.15179 18.85971 21 40 1e-01 Inf Inf 22 60 1e-01 27.01397 27.01590 23 80 1e-01 Inf Inf 24 100 1e-01 32.28480 32.49610 25 120 1e-01 Inf Inf [ FAIL 1 | WARN 2 | SKIP 0 | PASS 13 ] ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test-pvEBayes_object_S3_methods.R:11:3'): pvEBayes object associated functions ── Error in `apply(., 1, max)`: dim(X) must have a positive length Backtrace: ▆ 1. ├─pvEBayes::heatmap_pvEBayes(obj) at test-pvEBayes_object_S3_methods.R:11:3 2. │ └─... %>% order() 3. ├─base::order(.) 4. └─base::apply(., 1, max) [ FAIL 1 | WARN 2 | SKIP 0 | PASS 13 ] Error: Test failures Execution halted * checking PDF version of manual ... [5s/7s] OK * checking HTML version of manual ... [1s/2s] OK * checking for non-standard things in the check directory ... OK * DONE Status: 1 ERROR