• using R Under development (unstable) (2026-07-30 r90327)
• 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: 2026-07-31 17:03:14 UTC
• checking for file ‘protHMM/DESCRIPTION’ ... OK
• checking extension type ... Package
• this is package ‘protHMM’ version ‘0.1.1’
• 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 serialization versions ... OK
• checking whether package ‘protHMM’ 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 ... [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 ... [5s/7s] 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 installed files from ‘inst/doc’ ... OK
• checking files in ‘vignettes’ ... OK
• checking examples ... [5s/8s] OK
• checking for unstated dependencies in ‘tests’ ... OK
• checking tests ... [9s/14s] OK   Running ‘testthat.R’ [9s/14s]
• checking for unstated dependencies in vignettes ... OK
• checking package vignettes ... OK
• checking re-building of vignette outputs ... [7s/10s] OK
• checking PDF version of manual ... [4s/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/Rtmp0DWm15’ ‘~/tmp/scratch/Rtmp0Ocpig’   ‘~/tmp/scratch/Rtmp0Oh1HG’ ‘~/tmp/scratch/Rtmp1CVjEf’   ‘~/tmp/scratch/Rtmp1IFnDF’ ‘~/tmp/scratch/Rtmp2Ez5Hl’   ‘~/tmp/scratch/Rtmp3VfiHc’ ‘~/tmp/scratch/Rtmp3bo8Cu’   ‘~/tmp/scratch/Rtmp4XMDrP’ ‘~/tmp/scratch/Rtmp4XhZRR’   ‘~/tmp/scratch/Rtmp4yFRSa’ ‘~/tmp/scratch/Rtmp5b83c5’   ‘~/tmp/scratch/Rtmp5oKi14’ ‘~/tmp/scratch/Rtmp5oe8hU’   ‘~/tmp/scratch/Rtmp6b7Any’ ‘~/tmp/scratch/Rtmp7WnNaR’   ‘~/tmp/scratch/Rtmp7cTJfA’ ‘~/tmp/scratch/Rtmp9JWj47’   ‘~/tmp/scratch/Rtmp9cFtpy’ ‘~/tmp/scratch/Rtmp9z8ihB’   ‘~/tmp/scratch/RtmpA4L400’ ‘~/tmp/scratch/RtmpACTgnK’   ‘~/tmp/scratch/RtmpAX5Xoh’ ‘~/tmp/scratch/RtmpAbJ8dM’   ‘~/tmp/scratch/RtmpB5cbbK’ ‘~/tmp/scratch/RtmpBAeCAy’   ‘~/tmp/scratch/RtmpCMGgdL’ ‘~/tmp/scratch/RtmpEAdLHx’   ‘~/tmp/scratch/RtmpEzFwGc’ ‘~/tmp/scratch/RtmpF247QW’   ‘~/tmp/scratch/RtmpFcdFsY’ ‘~/tmp/scratch/RtmpH7FnsS’   ‘~/tmp/scratch/RtmpI0S5fO’ ‘~/tmp/scratch/RtmpI3Ious’   ‘~/tmp/scratch/RtmpIYaaAv’ ‘~/tmp/scratch/RtmpJJ3uGn’   ‘~/tmp/scratch/RtmpJajbOP’ ‘~/tmp/scratch/RtmpKNCmnW’   ‘~/tmp/scratch/RtmpKUAN08’ ‘~/tmp/scratch/RtmpKZaHsM’   ‘~/tmp/scratch/RtmpL3htBm’ ‘~/tmp/scratch/RtmpLliA7k’   ‘~/tmp/scratch/RtmpMhWou6’ ‘~/tmp/scratch/RtmpN4dMAK’   ‘~/tmp/scratch/RtmpNJNxW8’ ‘~/tmp/scratch/RtmpO9j1cU’   ‘~/tmp/scratch/RtmpOFZedH’ ‘~/tmp/scratch/RtmpONgyef’   ‘~/tmp/scratch/RtmpOPh3p8’ ‘~/tmp/scratch/RtmpOVWY4g’   ‘~/tmp/scratch/RtmpOk2DE3’ ‘~/tmp/scratch/RtmpOuGxYC’   ‘~/tmp/scratch/RtmpQ0Q80n’ ‘~/tmp/scratch/RtmpQHKhyI’   ‘~/tmp/scratch/RtmpR5Ooav’ ‘~/tmp/scratch/RtmpRNxlfc’   ‘~/tmp/scratch/RtmpRZUhDD’ ‘~/tmp/scratch/RtmpRf7WWM’   ‘~/tmp/scratch/RtmpS8M0ed’ ‘~/tmp/scratch/RtmpSArjhh’   ‘~/tmp/scratch/RtmpT1pSWo’ ‘~/tmp/scratch/RtmpT3Lil9’   ‘~/tmp/scratch/RtmpUUgfwy’ ‘~/tmp/scratch/RtmpUUyjuA’   ‘~/tmp/scratch/RtmpV7Nxd6’ ‘~/tmp/scratch/RtmpVEfLoF’   ‘~/tmp/scratch/RtmpVhYUxR’ ‘~/tmp/scratch/RtmpWFUfP3’   ‘~/tmp/scratch/RtmpWRDjfv’ ‘~/tmp/scratch/RtmpWa4GBr’   ‘~/tmp/scratch/RtmpWyNjyh’ ‘~/tmp/scratch/RtmpYWKHmD’   ‘~/tmp/scratch/RtmpYWjbZ9’ ‘~/tmp/scratch/RtmpYa7CPp’   ‘~/tmp/scratch/RtmpYkGIHq’ ‘~/tmp/scratch/RtmpZT96SO’   ‘~/tmp/scratch/RtmpaCOFJD’ ‘~/tmp/scratch/RtmpaU8g6Z’   ‘~/tmp/scratch/RtmpaiQHhk’ ‘~/tmp/scratch/Rtmpb6Rg8F’   ‘~/tmp/scratch/RtmpbrH8Zj’ ‘~/tmp/scratch/RtmpbshZDo’   ‘~/tmp/scratch/Rtmpe17bqb’ ‘~/tmp/scratch/RtmpeVaWc5’   ‘~/tmp/scratch/RtmpfRzS76’ ‘~/tmp/scratch/RtmpfW4nqx’   ‘~/tmp/scratch/Rtmpg0g1t0’ ‘~/tmp/scratch/Rtmpg6NETw’   ‘~/tmp/scratch/RtmpgDPOT4’ ‘~/tmp/scratch/RtmpjHcaLD’   ‘~/tmp/scratch/RtmpkRYMaO’ ‘~/tmp/scratch/RtmpkRphma’   ‘~/tmp/scratch/RtmplNY7rO’ ‘~/tmp/scratch/RtmplxiCtg’   ‘~/tmp/scratch/RtmpmGwJRn’ ‘~/tmp/scratch/RtmpmVT8iN’   ‘~/tmp/scratch/Rtmpmuzv0P’ ‘~/tmp/scratch/Rtmpn2sR50’   ‘~/tmp/scratch/RtmpnJgZWL’ ‘~/tmp/scratch/RtmpnYDINL’   ‘~/tmp/scratch/RtmpnvlMMR’ ‘~/tmp/scratch/RtmpoPmpNj’   ‘~/tmp/scratch/RtmppGQuqs’ ‘~/tmp/scratch/Rtmpq3yRfY’   ‘~/tmp/scratch/RtmpqfA49K’ ‘~/tmp/scratch/Rtmpqr4tNs’   ‘~/tmp/scratch/RtmprF6WPy’ ‘~/tmp/scratch/RtmprJCG1z’   ‘~/tmp/scratch/RtmptKTR3A’ ‘~/tmp/scratch/Rtmpu3ocJs’   ‘~/tmp/scratch/Rtmpu4YY8N’ ‘~/tmp/scratch/RtmpuOQJ2I’   ‘~/tmp/scratch/RtmpuZnfRr’ ‘~/tmp/scratch/RtmpvA4O7L’   ‘~/tmp/scratch/Rtmpw7iAkl’ ‘~/tmp/scratch/RtmpwS3ojb’   ‘~/tmp/scratch/RtmpwkarHy’ ‘~/tmp/scratch/Rtmpxq0INQ’   ‘~/tmp/scratch/RtmpxsTU7R’ ‘~/tmp/scratch/Rtmpy5RRdB’   ‘~/tmp/scratch/RtmpyVKTBP’ ‘~/tmp/scratch/RtmpzEmXcU’   ‘~/tmp/scratch/RtmpzXkHrT’ ‘~/tmp/scratch/xvfb-run.2r6aSZ’   ‘~/tmp/scratch/xvfb-run.3ysFa6’ ‘~/tmp/scratch/xvfb-run.5PizMe’   ‘~/tmp/scratch/xvfb-run.6aeg5H’ ‘~/tmp/scratch/xvfb-run.8LbWiQ’   ‘~/tmp/scratch/xvfb-run.8r6Lin’ ‘~/tmp/scratch/xvfb-run.8xPDuj’   ‘~/tmp/scratch/xvfb-run.90a2pR’ ‘~/tmp/scratch/xvfb-run.9TaXHZ’   ‘~/tmp/scratch/xvfb-run.Ah9dwN’ ‘~/tmp/scratch/xvfb-run.BIx1Cn’   ‘~/tmp/scratch/xvfb-run.BOps13’ ‘~/tmp/scratch/xvfb-run.DndxB1’   ‘~/tmp/scratch/xvfb-run.Ed3NY1’ ‘~/tmp/scratch/xvfb-run.G20U5n’   ‘~/tmp/scratch/xvfb-run.L0rSFa’ ‘~/tmp/scratch/xvfb-run.LrGY1v’   ‘~/tmp/scratch/xvfb-run.NfNQuo’ ‘~/tmp/scratch/xvfb-run.Pee7Ju’   ‘~/tmp/scratch/xvfb-run.Rfb62R’ ‘~/tmp/scratch/xvfb-run.SQvJoO’   ‘~/tmp/scratch/xvfb-run.Ssy7Ex’ ‘~/tmp/scratch/xvfb-run.UUkScJ’   ‘~/tmp/scratch/xvfb-run.V1f8As’ ‘~/tmp/scratch/xvfb-run.Y9o62I’   ‘~/tmp/scratch/xvfb-run.aRVzmN’ ‘~/tmp/scratch/xvfb-run.aYgeB0’   ‘~/tmp/scratch/xvfb-run.bEXll8’ ‘~/tmp/scratch/xvfb-run.bUTP4Z’   ‘~/tmp/scratch/xvfb-run.ckFwDm’ ‘~/tmp/scratch/xvfb-run.hgaRB1’   ‘~/tmp/scratch/xvfb-run.i81rpz’ ‘~/tmp/scratch/xvfb-run.kJUR13’   ‘~/tmp/scratch/xvfb-run.kyWk00’ ‘~/tmp/scratch/xvfb-run.lLe9ge’   ‘~/tmp/scratch/xvfb-run.lMrVyO’ ‘~/tmp/scratch/xvfb-run.lbUtBa’   ‘~/tmp/scratch/xvfb-run.p19mcv’ ‘~/tmp/scratch/xvfb-run.qBjB5j’   ‘~/tmp/scratch/xvfb-run.rNNXz2’ ‘~/tmp/scratch/xvfb-run.sHtZ17’   ‘~/tmp/scratch/xvfb-run.uH8G8k’ ‘~/tmp/scratch/xvfb-run.uYCACF’   ‘~/tmp/scratch/xvfb-run.vuUz1V’ ‘~/tmp/scratch/xvfb-run.wKBtri’   ‘~/tmp/scratch/xvfb-run.xkfN7k’ ‘~/tmp/scratch/xvfb-run.y3NHES’   ‘~/tmp/scratch/xvfb-run.yT6VwO’
• DONE

Status: 1 NOTE