- using R Under development (unstable) (2024-09-28 r87201)
- using platform: x86_64-pc-linux-gnu
- R was compiled by
Debian clang version 19.1.0 (4)
Debian flang-new version 19.1.0 (4)
- running under: Debian GNU/Linux trixie/sid
- using session charset: UTF-8
- checking for file ‘GenomeAdmixR/DESCRIPTION’ ... OK
- checking extension type ... Package
- this is package ‘GenomeAdmixR’ version ‘2.1.7’
- 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 serialization versions ... OK
- checking whether package ‘GenomeAdmixR’ can be installed ... OK
See the install log for details.
- used C++ compiler: ‘Debian clang version 19.1.0 (4)’
- checking C++ specification ... NOTE
Specified C++14: please drop specification unless essential
- checking package directory ... OK
- checking for future file timestamps ... 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 ... [1s/1s] OK
- checking whether the package can be loaded with stated dependencies ... [1s/1s] OK
- checking whether the package can be unloaded cleanly ... [0s/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 ... [11s/14s] OK
- checking Rd files ... [1s/1s] NOTE
checkRd: (-1) simulate_admixture.Rd:36: Lost braces
36 | \code{location}{ location of the marker under selection (in Morgan) }
| ^
checkRd: (-1) simulate_ancestry.Rd:49: Lost braces
49 | \code{location}{ location of the marker under selection (in Morgan) }
| ^
checkRd: (-1) simulate_ancestry_migration.Rd:59: Lost braces
59 | \code{location}{ location of the marker under selection (in Morgan) }
| ^
checkRd: (-1) simulate_sequence.Rd:51: Lost braces
51 | \code{location}{ location of the marker under selection (in Morgan) }
| ^
checkRd: (-1) simulate_sequence_migration.Rd:58: Lost braces
58 | \code{location}{ location of the marker under selection (in Morgan) }
| ^
- 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 data for ASCII and uncompressed saves ... 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 ... [10s/13s] OK
- checking for unstated dependencies in ‘tests’ ... OK
- checking tests ... [89s/111s] OK
Running ‘testthat.R’ [89s/111s]
- checking for unstated dependencies in vignettes ... OK
- checking package vignettes ... OK
- checking re-building of vignette outputs ... [117s/145s] OK
- checking PDF version of manual ... [7s/9s] OK
- checking HTML version of manual ... [1s/3s] OK
- checking for non-standard things in the check directory ... OK
- DONE
Status: 2 NOTEs