* using log directory ‘/srv/hornik/tmp/CRAN/polymapR.Rcheck’
* using R Under development (unstable) (2023-10-26 r85419)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    Debian clang version 16.0.6 (15)
    GNU Fortran (Debian 13.2.0-4) 13.2.0
* running under: Debian GNU/Linux trixie/sid
* using session charset: UTF-8
* checking for file ‘polymapR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘polymapR’ version ‘1.1.4’
* package encoding: UTF-8
* checking CRAN incoming feasibility ... [4s/5s] Note_to_CRAN_maintainers
Maintainer: ‘Peter Bourke <pbourkey@gmail.com>’
* 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 ‘polymapR’ can be installed ... [263s/263s] OK
* 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 R 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 ... NOTE
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘Mode’
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... [307s/307s] OK
* checking Rd files ... [0s/0s] NOTE
checkRd: (-1) add_dup_markers.Rd:19: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) add_dup_markers.Rd:20: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) calcSegtypeInfo.Rd:20: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) calcSegtypeInfo.Rd:21: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) calcSegtypeInfo.Rd:22: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) calcSegtypeInfo.Rd:23: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) calcSegtypeInfo.Rd:24: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) calcSegtypeInfo.Rd:25: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) calcSegtypeInfo.Rd:26-27: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) calcSegtypeInfo.Rd:28-31: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) calcSegtypeInfo.Rd:32-35: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) checkF1.Rd:41-43: Lost braces in \itemize; meant \describe ?
checkRd: (-1) checkF1.Rd:44-46: Lost braces in \itemize; meant \describe ?
checkRd: (-1) checkF1.Rd:47-49: Lost braces in \itemize; meant \describe ?
checkRd: (-1) checkF1.Rd:50-52: Lost braces in \itemize; meant \describe ?
checkRd: (-1) checkF1.Rd:53-55: Lost braces in \itemize; meant \describe ?
checkRd: (-1) checkF1.Rd:56-58: Lost braces in \itemize; meant \describe ?
checkRd: (-1) checkF1.Rd:59-61: Lost braces in \itemize; meant \describe ?
checkRd: (-1) check_maxP.Rd:13-15: Lost braces in \itemize; meant \describe ?
checkRd: (-1) check_maxP.Rd:16-18: Lost braces in \itemize; meant \describe ?
checkRd: (-1) check_maxP.Rd:19-21: Lost braces in \itemize; meant \describe ?
checkRd: (-1) check_maxP.Rd:22-24: Lost braces in \itemize; meant \describe ?
checkRd: (-1) check_maxP.Rd:25-27: Lost braces in \itemize; meant \describe ?
checkRd: (-1) check_maxP.Rd:28-30: Lost braces in \itemize; meant \describe ?
checkRd: (-1) check_maxP.Rd:31-33: Lost braces in \itemize; meant \describe ?
checkRd: (-1) finish_linkage_analysis.Rd:38-40: Lost braces in \itemize; meant \describe ?
checkRd: (-1) finish_linkage_analysis.Rd:41-43: Lost braces in \itemize; meant \describe ?
checkRd: (-1) finish_linkage_analysis.Rd:44-46: Lost braces in \itemize; meant \describe ?
checkRd: (-1) finish_linkage_analysis.Rd:47-49: Lost braces in \itemize; meant \describe ?
checkRd: (-1) finish_linkage_analysis.Rd:50-52: Lost braces in \itemize; meant \describe ?
checkRd: (-1) finish_linkage_analysis.Rd:53-55: Lost braces in \itemize; meant \describe ?
checkRd: (-1) finish_linkage_analysis.Rd:56-57: Lost braces in \itemize; meant \describe ?
checkRd: (-1) gp_overview.Rd:13-15: Lost braces in \itemize; meant \describe ?
checkRd: (-1) gp_overview.Rd:16-18: Lost braces in \itemize; meant \describe ?
checkRd: (-1) gp_overview.Rd:19-21: Lost braces in \itemize; meant \describe ?
checkRd: (-1) gp_overview.Rd:22-24: Lost braces in \itemize; meant \describe ?
checkRd: (-1) gp_overview.Rd:25-27: Lost braces in \itemize; meant \describe ?
checkRd: (-1) gp_overview.Rd:28-30: Lost braces in \itemize; meant \describe ?
checkRd: (-1) gp_overview.Rd:31-33: Lost braces in \itemize; meant \describe ?
checkRd: (-1) homologue_lg_assignment.Rd:38-40: Lost braces in \itemize; meant \describe ?
checkRd: (-1) homologue_lg_assignment.Rd:41-43: Lost braces in \itemize; meant \describe ?
checkRd: (-1) homologue_lg_assignment.Rd:44-46: Lost braces in \itemize; meant \describe ?
checkRd: (-1) homologue_lg_assignment.Rd:47-49: Lost braces in \itemize; meant \describe ?
checkRd: (-1) homologue_lg_assignment.Rd:50-52: Lost braces in \itemize; meant \describe ?
checkRd: (-1) homologue_lg_assignment.Rd:53-55: Lost braces in \itemize; meant \describe ?
checkRd: (-1) homologue_lg_assignment.Rd:56-57: Lost braces in \itemize; meant \describe ?
checkRd: (-1) linkage.Rd:72-74: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) linkage.Rd:75-77: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) linkage.Rd:78-80: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) linkage.Rd:81-83: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) linkage.Rd:84-86: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) linkage.gp.Rd:29-31: Lost braces in \itemize; meant \describe ?
checkRd: (-1) linkage.gp.Rd:32-34: Lost braces in \itemize; meant \describe ?
checkRd: (-1) linkage.gp.Rd:35-37: Lost braces in \itemize; meant \describe ?
checkRd: (-1) linkage.gp.Rd:38-40: Lost braces in \itemize; meant \describe ?
checkRd: (-1) linkage.gp.Rd:41-43: Lost braces in \itemize; meant \describe ?
checkRd: (-1) linkage.gp.Rd:44-46: Lost braces in \itemize; meant \describe ?
checkRd: (-1) linkage.gp.Rd:47-48: Lost braces in \itemize; meant \describe ?
checkRd: (-1) linkage.gp.Rd:92-94: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) linkage.gp.Rd:95-97: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) linkage.gp.Rd:98-100: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) linkage.gp.Rd:101-103: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) linkage.gp.Rd:104-106: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) screen_for_duplicate_individuals.gp.Rd:22-24: Lost braces in \itemize; meant \describe ?
checkRd: (-1) screen_for_duplicate_individuals.gp.Rd:25-27: Lost braces in \itemize; meant \describe ?
checkRd: (-1) screen_for_duplicate_individuals.gp.Rd:28-30: Lost braces in \itemize; meant \describe ?
checkRd: (-1) screen_for_duplicate_individuals.gp.Rd:31-33: Lost braces in \itemize; meant \describe ?
checkRd: (-1) screen_for_duplicate_individuals.gp.Rd:34-36: Lost braces in \itemize; meant \describe ?
checkRd: (-1) screen_for_duplicate_individuals.gp.Rd:37-39: Lost braces in \itemize; meant \describe ?
checkRd: (-1) screen_for_duplicate_individuals.gp.Rd:40-42: Lost braces in \itemize; meant \describe ?
checkRd: (-1) screen_for_duplicate_markers.Rd:41-42: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) screen_for_duplicate_markers.Rd:43-44: Lost braces in \itemize; \value handles \item{}{} directly
* checking Rd metadata ... WARNING
Rd files with duplicated alias 'polymapR':
  ‘polymapR-package.Rd’ ‘polymapR.Rd’
Rd files with duplicated alias 'polymapR-package':
  ‘polymapR-package.Rd’ ‘polymapR.Rd’
* 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 LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking R/sysdata.rda ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [8s/8s] OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking re-building of vignette outputs ... [8s/9s] 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: 1 WARNING, 2 NOTEs