* using log directory ‘/srv/hornik/tmp/CRAN_pretest/BAMMtools.Rcheck’
* using R Under development (unstable) (2024-09-11 r87117)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    Debian clang version 18.1.8 (9)
    Debian flang-new version 18.1.8 (9)
* running under: Debian GNU/Linux trixie/sid
* using session charset: UTF-8
* checking for file ‘BAMMtools/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘BAMMtools’ version ‘2.1.12’
* package encoding: UTF-8
* checking CRAN incoming feasibility ... [4s/14s] NOTE
Maintainer: ‘Pascal Title <ptitle@umich.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Dan",
                      family = "Rabosky",
                      role = "aut"),
               person(given = "Mike",
                      family = "Grundler",
                      role = "aut"),
               person(given = "Pascal",
                      family = "Title",
                      role = c("aut", "cre"),
                      email = "ptitle@umich.edu"),
               person(given = "Carlos",
                      family = "Anderson",
                      role = "aut"),
               person(given = "Jeff",
                      family = "Shi",
                      role = "aut"),
               person(given = "Joseph",
                      family = "Brown",
                      role = "aut"),
               person(given = "Huateng",
                      family = "Huang",
                      role = "aut"),
               person(given = "Jon",
                      family = "Mitchell",
                      role = "aut"))
as necessary.
* 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 ‘BAMMtools’ can be installed ... [5s/5s] OK
* used C compiler: ‘Debian clang version 18.1.8 (9)’
* 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 ... [0s/0s] OK
* checking whether the package can be loaded with stated dependencies ... [0s/0s] OK
* checking whether the package can be unloaded cleanly ... [0s/0s] OK
* checking whether the namespace can be loaded with stated dependencies ... [0s/0s] OK
* checking whether the namespace can be unloaded cleanly ... [0s/0s] OK
* checking loading without being on the library search path ... [0s/0s] 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 ... [9s/9s] OK
* checking Rd files ... [0s/0s] OK
* checking Rd metadata ... OK
* checking Rd line widths ... OK
* checking Rd cross-references ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  cohorts.Rd: rich.colors
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* 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 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 ... [27s/27s] OK
* checking PDF version of manual ... [4s/4s] OK
* checking HTML version of manual ... [1s/1s] OK
* checking for non-standard things in the check directory ... OK
* checking for detritus in the temp directory ... OK
* DONE
Status: 2 NOTEs