• 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 13:27:23 UTC
• checking for file ‘aroma.core/DESCRIPTION’ ... OK
• this is package ‘aroma.core’ version ‘3.3.2’
• checking CRAN incoming feasibility ... [3s/5s] OK
• checking package namespace information ... OK
• checking package dependencies ... INFO Packages suggested but not available for checking:   'sfit', 'expectile', 'HaarSeg', 'mpcbs'
• 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 ‘aroma.core’ can be installed ... OK See the install log for details.
• 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 whether startup messages can be suppressed ... [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 ... [43s/49s] 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 examples ... [4s/4s] OK
• checking for unstated dependencies in ‘tests’ ... OK
• checking tests ... [17s/25s] OK   Running ‘PairedPSCNData,SEG.R’ [0s/0s]   Running ‘PairedPSCNData.R’ [0s/1s]   Running ‘RawCopyNumbers,states.R’ [1s/1s]   Running ‘RawCopyNumbers.R’ [1s/1s]   Running ‘RawGenomicSignals.R’ [1s/2s]   Running ‘RawGenomicSignals.SEG,MP.R’ [1s/1s]   Running ‘RawGenomicSignals.SEG.R’ [1s/2s]   Running ‘RichDataFrame.R’ [1s/2s]   Running ‘SegmentedCopyNumbers.R’ [2s/3s]   Running ‘aromaSettings.R’ [1s/1s]   Running ‘binScatter.R’ [2s/2s]   Running ‘colBinnedSmoothing.R’ [1s/1s]   Running ‘colKernelSmoothing.R’ [1s/1s]   Running ‘fitGenotypeCone.R’ [1s/1s]   Running ‘fitMultiDimensionalCone.R’ [1s/1s]   Running ‘matrixBlockPolish.R’ [1s/2s]   Running ‘mergeBoxplotStats.R’ [1s/1s]
• checking PDF version of manual ... [13s/17s] OK
• checking HTML version of manual ... [5s/6s] 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/Rtmp05Hdrp’ ‘~/tmp/scratch/Rtmp0Busag’   ‘~/tmp/scratch/Rtmp0ZCrf2’ ‘~/tmp/scratch/Rtmp0pFBPU’   ‘~/tmp/scratch/Rtmp134mu6’ ‘~/tmp/scratch/Rtmp24bVVd’   ‘~/tmp/scratch/Rtmp2Xkt6D’ ‘~/tmp/scratch/Rtmp2pY2i2’   ‘~/tmp/scratch/Rtmp3gE5AV’ ‘~/tmp/scratch/Rtmp4cW4yd’   ‘~/tmp/scratch/Rtmp4xyens’ ‘~/tmp/scratch/Rtmp53Err0’   ‘~/tmp/scratch/Rtmp5BTisy’ ‘~/tmp/scratch/Rtmp68wtMH’   ‘~/tmp/scratch/Rtmp6Hjvjc’ ‘~/tmp/scratch/Rtmp6U0Ccw’   ‘~/tmp/scratch/Rtmp6vxbn4’ ‘~/tmp/scratch/Rtmp77SbQb’   ‘~/tmp/scratch/Rtmp957DCt’ ‘~/tmp/scratch/Rtmp9Jqulw’   ‘~/tmp/scratch/Rtmp9ns4ZJ’ ‘~/tmp/scratch/Rtmp9oRI97’   ‘~/tmp/scratch/Rtmp9sMpXV’ ‘~/tmp/scratch/Rtmp9yY17V’   ‘~/tmp/scratch/RtmpA6pLdM’ ‘~/tmp/scratch/RtmpAkwjwy’   ‘~/tmp/scratch/RtmpB1W4Dt’ ‘~/tmp/scratch/RtmpBKROsB’   ‘~/tmp/scratch/RtmpBNOL0H’ ‘~/tmp/scratch/RtmpBVlAlP’   ‘~/tmp/scratch/RtmpBwsDc9’ ‘~/tmp/scratch/RtmpBxpSrs’   ‘~/tmp/scratch/RtmpCQQoMO’ ‘~/tmp/scratch/RtmpCohKzG’   ‘~/tmp/scratch/RtmpDu7UsX’ ‘~/tmp/scratch/RtmpETlJYy’   ‘~/tmp/scratch/RtmpEuUxF8’ ‘~/tmp/scratch/RtmpF9ZdxG’   ‘~/tmp/scratch/RtmpFBJirM’ ‘~/tmp/scratch/RtmpFmj75E’   ‘~/tmp/scratch/RtmpGuefKf’ ‘~/tmp/scratch/RtmpHNHS97’   ‘~/tmp/scratch/RtmpHdsOTC’ ‘~/tmp/scratch/RtmpIHPHLG’   ‘~/tmp/scratch/RtmpIL0Qdb’ ‘~/tmp/scratch/RtmpJzJW3G’   ‘~/tmp/scratch/RtmpK0euU6’ ‘~/tmp/scratch/RtmpKI7SZn’   ‘~/tmp/scratch/RtmpKL7kSt’ ‘~/tmp/scratch/RtmpKwMLBm’   ‘~/tmp/scratch/RtmpL0SAVY’ ‘~/tmp/scratch/RtmpLIYS8T’   ‘~/tmp/scratch/RtmpMy3Wkj’ ‘~/tmp/scratch/RtmpN0gHrd’   ‘~/tmp/scratch/RtmpO4FHF6’ ‘~/tmp/scratch/RtmpO4XFoB’   ‘~/tmp/scratch/RtmpOEA5Dy’ ‘~/tmp/scratch/RtmpOEuj9S’   ‘~/tmp/scratch/RtmpOmCuoL’ ‘~/tmp/scratch/RtmpOzaguI’   ‘~/tmp/scratch/RtmpP1BRnO’ ‘~/tmp/scratch/RtmpQ5j2aI’   ‘~/tmp/scratch/RtmpQFfYaS’ ‘~/tmp/scratch/RtmpQtLB2j’   ‘~/tmp/scratch/RtmpRSAiaL’ ‘~/tmp/scratch/RtmpRSgpyn’   ‘~/tmp/scratch/RtmpRYvAjo’ ‘~/tmp/scratch/RtmpRcisz7’   ‘~/tmp/scratch/RtmpSbQ81O’ ‘~/tmp/scratch/RtmpSj4oWI’   ‘~/tmp/scratch/RtmpSt0wQt’ ‘~/tmp/scratch/RtmpTPoMUm’   ‘~/tmp/scratch/RtmpTS0ZaH’ ‘~/tmp/scratch/RtmpTWAS9p’   ‘~/tmp/scratch/RtmpTxG4mV’ ‘~/tmp/scratch/RtmpUU5Mli’   ‘~/tmp/scratch/RtmpUmVUsS’ ‘~/tmp/scratch/RtmpVUfeMq’   ‘~/tmp/scratch/RtmpW3X971’ ‘~/tmp/scratch/RtmpWUEmPn’   ‘~/tmp/scratch/RtmpWgJqFY’ ‘~/tmp/scratch/RtmpWmYu7j’   ‘~/tmp/scratch/RtmpX41pkF’ ‘~/tmp/scratch/RtmpXk9emO’   ‘~/tmp/scratch/RtmpXtO1rf’ ‘~/tmp/scratch/RtmpXuUmRq’   ‘~/tmp/scratch/RtmpY06wxW’ ‘~/tmp/scratch/RtmpY1mFgl’   ‘~/tmp/scratch/RtmpYvjdik’ ‘~/tmp/scratch/RtmpZ3Q2MX’   ‘~/tmp/scratch/Rtmpa2XvGo’ ‘~/tmp/scratch/RtmpaDoMq0’   ‘~/tmp/scratch/RtmpaENX8S’ ‘~/tmp/scratch/RtmpagXZCX’   ‘~/tmp/scratch/RtmpazSkno’ ‘~/tmp/scratch/Rtmpb8LEtP’   ‘~/tmp/scratch/RtmpciqQNv’ ‘~/tmp/scratch/Rtmpd1EJIj’   ‘~/tmp/scratch/RtmpdUOEIR’ ‘~/tmp/scratch/RtmpdqbFAV’   ‘~/tmp/scratch/RtmpeN7Vnw’ ‘~/tmp/scratch/RtmpfYklXo’   ‘~/tmp/scratch/RtmpfnGWNW’ ‘~/tmp/scratch/Rtmpg4P9fg’   ‘~/tmp/scratch/Rtmpg92Sbr’ ‘~/tmp/scratch/RtmpgFNYmk’   ‘~/tmp/scratch/RtmpgdTmN4’ ‘~/tmp/scratch/RtmpgydCB3’   ‘~/tmp/scratch/RtmpgzzFVo’ ‘~/tmp/scratch/RtmphG0iRa’   ‘~/tmp/scratch/RtmphOUtRf’ ‘~/tmp/scratch/Rtmpi2w1tj’   ‘~/tmp/scratch/Rtmpi315Iz’ ‘~/tmp/scratch/RtmpiVHXan’   ‘~/tmp/scratch/RtmpiwMM7k’ ‘~/tmp/scratch/RtmpjhAmXn’   ‘~/tmp/scratch/RtmpjrHvds’ ‘~/tmp/scratch/Rtmpk68BX4’   ‘~/tmp/scratch/RtmpkO6TL2’ ‘~/tmp/scratch/RtmpknvgP0’   ‘~/tmp/scratch/RtmpldKqOM’ ‘~/tmp/scratch/RtmplsIv1A’   ‘~/tmp/scratch/RtmplzAaty’ ‘~/tmp/scratch/RtmpmEvxYv’   ‘~/tmp/scratch/RtmpmKpmBT’ ‘~/tmp/scratch/RtmpmimTT8’   ‘~/tmp/scratch/RtmpmyiWb1’ ‘~/tmp/scratch/RtmpnBziBf’   ‘~/tmp/scratch/RtmpnTDE0o’ ‘~/tmp/scratch/Rtmpnt4lDI’   ‘~/tmp/scratch/RtmpnxAGLL’ ‘~/tmp/scratch/Rtmpo2hSV5’   ‘~/tmp/scratch/Rtmpo3EGmQ’ ‘~/tmp/scratch/RtmpohLChR’   ‘~/tmp/scratch/Rtmpp0OI9J’ ‘~/tmp/scratch/RtmppSPN8m’   ‘~/tmp/scratch/RtmpqAVvFu’ ‘~/tmp/scratch/RtmpqB4X03’   ‘~/tmp/scratch/RtmpqovsXn’ ‘~/tmp/scratch/Rtmpr3xnTB’   ‘~/tmp/scratch/RtmprIJY8b’ ‘~/tmp/scratch/RtmprmSPqM’   ‘~/tmp/scratch/Rtmps5eNgS’ ‘~/tmp/scratch/RtmpsBOQMN’   ‘~/tmp/scratch/Rtmpspx565’ ‘~/tmp/scratch/Rtmpt89hIN’   ‘~/tmp/scratch/RtmptZthvr’ ‘~/tmp/scratch/RtmptaLFrV’   ‘~/tmp/scratch/RtmpvoOeQv’ ‘~/tmp/scratch/RtmpwjdBva’   ‘~/tmp/scratch/RtmpwtNLYT’ ‘~/tmp/scratch/RtmpxNO457’   ‘~/tmp/scratch/RtmpxwheYr’ ‘~/tmp/scratch/RtmpyDsF8e’   ‘~/tmp/scratch/RtmpyU0YnW’ ‘~/tmp/scratch/RtmpyWNtR5’   ‘~/tmp/scratch/RtmpyvXqjJ’ ‘~/tmp/scratch/Rtmpz0t7PK’   ‘~/tmp/scratch/Rtmpz6ORaM’ ‘~/tmp/scratch/xvfb-run.0mv95A’   ‘~/tmp/scratch/xvfb-run.2mS8wx’ ‘~/tmp/scratch/xvfb-run.4frcYe’   ‘~/tmp/scratch/xvfb-run.5Mhvsv’ ‘~/tmp/scratch/xvfb-run.5QQt0K’   ‘~/tmp/scratch/xvfb-run.7YDKjx’ ‘~/tmp/scratch/xvfb-run.96a1qw’   ‘~/tmp/scratch/xvfb-run.9cv9NE’ ‘~/tmp/scratch/xvfb-run.A7yuHX’   ‘~/tmp/scratch/xvfb-run.D7kXtZ’ ‘~/tmp/scratch/xvfb-run.EpvzRq’   ‘~/tmp/scratch/xvfb-run.FGrTqR’ ‘~/tmp/scratch/xvfb-run.H7vK2d’   ‘~/tmp/scratch/xvfb-run.ItG88I’ ‘~/tmp/scratch/xvfb-run.JKESpO’   ‘~/tmp/scratch/xvfb-run.LXfdFS’ ‘~/tmp/scratch/xvfb-run.LeAmYu’   ‘~/tmp/scratch/xvfb-run.MEiTrd’ ‘~/tmp/scratch/xvfb-run.MlErSN’   ‘~/tmp/scratch/xvfb-run.NBw3L2’ ‘~/tmp/scratch/xvfb-run.NXGzpv’   ‘~/tmp/scratch/xvfb-run.PQ8O0d’ ‘~/tmp/scratch/xvfb-run.R3L4DC’   ‘~/tmp/scratch/xvfb-run.REUjfu’ ‘~/tmp/scratch/xvfb-run.TALACV’   ‘~/tmp/scratch/xvfb-run.TBhAiw’ ‘~/tmp/scratch/xvfb-run.Uaugvs’   ‘~/tmp/scratch/xvfb-run.V6A5IM’ ‘~/tmp/scratch/xvfb-run.VpmhMO’   ‘~/tmp/scratch/xvfb-run.WLjpHH’ ‘~/tmp/scratch/xvfb-run.X2xHh1’   ‘~/tmp/scratch/xvfb-run.YhNJdV’ ‘~/tmp/scratch/xvfb-run.aVUof4’   ‘~/tmp/scratch/xvfb-run.av9Q6d’ ‘~/tmp/scratch/xvfb-run.e8bp7j’   ‘~/tmp/scratch/xvfb-run.ehPILO’ ‘~/tmp/scratch/xvfb-run.fBCLyP’   ‘~/tmp/scratch/xvfb-run.fEv6fM’ ‘~/tmp/scratch/xvfb-run.fMXtDk’   ‘~/tmp/scratch/xvfb-run.fSRZ9I’ ‘~/tmp/scratch/xvfb-run.fYwqZo’   ‘~/tmp/scratch/xvfb-run.fxiSJL’ ‘~/tmp/scratch/xvfb-run.iYBtdV’   ‘~/tmp/scratch/xvfb-run.jtY6jd’ ‘~/tmp/scratch/xvfb-run.k2CsjM’   ‘~/tmp/scratch/xvfb-run.kHew9i’ ‘~/tmp/scratch/xvfb-run.kpNQoV’   ‘~/tmp/scratch/xvfb-run.kxT5qM’ ‘~/tmp/scratch/xvfb-run.lhXV2D’   ‘~/tmp/scratch/xvfb-run.mVdqyC’ ‘~/tmp/scratch/xvfb-run.nbrkXf’   ‘~/tmp/scratch/xvfb-run.ofESB3’ ‘~/tmp/scratch/xvfb-run.ojAMCo’   ‘~/tmp/scratch/xvfb-run.pj4pii’ ‘~/tmp/scratch/xvfb-run.qDSuBg’   ‘~/tmp/scratch/xvfb-run.qiBEQS’ ‘~/tmp/scratch/xvfb-run.quluor’   ‘~/tmp/scratch/xvfb-run.rduK8v’ ‘~/tmp/scratch/xvfb-run.sVI4pv’   ‘~/tmp/scratch/xvfb-run.sxj4pH’ ‘~/tmp/scratch/xvfb-run.t0kH5J’   ‘~/tmp/scratch/xvfb-run.tgnV0V’ ‘~/tmp/scratch/xvfb-run.uIoIQp’   ‘~/tmp/scratch/xvfb-run.x4j1ON’ ‘~/tmp/scratch/xvfb-run.xd14q4’   ‘~/tmp/scratch/xvfb-run.yy8hws’ ‘~/tmp/scratch/xvfb-run.z2Lhx9’   ‘~/tmp/scratch/xvfb-run.zU4OLp’
• DONE

Status: 1 NOTE