• 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 13:25:07 UTC
• checking for file ‘aphid/DESCRIPTION’ ... OK
• checking extension type ... Package
• this is package ‘aphid’ version ‘1.3.6’
• package encoding: UTF-8
• checking CRAN incoming feasibility ... [2s/3s] 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 ‘aphid’ can be installed ... OK See the install log for details.
• used C++ compiler: ‘g++-16 (Debian 16.1.0-3) 16.1.0’
• 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/1s] OK
• checking whether the package can be loaded with stated dependencies ... [0s/1s] OK
• checking whether the package can be unloaded cleanly ... [0s/1s] OK
• checking whether the namespace can be loaded with stated dependencies ... [0s/1s] OK
• checking whether the namespace can be unloaded cleanly ... [0s/1s] OK
• checking loading without being on the library search path ... [0s/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 ... [16s/22s] 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/0s] OK
• checking LazyData ... OK
• checking data for ASCII and uncompressed saves ... OK
• checking line endings in C/C++/Fortran sources/headers ... OK
• checking line endings in Makefiles ... OK
• checking compilation flags in Makevars ... OK
• checking for GNU extensions in Makefiles ... OK
• checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
• checking use of PKG_*FLAGS in Makefiles ... OK
• checking use of SHLIB_OPENMP_*FLAGS in Makefiles ... OK
• checking pragmas in C/C++ headers and code ... OK
• checking compilation flags used ... OK
• checking compiled code ... OK
• checking installed files from ‘inst/doc’ ... OK
• checking files in ‘vignettes’ ... OK
• checking examples ... [8s/11s] OK Examples with CPU (user + system) or elapsed time > 5s            user system elapsed derivePHMM 3.94 0.044 5.191
• checking for unstated dependencies in ‘tests’ ... OK
• checking tests ... [8s/9s] OK   Running ‘testthat.R’ [8s/9s]
• checking for unstated dependencies in vignettes ... OK
• checking package vignettes ... OK
• checking re-building of vignette outputs ... [6s/8s] OK
• checking PDF version of manual ... [5s/7s] 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/Rtmp0PZjmx’ ‘~/tmp/scratch/Rtmp0cvrQk’   ‘~/tmp/scratch/Rtmp1QOUpV’ ‘~/tmp/scratch/Rtmp23H3eL’   ‘~/tmp/scratch/Rtmp24fB3h’ ‘~/tmp/scratch/Rtmp2TyYBI’   ‘~/tmp/scratch/Rtmp3NBsSh’ ‘~/tmp/scratch/Rtmp3RtqR2’   ‘~/tmp/scratch/Rtmp4n3Fs4’ ‘~/tmp/scratch/Rtmp5E2DCy’   ‘~/tmp/scratch/Rtmp5IK4kb’ ‘~/tmp/scratch/Rtmp5MGw1J’   ‘~/tmp/scratch/Rtmp6XXg73’ ‘~/tmp/scratch/Rtmp7kpj0M’   ‘~/tmp/scratch/Rtmp8FUAlm’ ‘~/tmp/scratch/Rtmp9ikKn2’   ‘~/tmp/scratch/Rtmp9vgda4’ ‘~/tmp/scratch/RtmpABrtH2’   ‘~/tmp/scratch/RtmpANfOLm’ ‘~/tmp/scratch/RtmpAweFYj’   ‘~/tmp/scratch/RtmpB7yEpX’ ‘~/tmp/scratch/RtmpBYoy6o’   ‘~/tmp/scratch/RtmpC545cC’ ‘~/tmp/scratch/RtmpCARZsy’   ‘~/tmp/scratch/RtmpCKm7Uc’ ‘~/tmp/scratch/RtmpCmhg9e’   ‘~/tmp/scratch/RtmpDqnHyh’ ‘~/tmp/scratch/RtmpEGQvsQ’   ‘~/tmp/scratch/RtmpEKWL7c’ ‘~/tmp/scratch/RtmpF4Gk82’   ‘~/tmp/scratch/RtmpFFxT2p’ ‘~/tmp/scratch/RtmpFRmOKF’   ‘~/tmp/scratch/RtmpFlhAeS’ ‘~/tmp/scratch/RtmpG6tKUg’   ‘~/tmp/scratch/RtmpGHgQZw’ ‘~/tmp/scratch/RtmpH0V3xy’   ‘~/tmp/scratch/RtmpH2Xqq2’ ‘~/tmp/scratch/RtmpHIDtOE’   ‘~/tmp/scratch/RtmpIA03Vo’ ‘~/tmp/scratch/RtmpJID3tc’   ‘~/tmp/scratch/RtmpJQFMkO’ ‘~/tmp/scratch/RtmpJuCzGE’   ‘~/tmp/scratch/RtmpJz36KN’ ‘~/tmp/scratch/RtmpKN0iZJ’   ‘~/tmp/scratch/RtmpKOpm5j’ ‘~/tmp/scratch/RtmpLE7eVv’   ‘~/tmp/scratch/RtmpModPSu’ ‘~/tmp/scratch/RtmpN6AoBL’   ‘~/tmp/scratch/RtmpNUvYKt’ ‘~/tmp/scratch/RtmpNmEtbV’   ‘~/tmp/scratch/RtmpObPgfR’ ‘~/tmp/scratch/RtmpOuVApQ’   ‘~/tmp/scratch/RtmpOyImPb’ ‘~/tmp/scratch/RtmpP1r838’   ‘~/tmp/scratch/RtmpPFM2wN’ ‘~/tmp/scratch/RtmpPWE6nU’   ‘~/tmp/scratch/RtmpPhF2bf’ ‘~/tmp/scratch/RtmpPx4F86’   ‘~/tmp/scratch/RtmpRCnqM8’ ‘~/tmp/scratch/RtmpRRp3aQ’   ‘~/tmp/scratch/RtmpRSmZYy’ ‘~/tmp/scratch/RtmpRcWBPd’   ‘~/tmp/scratch/RtmpS3cQn8’ ‘~/tmp/scratch/RtmpSjfYz6’   ‘~/tmp/scratch/RtmpSssJ1P’ ‘~/tmp/scratch/RtmpT4RecU’   ‘~/tmp/scratch/RtmpT7Nz6o’ ‘~/tmp/scratch/RtmpTZsErT’   ‘~/tmp/scratch/RtmpTfGSkZ’ ‘~/tmp/scratch/RtmpTisUo3’   ‘~/tmp/scratch/RtmpTuvPmd’ ‘~/tmp/scratch/RtmpTxdxng’   ‘~/tmp/scratch/RtmpUcVKIw’ ‘~/tmp/scratch/RtmpVzEJG9’   ‘~/tmp/scratch/RtmpWAQtoP’ ‘~/tmp/scratch/RtmpWzJh3D’   ‘~/tmp/scratch/RtmpX0wKqu’ ‘~/tmp/scratch/RtmpXoGgb5’   ‘~/tmp/scratch/RtmpXyuvcS’ ‘~/tmp/scratch/RtmpYL9HF5’   ‘~/tmp/scratch/RtmpZIIw3y’ ‘~/tmp/scratch/RtmpZnGutw’   ‘~/tmp/scratch/RtmpZo2YAa’ ‘~/tmp/scratch/Rtmpa26vbt’   ‘~/tmp/scratch/RtmpaB0RS8’ ‘~/tmp/scratch/RtmpaGs7pa’   ‘~/tmp/scratch/RtmpantR4V’ ‘~/tmp/scratch/RtmpbZoG83’   ‘~/tmp/scratch/Rtmpbd55Y0’ ‘~/tmp/scratch/Rtmpc1yS6d’   ‘~/tmp/scratch/RtmpcaFwMF’ ‘~/tmp/scratch/RtmpceY7qW’   ‘~/tmp/scratch/Rtmpd0XKju’ ‘~/tmp/scratch/RtmpdJOQb9’   ‘~/tmp/scratch/Rtmpe0p2Nq’ ‘~/tmp/scratch/RtmpeUMsSb’   ‘~/tmp/scratch/RtmpeWczaZ’ ‘~/tmp/scratch/Rtmpey65Vc’   ‘~/tmp/scratch/RtmpfDhuXh’ ‘~/tmp/scratch/RtmpfE7ONQ’   ‘~/tmp/scratch/RtmpfXv8gI’ ‘~/tmp/scratch/RtmpgGlCeE’   ‘~/tmp/scratch/RtmpghRwJg’ ‘~/tmp/scratch/Rtmpgotdd9’   ‘~/tmp/scratch/RtmphcN5My’ ‘~/tmp/scratch/Rtmphs5maw’   ‘~/tmp/scratch/Rtmpi4JIJF’ ‘~/tmp/scratch/RtmpitaZAi’   ‘~/tmp/scratch/RtmpjVzId5’ ‘~/tmp/scratch/RtmpjgCEo4’   ‘~/tmp/scratch/RtmplFTdhY’ ‘~/tmp/scratch/RtmplGHKff’   ‘~/tmp/scratch/RtmpmBC2j3’ ‘~/tmp/scratch/RtmpmF43rK’   ‘~/tmp/scratch/RtmpmIZWn0’ ‘~/tmp/scratch/RtmpmLqHdd’   ‘~/tmp/scratch/RtmpmW7IYe’ ‘~/tmp/scratch/RtmpmhCMGZ’   ‘~/tmp/scratch/RtmpnZAlLu’ ‘~/tmp/scratch/Rtmpp5kolK’   ‘~/tmp/scratch/Rtmpp99thm’ ‘~/tmp/scratch/RtmppwrCCU’   ‘~/tmp/scratch/RtmpqVvO4P’ ‘~/tmp/scratch/Rtmpqo1i0C’   ‘~/tmp/scratch/RtmpriqVug’ ‘~/tmp/scratch/RtmprsBhZi’   ‘~/tmp/scratch/RtmprxRHgR’ ‘~/tmp/scratch/RtmpsPRXuI’   ‘~/tmp/scratch/RtmptUDdVk’ ‘~/tmp/scratch/RtmptsoQ0M’   ‘~/tmp/scratch/Rtmpty0CcA’ ‘~/tmp/scratch/Rtmpu6J3pu’   ‘~/tmp/scratch/RtmpuPFDc1’ ‘~/tmp/scratch/Rtmpumggr4’   ‘~/tmp/scratch/Rtmpv6qOxj’ ‘~/tmp/scratch/RtmpvE9nrB’   ‘~/tmp/scratch/RtmpvgB2rm’ ‘~/tmp/scratch/Rtmpw1JgvG’   ‘~/tmp/scratch/RtmpwE7OjR’ ‘~/tmp/scratch/RtmpxDNq8c’   ‘~/tmp/scratch/RtmpxER0pH’ ‘~/tmp/scratch/RtmpxEu4Ky’   ‘~/tmp/scratch/RtmpxTbSEd’ ‘~/tmp/scratch/Rtmpyr4ijp’   ‘~/tmp/scratch/Rtmpz051sO’ ‘~/tmp/scratch/Rtmpzl0VTd’   ‘~/tmp/scratch/cc6CM1Ur.s’   ‘~/tmp/scratch/quarto-session16eced51cb8b6c5d’   ‘~/tmp/scratch/xvfb-run.0s5dCE’ ‘~/tmp/scratch/xvfb-run.23FnP9’   ‘~/tmp/scratch/xvfb-run.2EHWUG’ ‘~/tmp/scratch/xvfb-run.3ArlDS’   ‘~/tmp/scratch/xvfb-run.8mm21V’ ‘~/tmp/scratch/xvfb-run.BHjI7O’   ‘~/tmp/scratch/xvfb-run.C8B0ST’ ‘~/tmp/scratch/xvfb-run.CrdgAT’   ‘~/tmp/scratch/xvfb-run.DOtej6’ ‘~/tmp/scratch/xvfb-run.DPhI91’   ‘~/tmp/scratch/xvfb-run.EHmNN2’ ‘~/tmp/scratch/xvfb-run.GvOfaA’   ‘~/tmp/scratch/xvfb-run.IS1kAX’ ‘~/tmp/scratch/xvfb-run.J28425’   ‘~/tmp/scratch/xvfb-run.J2hmsl’ ‘~/tmp/scratch/xvfb-run.JUQFct’   ‘~/tmp/scratch/xvfb-run.KSEISL’ ‘~/tmp/scratch/xvfb-run.LChWNL’   ‘~/tmp/scratch/xvfb-run.Mmpz3J’ ‘~/tmp/scratch/xvfb-run.NDO3Wz’   ‘~/tmp/scratch/xvfb-run.OX5xC0’ ‘~/tmp/scratch/xvfb-run.R5y9dq’   ‘~/tmp/scratch/xvfb-run.TmlnUO’ ‘~/tmp/scratch/xvfb-run.UwBv2j’   ‘~/tmp/scratch/xvfb-run.W0pwoN’ ‘~/tmp/scratch/xvfb-run.Y5BNt3’   ‘~/tmp/scratch/xvfb-run.YXuEoy’ ‘~/tmp/scratch/xvfb-run.YnKijH’   ‘~/tmp/scratch/xvfb-run.Yp7ZwV’ ‘~/tmp/scratch/xvfb-run.ZlIbIY’   ‘~/tmp/scratch/xvfb-run.bKkqEV’ ‘~/tmp/scratch/xvfb-run.cXdCG5’   ‘~/tmp/scratch/xvfb-run.hR8C7Z’ ‘~/tmp/scratch/xvfb-run.hcyaUy’   ‘~/tmp/scratch/xvfb-run.i13Ges’ ‘~/tmp/scratch/xvfb-run.jSpfj2’   ‘~/tmp/scratch/xvfb-run.junV01’ ‘~/tmp/scratch/xvfb-run.l1OtRj’   ‘~/tmp/scratch/xvfb-run.l6YqAp’ ‘~/tmp/scratch/xvfb-run.nWFlRR’   ‘~/tmp/scratch/xvfb-run.ngmdiE’ ‘~/tmp/scratch/xvfb-run.qVpU6h’   ‘~/tmp/scratch/xvfb-run.rMVR2x’ ‘~/tmp/scratch/xvfb-run.uIOj2x’   ‘~/tmp/scratch/xvfb-run.uJZgu7’ ‘~/tmp/scratch/xvfb-run.xhMbrS’   ‘~/tmp/scratch/xvfb-run.yUOC99’ ‘~/tmp/scratch/xvfb-run.yedmRK’
• DONE

Status: 1 NOTE