• 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 16:49:17 UTC
• checking for file ‘penetrance/DESCRIPTION’ ... OK
• checking extension type ... Package
• this is package ‘penetrance’ version ‘0.1.3’
• package encoding: UTF-8
• 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 ‘penetrance’ can be installed ... OK See the install log for details.
• 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 ... [2s/3s] OK
• checking whether the package can be loaded with stated dependencies ... [1s/2s] OK
• checking whether the package can be unloaded cleanly ... [1s/2s] OK
• checking whether the namespace can be loaded with stated dependencies ... [1s/2s] OK
• checking whether the namespace can be unloaded cleanly ... [1s/2s] 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 ... [12s/16s] 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 ... [0s/1s] OK
• checking LazyData ... OK
• checking data for ASCII and uncompressed saves ... OK
• checking installed files from ‘inst/doc’ ... OK
• checking files in ‘vignettes’ ... OK
• checking examples ... [2s/6s] OK
• checking for unstated dependencies in vignettes ... OK
• checking package vignettes ... OK
• checking re-building of vignette outputs ... [12s/17s] OK
• checking PDF version of manual ... [5s/7s] OK
• checking HTML version of manual ... [1s/2s] 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/Rtmp0KZSlN’ ‘~/tmp/scratch/Rtmp0Spig2’   ‘~/tmp/scratch/Rtmp0kjore’ ‘~/tmp/scratch/Rtmp0pocbi’   ‘~/tmp/scratch/Rtmp1RI8Rt’ ‘~/tmp/scratch/Rtmp2mDS1I’   ‘~/tmp/scratch/Rtmp3Ibfgq’ ‘~/tmp/scratch/Rtmp3Ph5Gb’   ‘~/tmp/scratch/Rtmp3jJU9N’ ‘~/tmp/scratch/Rtmp3jTn37’   ‘~/tmp/scratch/Rtmp4pvsJu’ ‘~/tmp/scratch/Rtmp4wRvHP’   ‘~/tmp/scratch/Rtmp57fJ9F’ ‘~/tmp/scratch/Rtmp5HNdn0’   ‘~/tmp/scratch/Rtmp5XSjeb’ ‘~/tmp/scratch/Rtmp5ZCA22’   ‘~/tmp/scratch/Rtmp6qwGT2’ ‘~/tmp/scratch/Rtmp8p7wKh’   ‘~/tmp/scratch/Rtmp9hT5C9’ ‘~/tmp/scratch/Rtmp9mNpDq’   ‘~/tmp/scratch/Rtmp9oo3Ra’ ‘~/tmp/scratch/Rtmp9wUWrv’   ‘~/tmp/scratch/RtmpA21wnQ’ ‘~/tmp/scratch/RtmpAD4onV’   ‘~/tmp/scratch/RtmpALsFnc’ ‘~/tmp/scratch/RtmpAM1lIs’   ‘~/tmp/scratch/RtmpAUegIe’ ‘~/tmp/scratch/RtmpCA2joE’   ‘~/tmp/scratch/RtmpCHES3l’ ‘~/tmp/scratch/RtmpCWGze7’   ‘~/tmp/scratch/RtmpCljagC’ ‘~/tmp/scratch/RtmpCxDIMP’   ‘~/tmp/scratch/RtmpDih5I1’ ‘~/tmp/scratch/RtmpE9LkQR’   ‘~/tmp/scratch/RtmpEPQ43Y’ ‘~/tmp/scratch/RtmpEoUmq6’   ‘~/tmp/scratch/RtmpEvrtWh’ ‘~/tmp/scratch/RtmpFJfm0u’   ‘~/tmp/scratch/RtmpFKmWvJ’ ‘~/tmp/scratch/RtmpFjvyrC’   ‘~/tmp/scratch/RtmpGPSrLv’ ‘~/tmp/scratch/RtmpGqAiK0’   ‘~/tmp/scratch/RtmpGrE6Z5’ ‘~/tmp/scratch/RtmpH8TK9z’   ‘~/tmp/scratch/RtmpHHFUdC’ ‘~/tmp/scratch/RtmpHJ79Ly’   ‘~/tmp/scratch/RtmpHsiSsZ’ ‘~/tmp/scratch/RtmpIywVP6’   ‘~/tmp/scratch/RtmpJ0ACGu’ ‘~/tmp/scratch/RtmpJLMe4J’   ‘~/tmp/scratch/RtmpJi5h4l’ ‘~/tmp/scratch/RtmpK3S2Md’   ‘~/tmp/scratch/RtmpKITJH9’ ‘~/tmp/scratch/RtmpKOzWIR’   ‘~/tmp/scratch/RtmpKYskpe’ ‘~/tmp/scratch/RtmpKaFViX’   ‘~/tmp/scratch/RtmpL8gEQf’ ‘~/tmp/scratch/RtmpLygutR’   ‘~/tmp/scratch/RtmpM8zYLt’ ‘~/tmp/scratch/RtmpMRp2Zo’   ‘~/tmp/scratch/RtmpNG4Mtc’ ‘~/tmp/scratch/RtmpNpRKPJ’   ‘~/tmp/scratch/RtmpP9oxTR’ ‘~/tmp/scratch/RtmpPL7WEi’   ‘~/tmp/scratch/RtmpPsDcI9’ ‘~/tmp/scratch/RtmpQvEplF’   ‘~/tmp/scratch/RtmpRApDTV’ ‘~/tmp/scratch/RtmpS9LUMY’   ‘~/tmp/scratch/RtmpT61HBI’ ‘~/tmp/scratch/RtmpToSpWD’   ‘~/tmp/scratch/RtmpTxvL1I’ ‘~/tmp/scratch/RtmpUFOCGm’   ‘~/tmp/scratch/RtmpVqKh3u’ ‘~/tmp/scratch/RtmpWCeM9L’   ‘~/tmp/scratch/RtmpWLIvX6’ ‘~/tmp/scratch/RtmpWPV9lt’   ‘~/tmp/scratch/RtmpXkexc8’ ‘~/tmp/scratch/RtmpY1Kue1’   ‘~/tmp/scratch/RtmpYaj3Fd’ ‘~/tmp/scratch/RtmpZNLpTB’   ‘~/tmp/scratch/RtmpaIKDxf’ ‘~/tmp/scratch/RtmpaNXWOY’   ‘~/tmp/scratch/RtmpaqCrGz’ ‘~/tmp/scratch/RtmpbIJ8jT’   ‘~/tmp/scratch/RtmpbMMXfp’ ‘~/tmp/scratch/Rtmpbmja0W’   ‘~/tmp/scratch/RtmpbuwhoI’ ‘~/tmp/scratch/RtmpcBc8ab’   ‘~/tmp/scratch/RtmpcRpTqA’ ‘~/tmp/scratch/RtmpckglzI’   ‘~/tmp/scratch/RtmpdCcXsY’ ‘~/tmp/scratch/RtmpdFRL33’   ‘~/tmp/scratch/Rtmpe8JFF1’ ‘~/tmp/scratch/Rtmped84NF’   ‘~/tmp/scratch/RtmpfBl2Fj’ ‘~/tmp/scratch/RtmpfBzQql’   ‘~/tmp/scratch/RtmpftLAcm’ ‘~/tmp/scratch/RtmpfwiUR6’   ‘~/tmp/scratch/RtmpgS2nA4’ ‘~/tmp/scratch/RtmpgSaahh’   ‘~/tmp/scratch/RtmpgaJQFD’ ‘~/tmp/scratch/RtmpghUMC6’   ‘~/tmp/scratch/Rtmph1FjRU’ ‘~/tmp/scratch/Rtmphw3fAK’   ‘~/tmp/scratch/RtmpiJAjV0’ ‘~/tmp/scratch/RtmpjGWG7H’   ‘~/tmp/scratch/RtmpjZOl1W’ ‘~/tmp/scratch/RtmpkOgy88’   ‘~/tmp/scratch/RtmpkviPO5’ ‘~/tmp/scratch/Rtmpl57Qeq’   ‘~/tmp/scratch/RtmplKV9KJ’ ‘~/tmp/scratch/RtmpmTiviu’   ‘~/tmp/scratch/Rtmpn9meGU’ ‘~/tmp/scratch/Rtmpo7IZD2’   ‘~/tmp/scratch/RtmpoDG3Gi’ ‘~/tmp/scratch/RtmppOw9sg’   ‘~/tmp/scratch/Rtmppar1ue’ ‘~/tmp/scratch/RtmpppRxxd’   ‘~/tmp/scratch/RtmpptJlJu’ ‘~/tmp/scratch/RtmpqJFTFg’   ‘~/tmp/scratch/RtmpqSvx9u’ ‘~/tmp/scratch/RtmprmaaI1’   ‘~/tmp/scratch/RtmpsSfdgO’ ‘~/tmp/scratch/Rtmpss3TpQ’   ‘~/tmp/scratch/RtmptLeMXK’ ‘~/tmp/scratch/RtmptTXPOk’   ‘~/tmp/scratch/Rtmptba2wh’ ‘~/tmp/scratch/Rtmpts3vIx’   ‘~/tmp/scratch/Rtmpu7guyM’ ‘~/tmp/scratch/RtmpuUaHkc’   ‘~/tmp/scratch/RtmpuldnZ6’ ‘~/tmp/scratch/RtmpulrZ91’   ‘~/tmp/scratch/RtmpunR9W9’ ‘~/tmp/scratch/RtmpvNVFd0’   ‘~/tmp/scratch/RtmpvVhkgC’ ‘~/tmp/scratch/RtmpvoGn0X’   ‘~/tmp/scratch/Rtmpvyug42’ ‘~/tmp/scratch/RtmpwPDkZl’   ‘~/tmp/scratch/RtmpwcChMI’ ‘~/tmp/scratch/RtmpwqMV2q’   ‘~/tmp/scratch/Rtmpxb10BP’ ‘~/tmp/scratch/RtmpxbCxtW’   ‘~/tmp/scratch/Rtmpz2ZtK6’ ‘~/tmp/scratch/RtmpzFBrpH’   ‘~/tmp/scratch/RtmpzhE7nS’ ‘~/tmp/scratch/xvfb-run.6QSGtN’   ‘~/tmp/scratch/xvfb-run.6WspnU’ ‘~/tmp/scratch/xvfb-run.6e9B4V’   ‘~/tmp/scratch/xvfb-run.6vHqkc’ ‘~/tmp/scratch/xvfb-run.8SbxYU’   ‘~/tmp/scratch/xvfb-run.94PZqX’ ‘~/tmp/scratch/xvfb-run.9D4FcE’   ‘~/tmp/scratch/xvfb-run.9GvZPY’ ‘~/tmp/scratch/xvfb-run.9WWGyI’   ‘~/tmp/scratch/xvfb-run.A8yzBH’ ‘~/tmp/scratch/xvfb-run.BUaf56’   ‘~/tmp/scratch/xvfb-run.C7flPf’ ‘~/tmp/scratch/xvfb-run.CrlYl2’   ‘~/tmp/scratch/xvfb-run.DCCNDU’ ‘~/tmp/scratch/xvfb-run.EnJOz0’   ‘~/tmp/scratch/xvfb-run.FEETg2’ ‘~/tmp/scratch/xvfb-run.FNus4l’   ‘~/tmp/scratch/xvfb-run.FTcjWB’ ‘~/tmp/scratch/xvfb-run.Fb7pm6’   ‘~/tmp/scratch/xvfb-run.G38SPs’ ‘~/tmp/scratch/xvfb-run.GeeLBh’   ‘~/tmp/scratch/xvfb-run.HDHf7a’ ‘~/tmp/scratch/xvfb-run.JXNXX7’   ‘~/tmp/scratch/xvfb-run.KEa067’ ‘~/tmp/scratch/xvfb-run.KV4C5u’   ‘~/tmp/scratch/xvfb-run.Kmq3Iw’ ‘~/tmp/scratch/xvfb-run.NGlV2K’   ‘~/tmp/scratch/xvfb-run.NayTIY’ ‘~/tmp/scratch/xvfb-run.ToGBvB’   ‘~/tmp/scratch/xvfb-run.UPUd1Y’ ‘~/tmp/scratch/xvfb-run.VPmpYD’   ‘~/tmp/scratch/xvfb-run.XaSpXp’ ‘~/tmp/scratch/xvfb-run.XkDDPX’   ‘~/tmp/scratch/xvfb-run.Yj7HX0’ ‘~/tmp/scratch/xvfb-run.ZCgr8n’   ‘~/tmp/scratch/xvfb-run.ZT9Xkt’ ‘~/tmp/scratch/xvfb-run.bNP0tY’   ‘~/tmp/scratch/xvfb-run.bgPYvG’ ‘~/tmp/scratch/xvfb-run.cicIxJ’   ‘~/tmp/scratch/xvfb-run.e9M9VH’ ‘~/tmp/scratch/xvfb-run.eJhPsr’   ‘~/tmp/scratch/xvfb-run.f56jhK’ ‘~/tmp/scratch/xvfb-run.fyNLdW’   ‘~/tmp/scratch/xvfb-run.gSqQIq’ ‘~/tmp/scratch/xvfb-run.k6Tt81’   ‘~/tmp/scratch/xvfb-run.kFBHYW’ ‘~/tmp/scratch/xvfb-run.kq3BbM’   ‘~/tmp/scratch/xvfb-run.mm5wKI’ ‘~/tmp/scratch/xvfb-run.pvjEsz’   ‘~/tmp/scratch/xvfb-run.rKHyhQ’ ‘~/tmp/scratch/xvfb-run.swWs3k’   ‘~/tmp/scratch/xvfb-run.t5WDQT’ ‘~/tmp/scratch/xvfb-run.u3FsO5’   ‘~/tmp/scratch/xvfb-run.uhvJ16’ ‘~/tmp/scratch/xvfb-run.yTQAXT’   ‘~/tmp/scratch/xvfb-run.zhdz5T’
• DONE

Status: 1 NOTE