• using R Under development (unstable) (2026-07-16 r90262)
• using platform: x86_64-pc-linux-gnu
• R was compiled by     gcc (GCC) 16.1.1 20260515 (Red Hat 16.1.1-2)     GNU Fortran (GCC) 16.1.1 20260515 (Red Hat 16.1.1-2)
• running under: Fedora Linux 44 (Server Edition)
• using session charset: UTF-8 * current time: 2026-07-16 17:51:59 UTC
• using option ‘--no-stop-on-test-error’
• checking for file ‘qtl2/DESCRIPTION’ ... OK
• this is package ‘qtl2’ version ‘0.44’
• 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 ‘qtl2’ can be installed ... [490s/381s] OK See the install log for details.
• used C++ compiler: ‘g++ (GCC) 16.1.1 20260515 (Red Hat 16.1.1-2)’
• checking package 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 ... OK
• checking whether the package can be loaded with stated dependencies ... OK
• checking whether the package can be unloaded cleanly ... OK
• checking whether the namespace can be loaded with stated dependencies ... OK
• checking whether the namespace can be unloaded cleanly ... OK
• checking loading without being on the library search path ... 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 ... [37s/40s] NOTE Found calls to structure() using deprecated special names:   qtl2/tests/testthat/test-calc_geno_freq.R (.Dim: 8, .Dimnames: 8, .Names: 2)   qtl2/tests/testthat/test-calcerrorlod.R (.Dim: 5, .Dimnames: 5)   qtl2/tests/testthat/test-compare_geno.R (.Dim: 3, .Dimnames: 3, .Names: 2)   qtl2/tests/testthat/test-compare_maps.R (.Names: 1)   qtl2/tests/testthat/test-control_files.R (.Names: 12)   qtl2/tests/testthat/test-count_xo.R (.Dim: 2, .Dimnames: 2)   qtl2/tests/testthat/test-create_gene_query_func.R (.Names: 1)   qtl2/tests/testthat/test-create_variant_query_func.R (.Names: 1)   qtl2/tests/testthat/test-est_herit.R (.Names: 1)   qtl2/tests/testthat/test-find_index_snp.R (.Names: 1)   qtl2/tests/testthat/test-find_peaks.R (.Label: 3, .Names: 3)   qtl2/tests/testthat/test-io.R (.Names: 4)   qtl2/tests/testthat/test-n_missing.R (.Names: 1)   qtl2/tests/testthat/test-reduce_markers.R (.Names: 7)   qtl2/tests/testthat/test-scan1_pg.R (.Dim: 2, .Dimnames: 2)   qtl2/tests/testthat/test-scan1snps.R (.Dim: 1, .Dimnames: 1)   qtl2/tests/testthat/test-simgeno.R (.Dim: 2, .Dimnames: 2) '.Dim' should be changed to 'dim'. '.Dimnames' should be changed to 'dimnames'. '.Names' should be changed to 'names'. '.Label' should be changed to 'levels'.
• 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 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 ... [15s/17s] OK
• checking for unstated dependencies in ‘tests’ ... OK
• checking tests ... [47s/50s] OK   Running ‘testthat.R’ [47s/50s]
• checking PDF version of manual ... OK
• checking HTML version of manual ... [9s/12s] OK
• checking for non-standard things in the check directory ... OK
• checking for detritus in the temp directory ... OK
• DONE

Status: 1 NOTE