• using R Under development (unstable) (2026-07-31 r90332)
• using platform: x86_64-pc-linux-gnu
• R was compiled by     gcc-16 (Debian 16.1.0-3) 16.1.0     GNU Fortran (Debian 16.1.0-3) 16.1.0
• running under: Debian GNU/Linux forky/sid
• using session charset: UTF-8 * current time: 2026-08-01 16:52:38 UTC
• checking for file ‘phyreg/DESCRIPTION’ ... OK
• checking extension type ... Package
• this is package ‘phyreg’ version ‘1.0.2’
• checking CRAN incoming feasibility ... [1s/1s] NOTE Maintainer: ‘Alan Grafen <alan.grafen@sjc.ox.ac.uk>’ No Authors@R field in DESCRIPTION. Please add one, modifying   Authors@R: person(given = "Alan",                     family = "Grafen",                     role = c("aut", "cre"),                     email = "alan.grafen@sjc.ox.ac.uk") 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 ‘phyreg’ can be installed ... OK See the install log for details.
• 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 ... [6s/8s] OK
• checking Rd files ... [0s/1s] 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 ... [0s/1s] OK
• checking data for ASCII and uncompressed saves ... OK
• checking examples ... [7s/7s] OK Examples with CPU (user + system) or elapsed time > 5s         user system elapsed phyreg 6.436 0.017 6.976
• checking PDF version of manual ... [5s/6s] OK
• checking HTML version of manual ... [1s/1s] OK
• checking for non-standard things in the check directory ... OK
• checking for new files in some other directories ... NOTE Found the following files/directories:   ‘~/tmp/scratch/Rtmp01DHOm’ ‘~/tmp/scratch/Rtmp0l3u9K’   ‘~/tmp/scratch/Rtmp0or3G5’ ‘~/tmp/scratch/Rtmp0ydVk1’   ‘~/tmp/scratch/Rtmp1MLC2n’ ‘~/tmp/scratch/Rtmp2DVd7X’   ‘~/tmp/scratch/Rtmp3eaOds’ ‘~/tmp/scratch/Rtmp3wPSTv’   ‘~/tmp/scratch/Rtmp4Azy16’ ‘~/tmp/scratch/Rtmp4Wemyh’   ‘~/tmp/scratch/Rtmp50drjY’ ‘~/tmp/scratch/Rtmp5v3Xkj’   ‘~/tmp/scratch/Rtmp6HkK1k’ ‘~/tmp/scratch/Rtmp6MEGRv’   ‘~/tmp/scratch/Rtmp6rGIDq’ ‘~/tmp/scratch/Rtmp7LfjeE’   ‘~/tmp/scratch/Rtmp7tPAph’ ‘~/tmp/scratch/Rtmp8PXM2e’   ‘~/tmp/scratch/Rtmp8UJgCZ’ ‘~/tmp/scratch/Rtmp9MOyUb’   ‘~/tmp/scratch/Rtmp9WZ8Ej’ ‘~/tmp/scratch/Rtmp9ZXykh’   ‘~/tmp/scratch/RtmpA8QwCU’ ‘~/tmp/scratch/RtmpAX7oAu’   ‘~/tmp/scratch/RtmpAi347x’ ‘~/tmp/scratch/RtmpBfYGNL’   ‘~/tmp/scratch/RtmpBiimgU’ ‘~/tmp/scratch/RtmpCEWpVI’   ‘~/tmp/scratch/RtmpCGxLQE’ ‘~/tmp/scratch/RtmpCn0JUP’   ‘~/tmp/scratch/RtmpDvykyz’ ‘~/tmp/scratch/RtmpEIfGm0’   ‘~/tmp/scratch/RtmpEwwZfm’ ‘~/tmp/scratch/RtmpGDewyo’   ‘~/tmp/scratch/RtmpHY1Mlv’ ‘~/tmp/scratch/RtmpHhpfHI’   ‘~/tmp/scratch/RtmpIfUaAs’ ‘~/tmp/scratch/RtmpJANulW’   ‘~/tmp/scratch/RtmpJQBf9z’ ‘~/tmp/scratch/RtmpJd7KFb’   ‘~/tmp/scratch/RtmpJy8T9B’ ‘~/tmp/scratch/RtmpKm8kzW’   ‘~/tmp/scratch/RtmpKriz6Q’ ‘~/tmp/scratch/RtmpL2XAGd’   ‘~/tmp/scratch/RtmpLYVEDe’ ‘~/tmp/scratch/RtmpLeDBw3’   ‘~/tmp/scratch/RtmpLgXosd’ ‘~/tmp/scratch/RtmpMEH4Et’   ‘~/tmp/scratch/RtmpNE8Ztj’ ‘~/tmp/scratch/RtmpNXgFsd’   ‘~/tmp/scratch/RtmpNyRwVl’ ‘~/tmp/scratch/RtmpO8xbjS’   ‘~/tmp/scratch/RtmpQ3S5j3’ ‘~/tmp/scratch/RtmpQ8sMZ8’   ‘~/tmp/scratch/RtmpQIRjM9’ ‘~/tmp/scratch/RtmpQUkNoe’   ‘~/tmp/scratch/RtmpRI8NvI’ ‘~/tmp/scratch/RtmpS3duu0’   ‘~/tmp/scratch/RtmpSfniGy’ ‘~/tmp/scratch/RtmpStHsU6’   ‘~/tmp/scratch/RtmpTGtS8o’ ‘~/tmp/scratch/RtmpThzzhj’   ‘~/tmp/scratch/RtmpTiBqIL’ ‘~/tmp/scratch/RtmpTt7rdl’   ‘~/tmp/scratch/RtmpV3ocUy’ ‘~/tmp/scratch/RtmpVNKLEh’   ‘~/tmp/scratch/RtmpW37Zy8’ ‘~/tmp/scratch/RtmpWcVDom’   ‘~/tmp/scratch/RtmpWoNgUv’ ‘~/tmp/scratch/RtmpWqx3wR’   ‘~/tmp/scratch/RtmpXYQAbh’ ‘~/tmp/scratch/RtmpZPzsap’   ‘~/tmp/scratch/RtmpZr3fWb’ ‘~/tmp/scratch/Rtmpbti7ZZ’   ‘~/tmp/scratch/RtmpcOVfc6’ ‘~/tmp/scratch/Rtmpd8Bakg’   ‘~/tmp/scratch/RtmpdDovBG’ ‘~/tmp/scratch/RtmpdwE1rA’   ‘~/tmp/scratch/RtmpeGfO9S’ ‘~/tmp/scratch/RtmpegqH9P’   ‘~/tmp/scratch/Rtmpetbkvq’ ‘~/tmp/scratch/RtmpfBcux5’   ‘~/tmp/scratch/RtmpgSoozq’ ‘~/tmp/scratch/RtmpgoGFTj’   ‘~/tmp/scratch/RtmpgrNFy4’ ‘~/tmp/scratch/Rtmphe9Dz0’   ‘~/tmp/scratch/RtmpiJHj6Q’ ‘~/tmp/scratch/RtmpiXSxGT’   ‘~/tmp/scratch/RtmpipPjUY’ ‘~/tmp/scratch/RtmpjuTnW0’   ‘~/tmp/scratch/RtmpkPsbxJ’ ‘~/tmp/scratch/RtmpleRT5f’   ‘~/tmp/scratch/RtmplgVNQm’ ‘~/tmp/scratch/RtmpnDTKrV’   ‘~/tmp/scratch/RtmpnE02E4’ ‘~/tmp/scratch/RtmpnjNzZb’   ‘~/tmp/scratch/Rtmpo9Ds7O’ ‘~/tmp/scratch/Rtmpp5SJcO’   ‘~/tmp/scratch/RtmppQlZK8’ ‘~/tmp/scratch/RtmppkP5AT’   ‘~/tmp/scratch/RtmpqBfLln’ ‘~/tmp/scratch/RtmpqFN5gd’   ‘~/tmp/scratch/RtmprK86tS’ ‘~/tmp/scratch/RtmprbvjZZ’   ‘~/tmp/scratch/Rtmprk4Zpn’ ‘~/tmp/scratch/RtmprtCYWr’   ‘~/tmp/scratch/Rtmps4ErQK’ ‘~/tmp/scratch/RtmpsAJvC3’   ‘~/tmp/scratch/RtmpsEBmMq’ ‘~/tmp/scratch/RtmpsyoWSG’   ‘~/tmp/scratch/RtmptUh38x’ ‘~/tmp/scratch/RtmptjMgup’   ‘~/tmp/scratch/RtmpwFY5AU’ ‘~/tmp/scratch/RtmpwTOpqf’   ‘~/tmp/scratch/RtmpwTPywC’ ‘~/tmp/scratch/RtmpwZ7CV0’   ‘~/tmp/scratch/Rtmpx5geCm’ ‘~/tmp/scratch/RtmpxNL6la’   ‘~/tmp/scratch/RtmpxYT21w’ ‘~/tmp/scratch/RtmpyplDPr’   ‘~/tmp/scratch/RtmpzWKE5Y’   ‘~/tmp/scratch/quarto-session71cad89da53e4060’   ‘~/tmp/scratch/xvfb-run.04lxi1’ ‘~/tmp/scratch/xvfb-run.2PJVdD’   ‘~/tmp/scratch/xvfb-run.3zKkJR’ ‘~/tmp/scratch/xvfb-run.4bxhAI’   ‘~/tmp/scratch/xvfb-run.5Q5cwv’ ‘~/tmp/scratch/xvfb-run.7vCUma’   ‘~/tmp/scratch/xvfb-run.CYCdiK’ ‘~/tmp/scratch/xvfb-run.Cjyz5w’   ‘~/tmp/scratch/xvfb-run.MDeK64’ ‘~/tmp/scratch/xvfb-run.MZOpDQ’   ‘~/tmp/scratch/xvfb-run.O83c6O’ ‘~/tmp/scratch/xvfb-run.PBFBcy’   ‘~/tmp/scratch/xvfb-run.PnBh11’ ‘~/tmp/scratch/xvfb-run.T7Q5GF’   ‘~/tmp/scratch/xvfb-run.UiyyAB’ ‘~/tmp/scratch/xvfb-run.Ulan66’   ‘~/tmp/scratch/xvfb-run.W9qPBt’ ‘~/tmp/scratch/xvfb-run.WFwiQV’   ‘~/tmp/scratch/xvfb-run.WVwlGN’ ‘~/tmp/scratch/xvfb-run.WXs6tR’   ‘~/tmp/scratch/xvfb-run.XunUFE’ ‘~/tmp/scratch/xvfb-run.YGyFvL’   ‘~/tmp/scratch/xvfb-run.asCi8z’ ‘~/tmp/scratch/xvfb-run.crAZIQ’   ‘~/tmp/scratch/xvfb-run.ddPYYF’ ‘~/tmp/scratch/xvfb-run.gJWJvB’   ‘~/tmp/scratch/xvfb-run.ifQeQ3’ ‘~/tmp/scratch/xvfb-run.ihyal8’   ‘~/tmp/scratch/xvfb-run.k4kcWS’ ‘~/tmp/scratch/xvfb-run.lPG3KK’   ‘~/tmp/scratch/xvfb-run.ptmcT3’ ‘~/tmp/scratch/xvfb-run.qQTGsk’   ‘~/tmp/scratch/xvfb-run.twP0OA’ ‘~/tmp/scratch/xvfb-run.uRGOaq’   ‘~/tmp/scratch/xvfb-run.v2quVF’ ‘~/tmp/scratch/xvfb-run.vrjnRr’   ‘~/tmp/scratch/xvfb-run.wPVdJl’ ‘~/tmp/scratch/xvfb-run.xnKlqk’   ‘~/tmp/scratch/xvfb-run.zOHaKt’
• DONE

Status: 2 NOTEs