• 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 17:42:58 UTC
• using option ‘--no-stop-on-test-error’
• checking for file ‘mSigTools/DESCRIPTION’ ... OK
• checking extension type ... Package
• this is package ‘mSigTools’ version ‘1.0.7’
• package encoding: UTF-8
• checking package namespace information ... OK
• checking package dependencies ... INFO Package suggested but not available for checking: ‘ICAMS’
• 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 ‘mSigTools’ can be installed ... OK See the install log for details.
• 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 ... NOTE Found calls to structure() using deprecated special names:   mSigTools/tests/testthat/test_TP_FP_FN_avg_sim.R (.Dim: 2, .Dimnames: 2)   mSigTools/tests/testthat/test_internal_matches.R (.Dim: 2, .Dimnames: 2)   mSigTools/tests/testthat/test_match_two_sig_sets.R (.Dim: 4, .Dimnames: 4)   mSigTools/tests/testthat/test_sig_dist_matrix.R (.Dim: 2, .Dimnames: 2) '.Dim' should be changed to 'dim'. '.Dimnames' should be changed to 'dimnames'.
• 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 examples ... OK
• checking for unstated dependencies in ‘tests’ ... OK
• checking tests ... [9s/10s] OK   Running ‘spelling.R’   Running ‘testthat.R’
• checking PDF version of manual ... 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 NOTE