Check results for 'signalHsmm'

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 17:51:04 UTC
checking for file ‘signalHsmm/DESCRIPTION’ ... OK
checking extension type ... Package
this is package ‘signalHsmm’ version ‘1.5’
package encoding: UTF-8
checking CRAN incoming feasibility ... [1s/2s] NOTE Maintainer: ‘Michal Burdukiewicz <michalburdukiewicz@gmail.com>’ Package CITATION file contains call(s) to old-style citEntry(). Please use bibentry() instead.
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 ‘signalHsmm’ 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 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 ... [1s/1s] OK
checking whether the package can be loaded with stated dependencies ... [1s/1s] OK
checking whether the package can be unloaded cleanly ... [1s/1s] OK
checking whether the namespace can be loaded with stated dependencies ... [1s/1s] OK
checking whether the namespace can be unloaded cleanly ... [1s/1s] 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 ... [6s/8s] NOTE Found calls to structure() using deprecated special names: signalHsmm/R/run_signalHsmm.R (.Dim: 3, .Names: 3, .Dimnames: 1) '.Dim' should be changed to 'dim'. '.Names' should be changed to 'names'. '.Dimnames' should be changed to 'dimnames'.
checking Rd files ... [0s/0s] NOTE checkRd: (-1) add_k_mer_state.Rd:33: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) add_k_mer_state.Rd:34: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) add_k_mer_state.Rd:35: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) add_k_mer_state.Rd:36: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) duration_viterbi.Rd:23: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) duration_viterbi.Rd:24: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) duration_viterbi.Rd:25: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) duration_viterbi.Rd:26: Lost braces in \itemize; \value handles \item{}{} directly
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 pragmas in C/C++ headers and code ... OK
checking compilation flags used ... OK
checking compiled code ... OK
checking examples ... [1s/2s] 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/Rtmp0IlJE2’ ‘~/tmp/scratch/Rtmp0kMoRP’ ‘~/tmp/scratch/Rtmp0xXtcr’ ‘~/tmp/scratch/Rtmp17V18a’ ‘~/tmp/scratch/Rtmp1Wr5KS’ ‘~/tmp/scratch/Rtmp21Jbre’ ‘~/tmp/scratch/Rtmp377z5z’ ‘~/tmp/scratch/Rtmp3arOyk’ ‘~/tmp/scratch/Rtmp3cy88B’ ‘~/tmp/scratch/Rtmp3drLfv’ ‘~/tmp/scratch/Rtmp3svOGB’ ‘~/tmp/scratch/Rtmp4094VB’ ‘~/tmp/scratch/Rtmp4ZRktN’ ‘~/tmp/scratch/Rtmp4yb42k’ ‘~/tmp/scratch/Rtmp8KF1rv’ ‘~/tmp/scratch/Rtmp8RIAZF’ ‘~/tmp/scratch/Rtmp8WYC14’ ‘~/tmp/scratch/Rtmp9FNCyp’ ‘~/tmp/scratch/Rtmp9Ozmfo’ ‘~/tmp/scratch/RtmpANihxp’ ‘~/tmp/scratch/RtmpAokSUa’ ‘~/tmp/scratch/RtmpArjEKQ’ ‘~/tmp/scratch/RtmpBWZq0b’ ‘~/tmp/scratch/RtmpBxWOrU’ ‘~/tmp/scratch/RtmpCAcBOE’ ‘~/tmp/scratch/RtmpCNO4w4’ ‘~/tmp/scratch/RtmpCmsnVA’ ‘~/tmp/scratch/RtmpCnKllA’ ‘~/tmp/scratch/RtmpCwEHwp’ ‘~/tmp/scratch/RtmpDLp7R0’ ‘~/tmp/scratch/RtmpDOJOYX’ ‘~/tmp/scratch/RtmpDPebUG’ ‘~/tmp/scratch/RtmpDeZG0H’ ‘~/tmp/scratch/RtmpFEwLK4’ ‘~/tmp/scratch/RtmpG8U9vL’ ‘~/tmp/scratch/RtmpGeDJyn’ ‘~/tmp/scratch/RtmpGsZC7A’ ‘~/tmp/scratch/RtmpJrSocH’ ‘~/tmp/scratch/RtmpKAP9Ds’ ‘~/tmp/scratch/RtmpKueyjM’ ‘~/tmp/scratch/RtmpLc7iG8’ ‘~/tmp/scratch/RtmpMPmSGp’ ‘~/tmp/scratch/RtmpMeaGww’ ‘~/tmp/scratch/RtmpMrgRAY’ ‘~/tmp/scratch/RtmpNTY4BC’ ‘~/tmp/scratch/RtmpNt6M8p’ ‘~/tmp/scratch/RtmpOHeJwt’ ‘~/tmp/scratch/RtmpOgRtRF’ ‘~/tmp/scratch/RtmpOmxWNF’ ‘~/tmp/scratch/RtmpOvarcM’ ‘~/tmp/scratch/RtmpPiNcDl’ ‘~/tmp/scratch/RtmpQdyxRH’ ‘~/tmp/scratch/RtmpRSymwz’ ‘~/tmp/scratch/RtmpRmIX0g’ ‘~/tmp/scratch/RtmpS2CmTn’ ‘~/tmp/scratch/RtmpS3lwy0’ ‘~/tmp/scratch/RtmpS7PlYG’ ‘~/tmp/scratch/RtmpS9QyhA’ ‘~/tmp/scratch/RtmpSDhKPs’ ‘~/tmp/scratch/RtmpSVec73’ ‘~/tmp/scratch/RtmpSuwyua’ ‘~/tmp/scratch/RtmpTPOOE3’ ‘~/tmp/scratch/RtmpTgpt48’ ‘~/tmp/scratch/RtmpUIMF00’ ‘~/tmp/scratch/RtmpUkl7Jx’ ‘~/tmp/scratch/RtmpWZRWuK’ ‘~/tmp/scratch/RtmpX5ygqS’ ‘~/tmp/scratch/RtmpYSZBsS’ ‘~/tmp/scratch/RtmpYipTzg’ ‘~/tmp/scratch/RtmpYx62RO’ ‘~/tmp/scratch/RtmpZ3CwoD’ ‘~/tmp/scratch/RtmpZ3PKvF’ ‘~/tmp/scratch/RtmpbDM75i’ ‘~/tmp/scratch/RtmpbLtiAZ’ ‘~/tmp/scratch/RtmpbMytFI’ ‘~/tmp/scratch/RtmpbWePxH’ ‘~/tmp/scratch/RtmpbZynhx’ ‘~/tmp/scratch/RtmpbkTmld’ ‘~/tmp/scratch/RtmpbnccHK’ ‘~/tmp/scratch/Rtmpbs9cDF’ ‘~/tmp/scratch/Rtmpc7lFrv’ ‘~/tmp/scratch/RtmpcvjGLB’ ‘~/tmp/scratch/Rtmpe3sn01’ ‘~/tmp/scratch/RtmpeDLpHO’ ‘~/tmp/scratch/RtmpezwgsY’ ‘~/tmp/scratch/RtmpgOFFMX’ ‘~/tmp/scratch/RtmpgOhR9w’ ‘~/tmp/scratch/RtmpgiagIr’ ‘~/tmp/scratch/RtmphVK1dz’ ‘~/tmp/scratch/RtmphnT2Pr’ ‘~/tmp/scratch/Rtmphz9naD’ ‘~/tmp/scratch/RtmpiKEjua’ ‘~/tmp/scratch/RtmpjSpPxa’ ‘~/tmp/scratch/RtmpjutIHC’ ‘~/tmp/scratch/RtmplyvWuK’ ‘~/tmp/scratch/RtmpmBbVsv’ ‘~/tmp/scratch/Rtmpo2nvoP’ ‘~/tmp/scratch/RtmpoCnNAn’ ‘~/tmp/scratch/RtmpobwTuO’ ‘~/tmp/scratch/RtmpoxhwBE’ ‘~/tmp/scratch/RtmppI1si1’ ‘~/tmp/scratch/RtmppnRonB’ ‘~/tmp/scratch/RtmpqhUlSL’ ‘~/tmp/scratch/Rtmpr5SYUL’ ‘~/tmp/scratch/RtmprGOrHg’ ‘~/tmp/scratch/RtmprQigIm’ ‘~/tmp/scratch/Rtmps58eaE’ ‘~/tmp/scratch/Rtmps7DP6l’ ‘~/tmp/scratch/RtmpsIv1l2’ ‘~/tmp/scratch/RtmpsOosx1’ ‘~/tmp/scratch/RtmpuAnGtK’ ‘~/tmp/scratch/Rtmpv8CCtZ’ ‘~/tmp/scratch/RtmpvckRlB’ ‘~/tmp/scratch/RtmpvkA2dE’ ‘~/tmp/scratch/RtmpvoR9T2’ ‘~/tmp/scratch/RtmpvvOd4c’ ‘~/tmp/scratch/Rtmpw3gWx0’ ‘~/tmp/scratch/RtmpwWEmR1’ ‘~/tmp/scratch/RtmpwYwmQb’ ‘~/tmp/scratch/RtmpwoYhk8’ ‘~/tmp/scratch/Rtmpx8WEfH’ ‘~/tmp/scratch/RtmpxcymJ1’ ‘~/tmp/scratch/Rtmpxrw8ux’ ‘~/tmp/scratch/RtmpyDTlfv’ ‘~/tmp/scratch/RtmpyRNmf2’ ‘~/tmp/scratch/RtmpzUq6Mf’ ‘~/tmp/scratch/Rtmpzaa5SV’ ‘~/tmp/scratch/quarto-sessiona659afbd7d8ec813’ ‘~/tmp/scratch/xvfb-run.0KoZsc’ ‘~/tmp/scratch/xvfb-run.0Vc8gu’ ‘~/tmp/scratch/xvfb-run.0w2vKo’ ‘~/tmp/scratch/xvfb-run.1Pq5cg’ ‘~/tmp/scratch/xvfb-run.3yd74w’ ‘~/tmp/scratch/xvfb-run.49ElBm’ ‘~/tmp/scratch/xvfb-run.4JP7KJ’ ‘~/tmp/scratch/xvfb-run.5a0RmT’ ‘~/tmp/scratch/xvfb-run.9kNZ3h’ ‘~/tmp/scratch/xvfb-run.AD5bxL’ ‘~/tmp/scratch/xvfb-run.Eeo3H3’ ‘~/tmp/scratch/xvfb-run.FTtcdc’ ‘~/tmp/scratch/xvfb-run.GIcSmX’ ‘~/tmp/scratch/xvfb-run.GdKlJc’ ‘~/tmp/scratch/xvfb-run.J0RPSg’ ‘~/tmp/scratch/xvfb-run.JdD01A’ ‘~/tmp/scratch/xvfb-run.JiNZ12’ ‘~/tmp/scratch/xvfb-run.KDdgMq’ ‘~/tmp/scratch/xvfb-run.LZ24Vv’ ‘~/tmp/scratch/xvfb-run.NvQgBS’ ‘~/tmp/scratch/xvfb-run.RNE55K’ ‘~/tmp/scratch/xvfb-run.Ti6DHQ’ ‘~/tmp/scratch/xvfb-run.TkMOrc’ ‘~/tmp/scratch/xvfb-run.UlozNX’ ‘~/tmp/scratch/xvfb-run.Usm4LW’ ‘~/tmp/scratch/xvfb-run.VIrQJG’ ‘~/tmp/scratch/xvfb-run.VYCkh5’ ‘~/tmp/scratch/xvfb-run.Zkina9’ ‘~/tmp/scratch/xvfb-run.aPTTlc’ ‘~/tmp/scratch/xvfb-run.bvCrNK’ ‘~/tmp/scratch/xvfb-run.cJLWZ2’ ‘~/tmp/scratch/xvfb-run.eEDnBk’ ‘~/tmp/scratch/xvfb-run.gE6ll0’ ‘~/tmp/scratch/xvfb-run.gv74bA’ ‘~/tmp/scratch/xvfb-run.kX1mpi’ ‘~/tmp/scratch/xvfb-run.kgf3YW’ ‘~/tmp/scratch/xvfb-run.nCmcaq’ ‘~/tmp/scratch/xvfb-run.tTe5rI’ ‘~/tmp/scratch/xvfb-run.vs3NGi’ ‘~/tmp/scratch/xvfb-run.wKpE7P’ ‘~/tmp/scratch/xvfb-run.yll5iY’ ‘~/tmp/scratch/xvfb-run.z6ssbf’
DONE

Status: 4 NOTEs