• using R Under development (unstable) (2026-05-27 r90083)
• using platform: x86_64-pc-linux-gnu
• R was compiled by     clang version 22.1.6 (https://github.com/llvm/llvm-project fc4aad7b5db3fff421df9a9637605b9ca5667881)     flang version 22.1.6 (https://github.com/llvm/llvm-project fc4aad7b5db3fff421df9a9637605b9ca5667881)
• running under: Fedora Linux 42 (Workstation Edition)
• using session charset: UTF-8 * current time: 2026-05-27 22:51:06 UTC
• using option ‘--no-stop-on-test-error’
• checking for file ‘harmony/DESCRIPTION’ ... OK
• this is package ‘harmony’ version ‘2.0.3’
• package encoding: UTF-8
• 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 ‘harmony’ can be installed ... [102s/288s] OK See the install log for details.
• used C++ compiler: ‘clang version 22.1.6 (https://github.com/llvm/llvm-project fc4aad7b5db3fff421df9a9637605b9ca5667881)’
• checking installed package size ... INFO   installed size is 6.4Mb   sub-directories of 1Mb or more:     data 2.7Mb     doc 2.8Mb
• checking package directory ... OK
• checking ‘build’ directory ... 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 ... [4s/14s] OK
• checking whether the package can be loaded with stated dependencies ... [4s/16s] OK
• checking whether the package can be unloaded cleanly ... [4s/15s] OK
• checking whether the namespace can be loaded with stated dependencies ... [3s/11s] OK
• checking whether the namespace can be unloaded cleanly ... [4s/20s] OK
• checking loading without being on the library search path ... [4s/14s] OK
• checking whether startup messages can be suppressed ... [4s/15s] 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 ... [19s/57s] OK
• checking Rd files ... 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 ... OK
• checking LazyData ... OK
• checking data for ASCII and uncompressed saves ... OK
• checking line endings in shell scripts ... OK
• checking line endings in C/C++/Fortran sources/headers ... OK
• checking line endings in Makefiles ... OK
• checking compilation flags in Makevars ... OK
• checking for GNU extensions in Makefiles ... OK
• checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
• checking use of PKG_*FLAGS in Makefiles ... OK
• checking use of SHLIB_OPENMP_*FLAGS in Makefiles ... OK
• checking pragmas in C/C++ headers and code ... OK
• checking compilation flags used ... OK
• checking compiled code ... OK
• checking installed files from ‘inst/doc’ ... OK
• checking files in ‘vignettes’ ... OK
• checking examples ... [7s/20s] OK
• checking for unstated dependencies in ‘tests’ ... OK
• checking tests ... [9s/34s] ERROR   Running ‘testthat.R’ [8s/32s] Running the tests in ‘tests/testthat.R’ failed. Complete output:   > library(testthat)   > library(harmony)   Loading required package: Rcpp   • This is Harmony2 version 2.0.3   • Read the guide: run vignette()   • Get help: Visit the website at https://korsunskylab.github.io/harmony2/ and   report issues on https://github.com/immunogenomics/harmony/issues   >   > test_check("harmony")   119exists, retrying for cluster 32 3.2314   120exists, retrying for cluster 42 3.22857   169exists, retrying for cluster 45 1.83073   504exists, retrying for cluster 15 3.27917   Saving _problems/test_two_variable-11.R   [ FAIL 1 | WARN 0 | SKIP 0 | PASS 13 ]      ══ Failed tests ════════════════════════════════════════════════════════════════   ── Error ('test_two_variable.R:5:1'): (code run outside of `test_that()`) ──────   <std::logic_error/C++Error/error/condition>   Error: inv(): use of LAPACK must be enabled   Backtrace:       ▆    1. ├─harmony::RunHarmony(...) at test_two_variable.R:5:1    2. └─harmony:::RunHarmony.default(...)    3. ├─base::tryCatch(...)    4. │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)    5. └─harmony:::harmonize(harmonyObj, max.iter.harmony, verbose)    6. └─harmonyObj$moe_correct_ridge_cpp()      [ FAIL 1 | WARN 0 | SKIP 0 | PASS 13 ]   Error:   ! Test failures.   Execution halted
• checking for unstated dependencies in vignettes ... OK
• checking package vignettes ... OK
• checking re-building of vignette outputs ... [170s/315s] OK
• checking PDF version of manual ... [7s/23s] OK
• checking HTML version of manual ... OK
• checking for non-standard things in the check directory ... OK
• checking for detritus in the temp directory ... OK
• DONE

Status: 1 ERROR