• using R Under development (unstable) (2026-08-02 r90338)
• 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: 2026-08-03 11:07:24 UTC
• checking for file ‘AlleleShift/DESCRIPTION’ ... OK
• checking extension type ... Package
• this is package ‘AlleleShift’ version ‘1.1-3’
• checking CRAN incoming feasibility ... [2s/2s] OK
• 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 ‘AlleleShift’ 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 ... [6s/8s] OK
• checking whether the package can be loaded with stated dependencies ... [4s/6s] OK
• checking whether the package can be unloaded cleanly ... [5s/6s] OK
• checking whether the namespace can be loaded with stated dependencies ... [4s/6s] OK
• checking whether the namespace can be unloaded cleanly ... [5s/6s] OK
• checking loading without being on the library search path ... [5s/6s] OK
• checking whether startup messages can be suppressed ... [5s/7s] 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 ... [23s/28s] OK
• checking Rd files ... [0s/0s] 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 ... [3s/4s] OK
• checking data for ASCII and uncompressed saves ... OK
• checking examples ... [16s/19s] OK
• checking PDF version of manual ... [4s/6s] OK
• checking HTML version of manual ... [0s/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/Rtmp0T05wz’ ‘~/tmp/scratch/Rtmp0Vg7pA’   ‘~/tmp/scratch/Rtmp0mKiku’ ‘~/tmp/scratch/Rtmp1uQ11X’   ‘~/tmp/scratch/Rtmp2Gqo5I’ ‘~/tmp/scratch/Rtmp2blt6S’   ‘~/tmp/scratch/Rtmp2pdadc’ ‘~/tmp/scratch/Rtmp4NBijF’   ‘~/tmp/scratch/Rtmp4jUHv4’ ‘~/tmp/scratch/Rtmp5DkCMq’   ‘~/tmp/scratch/Rtmp63W2UA’ ‘~/tmp/scratch/Rtmp6nbeqz’   ‘~/tmp/scratch/Rtmp6zpKD8’ ‘~/tmp/scratch/Rtmp7qZ8kE’   ‘~/tmp/scratch/Rtmp8tbWOt’ ‘~/tmp/scratch/Rtmp8ztO5K’   ‘~/tmp/scratch/Rtmp9V3P92’ ‘~/tmp/scratch/RtmpA7pjjO’   ‘~/tmp/scratch/RtmpAc6EkW’ ‘~/tmp/scratch/RtmpB4QwEY’   ‘~/tmp/scratch/RtmpCYRM1Q’ ‘~/tmp/scratch/RtmpCf1wmm’   ‘~/tmp/scratch/RtmpCpXmCm’ ‘~/tmp/scratch/RtmpDBTzRF’   ‘~/tmp/scratch/RtmpDdiA2r’ ‘~/tmp/scratch/RtmpDfJewH’   ‘~/tmp/scratch/RtmpDgheBt’ ‘~/tmp/scratch/RtmpE3Gxws’   ‘~/tmp/scratch/RtmpEe6VUh’ ‘~/tmp/scratch/RtmpEm3Vyc’   ‘~/tmp/scratch/RtmpF7VWGd’ ‘~/tmp/scratch/RtmpFF0WhU’   ‘~/tmp/scratch/RtmpGIoanH’ ‘~/tmp/scratch/RtmpGP6kKp’   ‘~/tmp/scratch/RtmpGedJGa’ ‘~/tmp/scratch/RtmpGwxjst’   ‘~/tmp/scratch/RtmpHWKbmX’ ‘~/tmp/scratch/RtmpHmpirt’   ‘~/tmp/scratch/RtmpIpC2Sf’ ‘~/tmp/scratch/RtmpJffM7K’   ‘~/tmp/scratch/RtmpK0W6PI’ ‘~/tmp/scratch/RtmpKPtTfS’   ‘~/tmp/scratch/RtmpKYgKjK’ ‘~/tmp/scratch/RtmpKZBwjc’   ‘~/tmp/scratch/RtmpKkBUc8’ ‘~/tmp/scratch/RtmpL8V2ZJ’   ‘~/tmp/scratch/RtmpLilobZ’ ‘~/tmp/scratch/RtmpMB7WbA’   ‘~/tmp/scratch/RtmpMBcPtv’ ‘~/tmp/scratch/RtmpMDCdE4’   ‘~/tmp/scratch/RtmpNGUzw5’ ‘~/tmp/scratch/RtmpNZ660N’   ‘~/tmp/scratch/RtmpOCGoIR’ ‘~/tmp/scratch/RtmpOcI0An’   ‘~/tmp/scratch/RtmpOcRjbz’ ‘~/tmp/scratch/RtmpPQWI7x’   ‘~/tmp/scratch/RtmpPmI7fy’ ‘~/tmp/scratch/RtmpQ42Uay’   ‘~/tmp/scratch/RtmpRbB3rK’ ‘~/tmp/scratch/RtmpRiKfoR’   ‘~/tmp/scratch/RtmpRm4sRB’ ‘~/tmp/scratch/RtmpS68yPS’   ‘~/tmp/scratch/RtmpSPuu6R’ ‘~/tmp/scratch/RtmpSR8hOU’   ‘~/tmp/scratch/RtmpSUlzpd’ ‘~/tmp/scratch/RtmpSxCf7f’   ‘~/tmp/scratch/RtmpSyVDra’ ‘~/tmp/scratch/RtmpTe2d1m’   ‘~/tmp/scratch/RtmpTm3ksN’ ‘~/tmp/scratch/RtmpTrI8GH’   ‘~/tmp/scratch/RtmpUSm3IF’ ‘~/tmp/scratch/RtmpUplXpv’   ‘~/tmp/scratch/RtmpUq5LpL’ ‘~/tmp/scratch/RtmpV4aVHh’   ‘~/tmp/scratch/RtmpVDJZ23’ ‘~/tmp/scratch/RtmpVmwUAe’   ‘~/tmp/scratch/RtmpW8ZNw1’ ‘~/tmp/scratch/RtmpWEocXB’   ‘~/tmp/scratch/RtmpWXiPXI’ ‘~/tmp/scratch/RtmpWrjc6Y’   ‘~/tmp/scratch/RtmpX94AL0’ ‘~/tmp/scratch/RtmpXfD3W0’   ‘~/tmp/scratch/RtmpXofHW7’ ‘~/tmp/scratch/RtmpYQ6nVU’   ‘~/tmp/scratch/RtmpYSSiyp’ ‘~/tmp/scratch/RtmpZ3GsK8’   ‘~/tmp/scratch/RtmpZ66SDU’ ‘~/tmp/scratch/RtmpZVezJ0’   ‘~/tmp/scratch/RtmpZb1vEW’ ‘~/tmp/scratch/Rtmpa7IHKt’   ‘~/tmp/scratch/RtmpaSZ0ki’ ‘~/tmp/scratch/RtmpaXbkTX’   ‘~/tmp/scratch/Rtmpaf4YJb’ ‘~/tmp/scratch/Rtmpal0Hjl’   ‘~/tmp/scratch/RtmpamelTg’ ‘~/tmp/scratch/Rtmpb9ou38’   ‘~/tmp/scratch/RtmpbiC22A’ ‘~/tmp/scratch/RtmpcIW5P5’   ‘~/tmp/scratch/RtmpcK1hPg’ ‘~/tmp/scratch/Rtmpco5W3k’   ‘~/tmp/scratch/RtmpcsZOoC’ ‘~/tmp/scratch/Rtmpd9v35l’   ‘~/tmp/scratch/RtmpeX3BHj’ ‘~/tmp/scratch/Rtmpeturii’   ‘~/tmp/scratch/Rtmpf8P1HL’ ‘~/tmp/scratch/RtmpfRB2cX’   ‘~/tmp/scratch/RtmpfUFnNx’ ‘~/tmp/scratch/Rtmpg5XuqR’   ‘~/tmp/scratch/RtmpgB1Kg1’ ‘~/tmp/scratch/RtmpgRyHo0’   ‘~/tmp/scratch/RtmpggKYa6’ ‘~/tmp/scratch/RtmphBFYIv’   ‘~/tmp/scratch/RtmphCGUt1’ ‘~/tmp/scratch/RtmphO93u8’   ‘~/tmp/scratch/Rtmphf10JY’ ‘~/tmp/scratch/RtmpiKaXoo’   ‘~/tmp/scratch/Rtmpj71DAL’ ‘~/tmp/scratch/Rtmpj8Js7h’   ‘~/tmp/scratch/RtmpjGmYG1’ ‘~/tmp/scratch/RtmpjgrqBk’   ‘~/tmp/scratch/RtmpkTxiL3’ ‘~/tmp/scratch/RtmplDsbFj’   ‘~/tmp/scratch/RtmplFjYII’ ‘~/tmp/scratch/Rtmpmd1yZ6’   ‘~/tmp/scratch/RtmpmeGwSN’ ‘~/tmp/scratch/RtmpnQ5sZR’   ‘~/tmp/scratch/RtmpnXawqc’ ‘~/tmp/scratch/RtmpoPQHQh’   ‘~/tmp/scratch/RtmpohKSD6’ ‘~/tmp/scratch/Rtmpojzxd9’   ‘~/tmp/scratch/RtmpqKXvAk’ ‘~/tmp/scratch/RtmpqS4oem’   ‘~/tmp/scratch/RtmprDIZEe’ ‘~/tmp/scratch/RtmprMR912’   ‘~/tmp/scratch/RtmpraR0om’ ‘~/tmp/scratch/RtmpsPDxOg’   ‘~/tmp/scratch/RtmptANB5l’ ‘~/tmp/scratch/Rtmpta5DgI’   ‘~/tmp/scratch/RtmptkKuak’ ‘~/tmp/scratch/RtmpueVz31’   ‘~/tmp/scratch/RtmpukmNYD’ ‘~/tmp/scratch/Rtmpul8pyQ’   ‘~/tmp/scratch/Rtmpvyj1NG’ ‘~/tmp/scratch/Rtmpw7Uazu’   ‘~/tmp/scratch/RtmpwkonbF’ ‘~/tmp/scratch/RtmpwpYEHI’   ‘~/tmp/scratch/RtmpwxuOE4’ ‘~/tmp/scratch/RtmpxbZVsG’   ‘~/tmp/scratch/Rtmpxn0Y9r’ ‘~/tmp/scratch/Rtmpy87OkP’   ‘~/tmp/scratch/Rtmpy9jEVX’ ‘~/tmp/scratch/RtmpylRzGJ’   ‘~/tmp/scratch/RtmpzKJ0PS’ ‘~/tmp/scratch/RtmpzKoCQR’   ‘~/tmp/scratch/RtmpzN07hl’ ‘~/tmp/scratch/RtmpzdSIVl’   ‘~/tmp/scratch/RtmpzthcgS’ ‘~/tmp/scratch/ar3hUDai’   ‘~/tmp/scratch/xvfb-run.02vxCj’ ‘~/tmp/scratch/xvfb-run.1DEn73’   ‘~/tmp/scratch/xvfb-run.2ocHqS’ ‘~/tmp/scratch/xvfb-run.3LSEZs’   ‘~/tmp/scratch/xvfb-run.5F7SWB’ ‘~/tmp/scratch/xvfb-run.5Qtpix’   ‘~/tmp/scratch/xvfb-run.6crVpw’ ‘~/tmp/scratch/xvfb-run.7ZeJcZ’   ‘~/tmp/scratch/xvfb-run.8ONDxP’ ‘~/tmp/scratch/xvfb-run.8pp1Y4’   ‘~/tmp/scratch/xvfb-run.8zykXN’ ‘~/tmp/scratch/xvfb-run.A7xOiS’   ‘~/tmp/scratch/xvfb-run.AyllRn’ ‘~/tmp/scratch/xvfb-run.B7YVFp’   ‘~/tmp/scratch/xvfb-run.BFf4gn’ ‘~/tmp/scratch/xvfb-run.Brmoh3’   ‘~/tmp/scratch/xvfb-run.DQbn9r’ ‘~/tmp/scratch/xvfb-run.EHWBny’   ‘~/tmp/scratch/xvfb-run.EibPy8’ ‘~/tmp/scratch/xvfb-run.F39KnD’   ‘~/tmp/scratch/xvfb-run.G2DDyn’ ‘~/tmp/scratch/xvfb-run.GjrtXr’   ‘~/tmp/scratch/xvfb-run.GkYU7K’ ‘~/tmp/scratch/xvfb-run.Gvnvit’   ‘~/tmp/scratch/xvfb-run.HUtsbc’ ‘~/tmp/scratch/xvfb-run.HiNXI5’   ‘~/tmp/scratch/xvfb-run.JHd7F7’ ‘~/tmp/scratch/xvfb-run.Jl6p5X’   ‘~/tmp/scratch/xvfb-run.KL0vhq’ ‘~/tmp/scratch/xvfb-run.L4qOKC’   ‘~/tmp/scratch/xvfb-run.LB10fV’ ‘~/tmp/scratch/xvfb-run.LaqbVr’   ‘~/tmp/scratch/xvfb-run.Llhx6q’ ‘~/tmp/scratch/xvfb-run.MBTe8W’   ‘~/tmp/scratch/xvfb-run.NDWSNt’ ‘~/tmp/scratch/xvfb-run.NK0Xnh’   ‘~/tmp/scratch/xvfb-run.On2tj7’ ‘~/tmp/scratch/xvfb-run.QPofIt’   ‘~/tmp/scratch/xvfb-run.QlM4G1’ ‘~/tmp/scratch/xvfb-run.QlimLT’   ‘~/tmp/scratch/xvfb-run.QuC2La’ ‘~/tmp/scratch/xvfb-run.R91YqY’   ‘~/tmp/scratch/xvfb-run.SlcshC’ ‘~/tmp/scratch/xvfb-run.T5fijU’   ‘~/tmp/scratch/xvfb-run.T6eL8t’ ‘~/tmp/scratch/xvfb-run.V08GRY’   ‘~/tmp/scratch/xvfb-run.VAdwoI’ ‘~/tmp/scratch/xvfb-run.VUwuw0’   ‘~/tmp/scratch/xvfb-run.VoSSp7’ ‘~/tmp/scratch/xvfb-run.VtMHKm’   ‘~/tmp/scratch/xvfb-run.Yaeys6’ ‘~/tmp/scratch/xvfb-run.Zao1vx’   ‘~/tmp/scratch/xvfb-run.cMGNJu’ ‘~/tmp/scratch/xvfb-run.dJ63qQ’   ‘~/tmp/scratch/xvfb-run.e1iMSY’ ‘~/tmp/scratch/xvfb-run.erIP3S’   ‘~/tmp/scratch/xvfb-run.g3nEam’ ‘~/tmp/scratch/xvfb-run.hH8qUe’   ‘~/tmp/scratch/xvfb-run.hMtwvc’ ‘~/tmp/scratch/xvfb-run.if9mQd’   ‘~/tmp/scratch/xvfb-run.jTgZRb’ ‘~/tmp/scratch/xvfb-run.jnyRXd’   ‘~/tmp/scratch/xvfb-run.jyTLCq’ ‘~/tmp/scratch/xvfb-run.kzTOTI’   ‘~/tmp/scratch/xvfb-run.plw9JM’ ‘~/tmp/scratch/xvfb-run.rDJJel’   ‘~/tmp/scratch/xvfb-run.rR6oLg’ ‘~/tmp/scratch/xvfb-run.siyc4j’   ‘~/tmp/scratch/xvfb-run.tC7Q6e’ ‘~/tmp/scratch/xvfb-run.w2DNk0’   ‘~/tmp/scratch/xvfb-run.wAIcYi’ ‘~/tmp/scratch/xvfb-run.wqeoYe’   ‘~/tmp/scratch/xvfb-run.wx3oRC’ ‘~/tmp/scratch/xvfb-run.zJjmQh’   ‘~/tmp/scratch/xvfb-run.zcBcEq’ ‘~/tmp/scratch/xvfb-run.ztYlDD’
• DONE

Status: 1 NOTE