• 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 17:45:10 UTC
• checking for file ‘seqHMM/DESCRIPTION’ ... OK
• this is package ‘seqHMM’ version ‘2.2.0’
• package encoding: UTF-8
• checking CRAN incoming feasibility ... [3s/4s] 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 ‘seqHMM’ 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 ... [3s/5s] OK
• checking whether the package can be loaded with stated dependencies ... [2s/3s] OK
• checking whether the package can be unloaded cleanly ... [2s/3s] OK
• checking whether the namespace can be loaded with stated dependencies ... [3s/4s] OK
• checking whether the namespace can be unloaded cleanly ... [3s/3s] OK
• checking loading without being on the library search path ... [3s/4s] OK
• checking whether startup messages can be suppressed ... [3s/3s] 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 ... [37s/42s] OK
• checking Rd files ... [1s/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 ... [3s/3s] 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 sizes of PDF files under ‘inst/doc’ ... OK
• checking installed files from ‘inst/doc’ ... OK
• checking files in ‘vignettes’ ... OK
• checking examples ... [21s/22s] OK
• checking for unstated dependencies in ‘tests’ ... OK
• checking tests ... [134s/109s] OK   Running ‘testthat.R’ [134s/109s]
• checking for unstated dependencies in vignettes ... OK
• checking package vignettes ... OK
• checking re-building of vignette outputs ... [84s/95s] OK
• checking PDF version of manual ... [7s/10s] OK
• checking HTML version of manual ... [3s/3s] 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/Rtmp0nJvmH’ ‘~/tmp/scratch/Rtmp0xXtcr’   ‘~/tmp/scratch/Rtmp1N3O2k’ ‘~/tmp/scratch/Rtmp1Wr5KS’   ‘~/tmp/scratch/Rtmp280phy’ ‘~/tmp/scratch/Rtmp2dsM4t’   ‘~/tmp/scratch/Rtmp2qqvyq’ ‘~/tmp/scratch/Rtmp377z5z’   ‘~/tmp/scratch/Rtmp3WHu3o’ ‘~/tmp/scratch/Rtmp3arOyk’   ‘~/tmp/scratch/Rtmp3svOGB’ ‘~/tmp/scratch/Rtmp3vOor1’   ‘~/tmp/scratch/Rtmp4094VB’ ‘~/tmp/scratch/Rtmp4DbdtP’   ‘~/tmp/scratch/Rtmp4I4osq’ ‘~/tmp/scratch/Rtmp4P5ma0’   ‘~/tmp/scratch/Rtmp4UEdIY’ ‘~/tmp/scratch/Rtmp507j7n’   ‘~/tmp/scratch/Rtmp609RjP’ ‘~/tmp/scratch/Rtmp6NmC3m’   ‘~/tmp/scratch/Rtmp6QvlCl’ ‘~/tmp/scratch/Rtmp6XtruW’   ‘~/tmp/scratch/Rtmp7NWkhH’ ‘~/tmp/scratch/Rtmp7TyFpK’   ‘~/tmp/scratch/Rtmp7ZZ9Wp’ ‘~/tmp/scratch/Rtmp7jkVfh’   ‘~/tmp/scratch/Rtmp7kyMMl’ ‘~/tmp/scratch/Rtmp8KCwWi’   ‘~/tmp/scratch/Rtmp8RIAZF’ ‘~/tmp/scratch/Rtmp8WYC14’   ‘~/tmp/scratch/Rtmp8gaRwX’ ‘~/tmp/scratch/Rtmp8wA28l’   ‘~/tmp/scratch/Rtmp93woZG’ ‘~/tmp/scratch/Rtmp9qsqPB’   ‘~/tmp/scratch/RtmpAKsEh3’ ‘~/tmp/scratch/RtmpAokSUa’   ‘~/tmp/scratch/RtmpAvd6GX’ ‘~/tmp/scratch/RtmpBHVLFd’   ‘~/tmp/scratch/RtmpBV5W5i’ ‘~/tmp/scratch/RtmpBWZq0b’   ‘~/tmp/scratch/RtmpCAcBOE’ ‘~/tmp/scratch/RtmpCNO4w4’   ‘~/tmp/scratch/RtmpCnKllA’ ‘~/tmp/scratch/RtmpD4i73g’   ‘~/tmp/scratch/RtmpDKYMAD’ ‘~/tmp/scratch/RtmpDLp7R0’   ‘~/tmp/scratch/RtmpDNsG8F’ ‘~/tmp/scratch/RtmpDOJOYX’   ‘~/tmp/scratch/RtmpDPebUG’ ‘~/tmp/scratch/RtmpE5NVSX’   ‘~/tmp/scratch/RtmpESB5oB’ ‘~/tmp/scratch/RtmpFAVe4w’   ‘~/tmp/scratch/RtmpFEwLK4’ ‘~/tmp/scratch/RtmpFkjLff’   ‘~/tmp/scratch/RtmpFupxDE’ ‘~/tmp/scratch/RtmpGeDJyn’   ‘~/tmp/scratch/RtmpHhixmV’ ‘~/tmp/scratch/RtmpICxRPk’   ‘~/tmp/scratch/RtmpIJywNV’ ‘~/tmp/scratch/RtmpJ4tynV’   ‘~/tmp/scratch/RtmpJVohCJ’ ‘~/tmp/scratch/RtmpJYFbhZ’   ‘~/tmp/scratch/RtmpKxu1Po’ ‘~/tmp/scratch/RtmpLRF539’   ‘~/tmp/scratch/RtmpLc7iG8’ ‘~/tmp/scratch/RtmpLupaaU’   ‘~/tmp/scratch/RtmpM5PwJN’ ‘~/tmp/scratch/RtmpMDioS7’   ‘~/tmp/scratch/RtmpMgAUb9’ ‘~/tmp/scratch/RtmpNt6M8p’   ‘~/tmp/scratch/RtmpOHeJwt’ ‘~/tmp/scratch/RtmpOmgtZG’   ‘~/tmp/scratch/RtmpOmxWNF’ ‘~/tmp/scratch/RtmpOqBq4l’   ‘~/tmp/scratch/RtmpP0zUyq’ ‘~/tmp/scratch/RtmpQcgN8m’   ‘~/tmp/scratch/RtmpQdyxRH’ ‘~/tmp/scratch/RtmpR2aPkn’   ‘~/tmp/scratch/RtmpReX959’ ‘~/tmp/scratch/RtmpS2CmTn’   ‘~/tmp/scratch/RtmpSbTwzZ’ ‘~/tmp/scratch/RtmpUIMF00’   ‘~/tmp/scratch/RtmpUZkF7F’ ‘~/tmp/scratch/RtmpUhwQlj’   ‘~/tmp/scratch/RtmpUlABVL’ ‘~/tmp/scratch/RtmpVMHYDq’   ‘~/tmp/scratch/RtmpVQdExr’ ‘~/tmp/scratch/RtmpVtILIn’   ‘~/tmp/scratch/RtmpVzNaEw’ ‘~/tmp/scratch/RtmpW6F8Jl’   ‘~/tmp/scratch/RtmpWDoPMZ’ ‘~/tmp/scratch/RtmpWZRWuK’   ‘~/tmp/scratch/RtmpWgGOTu’ ‘~/tmp/scratch/RtmpWousyR’   ‘~/tmp/scratch/RtmpXEIozB’ ‘~/tmp/scratch/RtmpXu3EvI’   ‘~/tmp/scratch/RtmpXyJ2Fn’ ‘~/tmp/scratch/RtmpY9Jvkp’   ‘~/tmp/scratch/RtmpY9vm1l’ ‘~/tmp/scratch/RtmpYF1nJI’   ‘~/tmp/scratch/RtmpYSZBsS’ ‘~/tmp/scratch/RtmpYipTzg’   ‘~/tmp/scratch/RtmpYrhvxO’ ‘~/tmp/scratch/RtmpYx62RO’   ‘~/tmp/scratch/RtmpZ3CwoD’ ‘~/tmp/scratch/RtmpaMsapQ’   ‘~/tmp/scratch/RtmpaWXgwK’ ‘~/tmp/scratch/RtmpbDM75i’   ‘~/tmp/scratch/RtmpbMytFI’ ‘~/tmp/scratch/RtmpbVAr78’   ‘~/tmp/scratch/RtmpbWHBOu’ ‘~/tmp/scratch/RtmpbZynhx’   ‘~/tmp/scratch/Rtmpbbrang’ ‘~/tmp/scratch/RtmpbkIyy6’   ‘~/tmp/scratch/RtmpbkTmld’ ‘~/tmp/scratch/RtmpbnccHK’   ‘~/tmp/scratch/Rtmpbs9cDF’ ‘~/tmp/scratch/RtmpcvjGLB’   ‘~/tmp/scratch/Rtmpdbzjsv’ ‘~/tmp/scratch/RtmpdnGzjb’   ‘~/tmp/scratch/RtmpeDLpHO’ ‘~/tmp/scratch/RtmpeppLf3’   ‘~/tmp/scratch/RtmpexiVmD’ ‘~/tmp/scratch/RtmpezwgsY’   ‘~/tmp/scratch/RtmpfpjI9c’ ‘~/tmp/scratch/Rtmpft043h’   ‘~/tmp/scratch/RtmpgOFFMX’ ‘~/tmp/scratch/RtmpgrEgXm’   ‘~/tmp/scratch/RtmpgwnMIk’ ‘~/tmp/scratch/RtmphLB5Iw’   ‘~/tmp/scratch/RtmphTwZ1t’ ‘~/tmp/scratch/RtmphnT2Pr’   ‘~/tmp/scratch/RtmpiKEjua’ ‘~/tmp/scratch/RtmpiWNs3A’   ‘~/tmp/scratch/RtmpiWheGC’ ‘~/tmp/scratch/Rtmpio07A0’   ‘~/tmp/scratch/RtmpiuIKBD’ ‘~/tmp/scratch/RtmpjSpPxa’   ‘~/tmp/scratch/RtmpjvvGQu’ ‘~/tmp/scratch/Rtmpkirsug’   ‘~/tmp/scratch/Rtmpkm1Bgt’ ‘~/tmp/scratch/RtmplyvWuK’   ‘~/tmp/scratch/RtmpmJyK2c’ ‘~/tmp/scratch/RtmpnAqaZo’   ‘~/tmp/scratch/RtmpnZE2cr’ ‘~/tmp/scratch/Rtmpo2nvoP’   ‘~/tmp/scratch/RtmpoAsUYU’ ‘~/tmp/scratch/RtmpoRWR5t’   ‘~/tmp/scratch/RtmpobmedF’ ‘~/tmp/scratch/Rtmpoifprq’   ‘~/tmp/scratch/RtmpoxhwBE’ ‘~/tmp/scratch/Rtmpp4MzDv’   ‘~/tmp/scratch/RtmppI1si1’ ‘~/tmp/scratch/RtmppyERuh’   ‘~/tmp/scratch/Rtmpr5SYUL’ ‘~/tmp/scratch/Rtmpr9qS6W’   ‘~/tmp/scratch/RtmprGOrHg’ ‘~/tmp/scratch/Rtmpra0yct’   ‘~/tmp/scratch/Rtmpra4GvS’ ‘~/tmp/scratch/RtmprgzOai’   ‘~/tmp/scratch/Rtmps7DP6l’ ‘~/tmp/scratch/RtmpsIv1l2’   ‘~/tmp/scratch/RtmpsOosx1’ ‘~/tmp/scratch/RtmpsrYjZi’   ‘~/tmp/scratch/RtmptHWoqB’ ‘~/tmp/scratch/RtmptZJxZx’   ‘~/tmp/scratch/RtmptpzpSJ’ ‘~/tmp/scratch/RtmpuAnGtK’   ‘~/tmp/scratch/Rtmpug4WFY’ ‘~/tmp/scratch/RtmpuhDwUC’   ‘~/tmp/scratch/RtmpvHec3j’ ‘~/tmp/scratch/RtmpvoR9T2’   ‘~/tmp/scratch/Rtmpw3gWx0’ ‘~/tmp/scratch/RtmpwFt7Il’   ‘~/tmp/scratch/RtmpwNpqlT’ ‘~/tmp/scratch/RtmpwQof6Z’   ‘~/tmp/scratch/Rtmpx2ndpR’ ‘~/tmp/scratch/RtmpxvHkgP’   ‘~/tmp/scratch/Rtmpy9lHIh’ ‘~/tmp/scratch/RtmpyDTlfv’   ‘~/tmp/scratch/RtmpyTDKLr’ ‘~/tmp/scratch/RtmpzzFYbz’   ‘~/tmp/scratch/cc1CKpGA.cdtor.o’ ‘~/tmp/scratch/ccLsztKs.cdtor.c’   ‘~/tmp/scratch/cczEjkSz.res’   ‘~/tmp/scratch/quarto-session7ebaeeb5358cc14b’   ‘~/tmp/scratch/xvfb-run.0KoZsc’ ‘~/tmp/scratch/xvfb-run.0Vc8gu’   ‘~/tmp/scratch/xvfb-run.0w2vKo’ ‘~/tmp/scratch/xvfb-run.1Pq5cg’   ‘~/tmp/scratch/xvfb-run.23UKS2’ ‘~/tmp/scratch/xvfb-run.3O7CDf’   ‘~/tmp/scratch/xvfb-run.3yd74w’ ‘~/tmp/scratch/xvfb-run.47WxKE’   ‘~/tmp/scratch/xvfb-run.4JP7KJ’ ‘~/tmp/scratch/xvfb-run.5OND4q’   ‘~/tmp/scratch/xvfb-run.5a0RmT’ ‘~/tmp/scratch/xvfb-run.9cYXqc’   ‘~/tmp/scratch/xvfb-run.9kNZ3h’ ‘~/tmp/scratch/xvfb-run.AD5bxL’   ‘~/tmp/scratch/xvfb-run.AGEOnB’ ‘~/tmp/scratch/xvfb-run.D5HJ9a’   ‘~/tmp/scratch/xvfb-run.EYJKK5’ ‘~/tmp/scratch/xvfb-run.Eeo3H3’   ‘~/tmp/scratch/xvfb-run.EypPJz’ ‘~/tmp/scratch/xvfb-run.EzGfVN’   ‘~/tmp/scratch/xvfb-run.FTtcdc’ ‘~/tmp/scratch/xvfb-run.GIcSmX’   ‘~/tmp/scratch/xvfb-run.GO8ciy’ ‘~/tmp/scratch/xvfb-run.Gd6L3A’   ‘~/tmp/scratch/xvfb-run.GdKlJc’ ‘~/tmp/scratch/xvfb-run.IBdwrD’   ‘~/tmp/scratch/xvfb-run.IuI8Lp’ ‘~/tmp/scratch/xvfb-run.J0RPSg’   ‘~/tmp/scratch/xvfb-run.JdD01A’ ‘~/tmp/scratch/xvfb-run.JdphuK’   ‘~/tmp/scratch/xvfb-run.JiNZ12’ ‘~/tmp/scratch/xvfb-run.MdGWQu’   ‘~/tmp/scratch/xvfb-run.Mt4BBX’ ‘~/tmp/scratch/xvfb-run.NvQgBS’   ‘~/tmp/scratch/xvfb-run.QTzDee’ ‘~/tmp/scratch/xvfb-run.RNE55K’   ‘~/tmp/scratch/xvfb-run.TNinz4’ ‘~/tmp/scratch/xvfb-run.Ti6DHQ’   ‘~/tmp/scratch/xvfb-run.TkMOrc’ ‘~/tmp/scratch/xvfb-run.UPwdv8’   ‘~/tmp/scratch/xvfb-run.UlozNX’ ‘~/tmp/scratch/xvfb-run.Usm4LW’   ‘~/tmp/scratch/xvfb-run.V3aU8b’ ‘~/tmp/scratch/xvfb-run.VIrQJG’   ‘~/tmp/scratch/xvfb-run.VYCkh5’ ‘~/tmp/scratch/xvfb-run.WF3grA’   ‘~/tmp/scratch/xvfb-run.Z4tdwu’ ‘~/tmp/scratch/xvfb-run.ZUAtAe’   ‘~/tmp/scratch/xvfb-run.Zkina9’ ‘~/tmp/scratch/xvfb-run.aPTTlc’   ‘~/tmp/scratch/xvfb-run.bL5Jd4’ ‘~/tmp/scratch/xvfb-run.bvCrNK’   ‘~/tmp/scratch/xvfb-run.cJLWZ2’ ‘~/tmp/scratch/xvfb-run.dgf6SR’   ‘~/tmp/scratch/xvfb-run.eEDnBk’ ‘~/tmp/scratch/xvfb-run.eGBbDP’   ‘~/tmp/scratch/xvfb-run.ebZqBD’ ‘~/tmp/scratch/xvfb-run.eetjpC’   ‘~/tmp/scratch/xvfb-run.g5LNxC’ ‘~/tmp/scratch/xvfb-run.gE6ll0’   ‘~/tmp/scratch/xvfb-run.gUMejD’ ‘~/tmp/scratch/xvfb-run.gdpyyg’   ‘~/tmp/scratch/xvfb-run.kX1mpi’ ‘~/tmp/scratch/xvfb-run.kgf3YW’   ‘~/tmp/scratch/xvfb-run.qAXzXu’ ‘~/tmp/scratch/xvfb-run.qiPIS4’   ‘~/tmp/scratch/xvfb-run.tTe5rI’ ‘~/tmp/scratch/xvfb-run.uFlQIM’   ‘~/tmp/scratch/xvfb-run.uudFdP’ ‘~/tmp/scratch/xvfb-run.vQ8t24’   ‘~/tmp/scratch/xvfb-run.vQA8bz’ ‘~/tmp/scratch/xvfb-run.vs3NGi’   ‘~/tmp/scratch/xvfb-run.vxMsNz’ ‘~/tmp/scratch/xvfb-run.w4sFr5’   ‘~/tmp/scratch/xvfb-run.wKpE7P’ ‘~/tmp/scratch/xvfb-run.wzJt08’   ‘~/tmp/scratch/xvfb-run.yll5iY’ ‘~/tmp/scratch/xvfb-run.z6ssbf’   ‘~/tmp/scratch/xvfb-run.zNbJDb’ ‘~/tmp/scratch/xvfb-run.zvPewB’
• DONE

Status: 1 NOTE