• 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 16:38:25 UTC
• checking for file ‘ontologyIndex/DESCRIPTION’ ... OK
• checking extension type ... Package
• this is package ‘ontologyIndex’ version ‘2.12’
• package encoding: UTF-8
• checking CRAN incoming feasibility ... [1s/2s] NOTE Maintainer: ‘Daniel Greene <dg333@cam.ac.uk>’ No Authors@R field in DESCRIPTION. Please add one, modifying   Authors@R: person(given = "Daniel",                     family = "Greene",                     role = c("aut", "cre"),                     email = "dg333@cam.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 whether package ‘ontologyIndex’ 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 ... [4s/5s] 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 ... [5s/7s] OK
• checking data for ASCII and uncompressed saves ... OK
• checking installed files from ‘inst/doc’ ... OK
• checking files in ‘vignettes’ ... OK
• checking examples ... [3s/4s] OK
• checking for unstated dependencies in vignettes ... OK
• checking package vignettes ... OK
• checking re-building of vignette outputs ... [4s/6s] 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/Rtmp1u8HT3’ ‘~/tmp/scratch/Rtmp2VcyDu’   ‘~/tmp/scratch/Rtmp3GjSGG’ ‘~/tmp/scratch/Rtmp4A5eiw’   ‘~/tmp/scratch/Rtmp4b6rOp’ ‘~/tmp/scratch/Rtmp6AdyBV’   ‘~/tmp/scratch/Rtmp6O1yoA’ ‘~/tmp/scratch/Rtmp7BSOUX’   ‘~/tmp/scratch/Rtmp7a3ThB’ ‘~/tmp/scratch/Rtmp8BAJcC’   ‘~/tmp/scratch/Rtmp8CgOT7’ ‘~/tmp/scratch/Rtmp8NuCto’   ‘~/tmp/scratch/Rtmp8XRQK5’ ‘~/tmp/scratch/Rtmp8tqqEO’   ‘~/tmp/scratch/Rtmp9jsJgD’ ‘~/tmp/scratch/RtmpA4a7JX’   ‘~/tmp/scratch/RtmpAqZseq’ ‘~/tmp/scratch/RtmpB8DNpE’   ‘~/tmp/scratch/RtmpBS6gqe’ ‘~/tmp/scratch/RtmpBmlhOF’   ‘~/tmp/scratch/RtmpBqqm5X’ ‘~/tmp/scratch/RtmpBs71M7’   ‘~/tmp/scratch/RtmpByQ0tN’ ‘~/tmp/scratch/RtmpC2sGto’   ‘~/tmp/scratch/RtmpCRHUM7’ ‘~/tmp/scratch/RtmpCSWyDP’   ‘~/tmp/scratch/RtmpCcJVCN’ ‘~/tmp/scratch/RtmpDBfcJs’   ‘~/tmp/scratch/RtmpDbhEiB’ ‘~/tmp/scratch/RtmpDvsVnG’   ‘~/tmp/scratch/RtmpDzkBc9’ ‘~/tmp/scratch/RtmpERJVPE’   ‘~/tmp/scratch/RtmpEWKtOV’ ‘~/tmp/scratch/RtmpEX7e8B’   ‘~/tmp/scratch/RtmpEixFaI’ ‘~/tmp/scratch/RtmpF1bqkR’   ‘~/tmp/scratch/RtmpF95KYb’ ‘~/tmp/scratch/RtmpFiOx93’   ‘~/tmp/scratch/RtmpGAxJFV’ ‘~/tmp/scratch/RtmpGSfwHq’   ‘~/tmp/scratch/RtmpGYHhAg’ ‘~/tmp/scratch/RtmpH2v1jJ’   ‘~/tmp/scratch/RtmpHUzjn2’ ‘~/tmp/scratch/RtmpHbFlaD’   ‘~/tmp/scratch/RtmpI6nu89’ ‘~/tmp/scratch/RtmpISH8O1’   ‘~/tmp/scratch/RtmpIvjc6O’ ‘~/tmp/scratch/RtmpJMrrbF’   ‘~/tmp/scratch/RtmpJkWYUo’ ‘~/tmp/scratch/RtmpKKrW7O’   ‘~/tmp/scratch/RtmpKlyyZT’ ‘~/tmp/scratch/RtmpM6qIy5’   ‘~/tmp/scratch/RtmpMGtV4b’ ‘~/tmp/scratch/RtmpMzziu1’   ‘~/tmp/scratch/RtmpN3gYzX’ ‘~/tmp/scratch/RtmpNe8Vhp’   ‘~/tmp/scratch/RtmpOIOiwY’ ‘~/tmp/scratch/RtmpOWqoQq’   ‘~/tmp/scratch/RtmpOZ56SZ’ ‘~/tmp/scratch/RtmpOlBtrZ’   ‘~/tmp/scratch/RtmpP0jjDz’ ‘~/tmp/scratch/RtmpPEzyso’   ‘~/tmp/scratch/RtmpQDnKmZ’ ‘~/tmp/scratch/RtmpQExOjF’   ‘~/tmp/scratch/RtmpSNRmho’ ‘~/tmp/scratch/RtmpT6ujFn’   ‘~/tmp/scratch/RtmpTciKME’ ‘~/tmp/scratch/RtmpUdWrKU’   ‘~/tmp/scratch/RtmpV7ej3e’ ‘~/tmp/scratch/RtmpVKGaaE’   ‘~/tmp/scratch/RtmpVu3BxV’ ‘~/tmp/scratch/RtmpVyWsPO’   ‘~/tmp/scratch/RtmpW7Rj1p’ ‘~/tmp/scratch/RtmpWatFcv’   ‘~/tmp/scratch/RtmpX4pb9U’ ‘~/tmp/scratch/RtmpXAZCnX’   ‘~/tmp/scratch/RtmpYbfOxM’ ‘~/tmp/scratch/RtmpYj5hbj’   ‘~/tmp/scratch/RtmpYscTHg’ ‘~/tmp/scratch/RtmpZBqSJD’   ‘~/tmp/scratch/RtmpZvTFlY’ ‘~/tmp/scratch/Rtmpa1v0L3’   ‘~/tmp/scratch/Rtmpa7a8Z2’ ‘~/tmp/scratch/RtmpaAXJU0’   ‘~/tmp/scratch/RtmpaLsXP3’ ‘~/tmp/scratch/RtmpbHZN2h’   ‘~/tmp/scratch/RtmpbXjpjH’ ‘~/tmp/scratch/RtmpbcCYWL’   ‘~/tmp/scratch/RtmpbwSMha’ ‘~/tmp/scratch/RtmpcK58zZ’   ‘~/tmp/scratch/Rtmpd63Y6M’ ‘~/tmp/scratch/RtmpdmlpHH’   ‘~/tmp/scratch/RtmpeWjFDf’ ‘~/tmp/scratch/Rtmpeh73aL’   ‘~/tmp/scratch/RtmpfUMq4W’ ‘~/tmp/scratch/RtmpfaEXAw’   ‘~/tmp/scratch/Rtmpgev9WM’ ‘~/tmp/scratch/Rtmpgk7wql’   ‘~/tmp/scratch/Rtmph6CbaP’ ‘~/tmp/scratch/RtmphM0iLk’   ‘~/tmp/scratch/RtmphObaI8’ ‘~/tmp/scratch/RtmphwLdEP’   ‘~/tmp/scratch/Rtmpi0akBw’ ‘~/tmp/scratch/Rtmpi4pDqi’   ‘~/tmp/scratch/Rtmpic4iGr’ ‘~/tmp/scratch/RtmpkDUMBk’   ‘~/tmp/scratch/RtmplVEPOI’ ‘~/tmp/scratch/RtmplahQjf’   ‘~/tmp/scratch/RtmpnE9Tsp’ ‘~/tmp/scratch/RtmpnLApFg’   ‘~/tmp/scratch/RtmpnQwgUs’ ‘~/tmp/scratch/RtmpnlJD6Z’   ‘~/tmp/scratch/Rtmpo3nbmI’ ‘~/tmp/scratch/RtmpoADcLm’   ‘~/tmp/scratch/RtmpoyXELp’ ‘~/tmp/scratch/RtmppnyGqa’   ‘~/tmp/scratch/RtmpqOR9qY’ ‘~/tmp/scratch/RtmpsBkERu’   ‘~/tmp/scratch/RtmpsTiPw5’ ‘~/tmp/scratch/RtmpuHDRez’   ‘~/tmp/scratch/RtmpvMMKRD’ ‘~/tmp/scratch/Rtmpvg5er1’   ‘~/tmp/scratch/Rtmpvkyzhw’ ‘~/tmp/scratch/Rtmpwu3DAi’   ‘~/tmp/scratch/RtmpxgyHSU’ ‘~/tmp/scratch/Rtmpy22muk’   ‘~/tmp/scratch/RtmpyGuafO’ ‘~/tmp/scratch/RtmpyKfJH5’   ‘~/tmp/scratch/RtmpyPjCAs’ ‘~/tmp/scratch/Rtmpylu3Xj’   ‘~/tmp/scratch/RtmpynDQf9’ ‘~/tmp/scratch/RtmpzTEvIU’   ‘~/tmp/scratch/xvfb-run.0GWTJ7’ ‘~/tmp/scratch/xvfb-run.28KPwP’   ‘~/tmp/scratch/xvfb-run.3hG4lW’ ‘~/tmp/scratch/xvfb-run.4FYgSh’   ‘~/tmp/scratch/xvfb-run.5xZdPn’ ‘~/tmp/scratch/xvfb-run.6Kw6os’   ‘~/tmp/scratch/xvfb-run.7KlJn1’ ‘~/tmp/scratch/xvfb-run.9FGJjc’   ‘~/tmp/scratch/xvfb-run.9FtxXh’ ‘~/tmp/scratch/xvfb-run.9UliG7’   ‘~/tmp/scratch/xvfb-run.A3Zi0s’ ‘~/tmp/scratch/xvfb-run.A6GaYe’   ‘~/tmp/scratch/xvfb-run.Ab3A4t’ ‘~/tmp/scratch/xvfb-run.BXh0Wn’   ‘~/tmp/scratch/xvfb-run.BgpOLS’ ‘~/tmp/scratch/xvfb-run.Cne1zj’   ‘~/tmp/scratch/xvfb-run.EqLHNP’ ‘~/tmp/scratch/xvfb-run.FpqiOf’   ‘~/tmp/scratch/xvfb-run.GzNmg4’ ‘~/tmp/scratch/xvfb-run.LHlftw’   ‘~/tmp/scratch/xvfb-run.Mlc57y’ ‘~/tmp/scratch/xvfb-run.MuKX2N’   ‘~/tmp/scratch/xvfb-run.PjNmck’ ‘~/tmp/scratch/xvfb-run.PuLOk8’   ‘~/tmp/scratch/xvfb-run.Qo4mga’ ‘~/tmp/scratch/xvfb-run.UD65sY’   ‘~/tmp/scratch/xvfb-run.UozOOP’ ‘~/tmp/scratch/xvfb-run.ZL2ibD’   ‘~/tmp/scratch/xvfb-run.afZwTn’ ‘~/tmp/scratch/xvfb-run.an3uaw’   ‘~/tmp/scratch/xvfb-run.b0Zrep’ ‘~/tmp/scratch/xvfb-run.cWgkSb’   ‘~/tmp/scratch/xvfb-run.dhahGg’ ‘~/tmp/scratch/xvfb-run.fmVWvG’   ‘~/tmp/scratch/xvfb-run.i1X9fw’ ‘~/tmp/scratch/xvfb-run.iKoofW’   ‘~/tmp/scratch/xvfb-run.iiLiEA’ ‘~/tmp/scratch/xvfb-run.jwX2yQ’   ‘~/tmp/scratch/xvfb-run.ka0vEo’ ‘~/tmp/scratch/xvfb-run.mvoIwN’   ‘~/tmp/scratch/xvfb-run.q37db0’ ‘~/tmp/scratch/xvfb-run.rV6YgG’   ‘~/tmp/scratch/xvfb-run.t9RlP6’ ‘~/tmp/scratch/xvfb-run.tfEzOk’   ‘~/tmp/scratch/xvfb-run.uLCCiA’ ‘~/tmp/scratch/xvfb-run.wC2rh5’   ‘~/tmp/scratch/xvfb-run.wF76Dx’ ‘~/tmp/scratch/xvfb-run.wQ7pXj’   ‘~/tmp/scratch/xvfb-run.zg3VIj’   ‘/dev/shm/sm_segment.gimli1.1001.269f0000.0’   ‘/dev/shm/sm_segment.gimli1.1001.883b0000.0’   ‘/dev/shm/sm_segment.gimli1.1001.a170000.0’   ‘/dev/shm/sm_segment.gimli1.1001.cc4c0000.0’   ‘/dev/shm/sm_segment.gimli1.1001.ccba0000.0’   ‘~/.cache/pocl/uncached/tempfile_3F7zNt’   ‘~/.cache/pocl/uncached/tempfile_Erbkod’   ‘~/.cache/pocl/uncached/tempfile_X7BLrX’   ‘~/.cache/pocl/uncached/tempfile_Yp5YCO’   ‘~/.cache/pocl/uncached/tempfile_a7hbnU’
• DONE

Status: 2 NOTEs