• 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 16:31:19 UTC
• checking for file ‘nlme/DESCRIPTION’ ... OK
• this is package ‘nlme’ version ‘3.1-170’
• 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 ‘nlme’ can be installed ... OK See the install log for details.
• used C compiler: ‘gcc-16 (Debian 16.1.0-3) 16.1.0’
• used Fortran compiler: ‘GNU Fortran (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 ... [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 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 ... [36s/46s] OK
• checking Rd files ... [2s/3s] 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 usage of KIND in Fortran files ... OK
• checking examples ... [26s/31s] OK
• checking for unstated dependencies in ‘tests’ ... OK
• checking tests ... [35s/45s] OK   Processing ‘extras.Rin’   Running ‘anova.gls.R’ [1s/1s]   Running ‘augPred_lab.R’ [9s/11s]   Running ‘augPredmissing.R’ [0s/1s]   Running ‘coef.R’ [0s/0s]   Comparing ‘coef.Rout’ to ‘coef.Rout.save’ ... OK   Running ‘contrMat.R’ [0s/1s]   Running ‘corMatrix.R’ [0s/1s]   Running ‘corStruct.R’ [0s/0s]   Running ‘data.frame.R’ [0s/0s]   Running ‘deparse.R’ [0s/1s]   Running ‘deviance.R’ [1s/1s]   Running ‘fitted.R’ [0s/1s]   Running ‘getData.R’ [0s/1s]   Running ‘getVarCov.R’ [1s/1s]   Running ‘gls.R’ [1s/1s]   Running ‘gnls-ch8.R’ [1s/1s]   Running ‘lmList.R’ [1s/1s]   Running ‘lme.R’ [2s/3s]   Comparing ‘lme.Rout’ to ‘lme.Rout.save’ ... OK   Running ‘missing.R’ [0s/1s]   Comparing ‘missing.Rout’ to ‘missing.Rout.save’ ... OK   Running ‘nlme.R’ [1s/2s]   Running ‘nlme2.R’ [1s/1s]   Running ‘predict.lme.R’ [2s/2s]   Running ‘scoping.R’ [1s/1s]   Running ‘sigma-fixed-etc.R’ [8s/10s]   Running ‘updateLme.R’ [1s/1s]   Running ‘varConstProp.R’ [1s/1s]   Running ‘varFixed.R’ [0s/1s]   Running ‘varIdent.R’ [0s/0s]
• checking PDF version of manual ... [15s/18s] OK
• checking HTML version of manual ... [10s/13s] 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/Rtmp01I6EX’ ‘~/tmp/scratch/Rtmp0xtIOD’   ‘~/tmp/scratch/Rtmp1KVyG2’ ‘~/tmp/scratch/Rtmp1gc3Ac’   ‘~/tmp/scratch/Rtmp2Js9ZL’ ‘~/tmp/scratch/Rtmp2dbIn7’   ‘~/tmp/scratch/Rtmp3ViHHJ’ ‘~/tmp/scratch/Rtmp4BIT3o’   ‘~/tmp/scratch/Rtmp4nsw2C’ ‘~/tmp/scratch/Rtmp4nwDr9’   ‘~/tmp/scratch/Rtmp5habo7’ ‘~/tmp/scratch/Rtmp6EUXay’   ‘~/tmp/scratch/Rtmp74xzuu’ ‘~/tmp/scratch/Rtmp7U1qGe’   ‘~/tmp/scratch/Rtmp7czhAQ’ ‘~/tmp/scratch/Rtmp7jeo5D’   ‘~/tmp/scratch/Rtmp80CWdM’ ‘~/tmp/scratch/Rtmp8fJo0b’   ‘~/tmp/scratch/Rtmp9rZ79U’ ‘~/tmp/scratch/RtmpAuauAJ’   ‘~/tmp/scratch/RtmpBMfwqv’ ‘~/tmp/scratch/RtmpBWaxLo’   ‘~/tmp/scratch/RtmpBXmUTj’ ‘~/tmp/scratch/RtmpBaUH4J’   ‘~/tmp/scratch/RtmpC9NlSb’ ‘~/tmp/scratch/RtmpCSMvsR’   ‘~/tmp/scratch/RtmpCZgvjx’ ‘~/tmp/scratch/RtmpCaVFqi’   ‘~/tmp/scratch/RtmpD4xK5x’ ‘~/tmp/scratch/RtmpD5uXZH’   ‘~/tmp/scratch/RtmpDBszFm’ ‘~/tmp/scratch/RtmpDu4Q5s’   ‘~/tmp/scratch/RtmpECBmqJ’ ‘~/tmp/scratch/RtmpElJWfa’   ‘~/tmp/scratch/RtmpEvDHXq’ ‘~/tmp/scratch/RtmpF7oWsi’   ‘~/tmp/scratch/RtmpFmVRsw’ ‘~/tmp/scratch/RtmpG02Q7h’   ‘~/tmp/scratch/RtmpGW6wyl’ ‘~/tmp/scratch/RtmpGwtfSn’   ‘~/tmp/scratch/RtmpHhewCJ’ ‘~/tmp/scratch/RtmpHrSEWP’   ‘~/tmp/scratch/RtmpHttMps’ ‘~/tmp/scratch/RtmpHyhy6s’   ‘~/tmp/scratch/RtmpIs053E’ ‘~/tmp/scratch/RtmpJLBxPC’   ‘~/tmp/scratch/RtmpJgghkp’ ‘~/tmp/scratch/RtmpK2VpDI’   ‘~/tmp/scratch/RtmpK4OeAe’ ‘~/tmp/scratch/RtmpKGaKUa’   ‘~/tmp/scratch/RtmpKIMwhp’ ‘~/tmp/scratch/RtmpKMbhzC’   ‘~/tmp/scratch/RtmpKn9dDd’ ‘~/tmp/scratch/RtmpLHvd36’   ‘~/tmp/scratch/RtmpLYGxIa’ ‘~/tmp/scratch/RtmpMZzG1D’   ‘~/tmp/scratch/RtmpNCBDkQ’ ‘~/tmp/scratch/RtmpNIl9G2’   ‘~/tmp/scratch/RtmpNef0jO’ ‘~/tmp/scratch/RtmpNfiU94’   ‘~/tmp/scratch/RtmpP1Ath4’ ‘~/tmp/scratch/RtmpP9NCDB’   ‘~/tmp/scratch/RtmpP9ZO0g’ ‘~/tmp/scratch/RtmpPI35eM’   ‘~/tmp/scratch/RtmpPVDTwY’ ‘~/tmp/scratch/RtmpPhhuoy’   ‘~/tmp/scratch/RtmpQAp3u8’ ‘~/tmp/scratch/RtmpQtozb6’   ‘~/tmp/scratch/RtmpRImZh3’ ‘~/tmp/scratch/RtmpRTXvfC’   ‘~/tmp/scratch/RtmpRhAMOL’ ‘~/tmp/scratch/RtmpRoYMaG’   ‘~/tmp/scratch/RtmpRtkqdS’ ‘~/tmp/scratch/RtmpSBmIBf’   ‘~/tmp/scratch/RtmpSUpHwG’ ‘~/tmp/scratch/RtmpT1CdJZ’   ‘~/tmp/scratch/RtmpU8vWXO’ ‘~/tmp/scratch/RtmpUGfFM6’   ‘~/tmp/scratch/RtmpUkbm0a’ ‘~/tmp/scratch/RtmpVWozmY’   ‘~/tmp/scratch/RtmpVvDwes’ ‘~/tmp/scratch/RtmpWJDPP5’   ‘~/tmp/scratch/RtmpWKJbnB’ ‘~/tmp/scratch/RtmpWkNRpr’   ‘~/tmp/scratch/RtmpWnfM0z’ ‘~/tmp/scratch/RtmpYJYlO1’   ‘~/tmp/scratch/RtmpYMbjp8’ ‘~/tmp/scratch/RtmpYW3tJJ’   ‘~/tmp/scratch/RtmpYceg8D’ ‘~/tmp/scratch/RtmpYmK1hb’   ‘~/tmp/scratch/RtmpYuQfKo’ ‘~/tmp/scratch/RtmpZrhAZO’   ‘~/tmp/scratch/RtmpaYXuug’ ‘~/tmp/scratch/Rtmpb3YfIb’   ‘~/tmp/scratch/RtmpbxCLhq’ ‘~/tmp/scratch/RtmpcVzNSK’   ‘~/tmp/scratch/RtmpcefMz8’ ‘~/tmp/scratch/Rtmpcwjzg6’   ‘~/tmp/scratch/RtmpdV6dn7’ ‘~/tmp/scratch/Rtmpdwd74z’   ‘~/tmp/scratch/Rtmpee27RV’ ‘~/tmp/scratch/RtmpehAUpo’   ‘~/tmp/scratch/Rtmpf8Fruv’ ‘~/tmp/scratch/RtmpfOcCJ5’   ‘~/tmp/scratch/Rtmpg6aB9m’ ‘~/tmp/scratch/RtmpgNImMC’   ‘~/tmp/scratch/RtmphLWctz’ ‘~/tmp/scratch/RtmphmCCfy’   ‘~/tmp/scratch/RtmpiD3QkQ’ ‘~/tmp/scratch/RtmpiqRZxV’   ‘~/tmp/scratch/RtmpjSttw8’ ‘~/tmp/scratch/RtmpjbizPF’   ‘~/tmp/scratch/Rtmpk3xqEa’ ‘~/tmp/scratch/Rtmpkcml8z’   ‘~/tmp/scratch/RtmplDolVZ’ ‘~/tmp/scratch/RtmplPXg4c’   ‘~/tmp/scratch/RtmplSy58h’ ‘~/tmp/scratch/RtmplmxkUn’   ‘~/tmp/scratch/RtmpmQ3GRi’ ‘~/tmp/scratch/Rtmpme7Tj3’   ‘~/tmp/scratch/RtmpmperT9’ ‘~/tmp/scratch/RtmpnFAJLQ’   ‘~/tmp/scratch/RtmpoLdwaY’ ‘~/tmp/scratch/RtmpoNqana’   ‘~/tmp/scratch/RtmpoyoQOs’ ‘~/tmp/scratch/RtmppYcYH5’   ‘~/tmp/scratch/Rtmppx7Knd’ ‘~/tmp/scratch/RtmpqHQU7f’   ‘~/tmp/scratch/RtmpqjmBkA’ ‘~/tmp/scratch/RtmprDPzcu’   ‘~/tmp/scratch/RtmprTHggh’ ‘~/tmp/scratch/RtmprX9ekb’   ‘~/tmp/scratch/Rtmps72cKe’ ‘~/tmp/scratch/RtmptOm140’   ‘~/tmp/scratch/RtmptVCt07’ ‘~/tmp/scratch/Rtmpu34HOa’   ‘~/tmp/scratch/Rtmpu4kmtJ’ ‘~/tmp/scratch/RtmpuSJ8vJ’   ‘~/tmp/scratch/RtmpufrPay’ ‘~/tmp/scratch/RtmpuxhpoP’   ‘~/tmp/scratch/Rtmpv65Xwf’ ‘~/tmp/scratch/Rtmpw9P4op’   ‘~/tmp/scratch/RtmpwjhR5T’ ‘~/tmp/scratch/Rtmpx3WR1h’   ‘~/tmp/scratch/RtmpxVa89T’ ‘~/tmp/scratch/RtmpxjIf2l’   ‘~/tmp/scratch/RtmpxnyJk5’ ‘~/tmp/scratch/RtmpyRcXL6’   ‘~/tmp/scratch/Rtmpyx9qCX’ ‘~/tmp/scratch/RtmpzL38wj’   ‘~/tmp/scratch/RtmpzhCFiX’ ‘~/tmp/scratch/RtmpzkXdQA’   ‘~/tmp/scratch/RtmpzvzCFb’ ‘~/tmp/scratch/xvfb-run.0oa8kw’   ‘~/tmp/scratch/xvfb-run.131tm8’ ‘~/tmp/scratch/xvfb-run.1eRoEH’   ‘~/tmp/scratch/xvfb-run.28Ubwe’ ‘~/tmp/scratch/xvfb-run.5BvY1q’   ‘~/tmp/scratch/xvfb-run.5oR05o’ ‘~/tmp/scratch/xvfb-run.5yPXRU’   ‘~/tmp/scratch/xvfb-run.5zJwYH’ ‘~/tmp/scratch/xvfb-run.6357Go’   ‘~/tmp/scratch/xvfb-run.6geu0D’ ‘~/tmp/scratch/xvfb-run.79RHNU’   ‘~/tmp/scratch/xvfb-run.7gi2nD’ ‘~/tmp/scratch/xvfb-run.8Urj5O’   ‘~/tmp/scratch/xvfb-run.8lVaRH’ ‘~/tmp/scratch/xvfb-run.9oqDDA’   ‘~/tmp/scratch/xvfb-run.Af4l8o’ ‘~/tmp/scratch/xvfb-run.AoJbhj’   ‘~/tmp/scratch/xvfb-run.BjC39G’ ‘~/tmp/scratch/xvfb-run.CZMZb2’   ‘~/tmp/scratch/xvfb-run.DY9blw’ ‘~/tmp/scratch/xvfb-run.E4PVbu’   ‘~/tmp/scratch/xvfb-run.E4tJsz’ ‘~/tmp/scratch/xvfb-run.E5VeOX’   ‘~/tmp/scratch/xvfb-run.EDTdeA’ ‘~/tmp/scratch/xvfb-run.GOf9eX’   ‘~/tmp/scratch/xvfb-run.GS75c2’ ‘~/tmp/scratch/xvfb-run.HuJfPh’   ‘~/tmp/scratch/xvfb-run.IJI1qJ’ ‘~/tmp/scratch/xvfb-run.IfaT9q’   ‘~/tmp/scratch/xvfb-run.JjCXJV’ ‘~/tmp/scratch/xvfb-run.NTifAd’   ‘~/tmp/scratch/xvfb-run.NrWKY5’ ‘~/tmp/scratch/xvfb-run.PgICQ6’   ‘~/tmp/scratch/xvfb-run.Pt0bl3’ ‘~/tmp/scratch/xvfb-run.QHla3o’   ‘~/tmp/scratch/xvfb-run.R15p5H’ ‘~/tmp/scratch/xvfb-run.Smnicx’   ‘~/tmp/scratch/xvfb-run.TiUjhu’ ‘~/tmp/scratch/xvfb-run.V3c5Gc’   ‘~/tmp/scratch/xvfb-run.VCaRn1’ ‘~/tmp/scratch/xvfb-run.VXT7PT’   ‘~/tmp/scratch/xvfb-run.WQMyUN’ ‘~/tmp/scratch/xvfb-run.ZwjX8c’   ‘~/tmp/scratch/xvfb-run.aXa1PV’ ‘~/tmp/scratch/xvfb-run.aoNdPP’   ‘~/tmp/scratch/xvfb-run.ascCz5’ ‘~/tmp/scratch/xvfb-run.cQAfbW’   ‘~/tmp/scratch/xvfb-run.cX8E2Z’ ‘~/tmp/scratch/xvfb-run.gOacpU’   ‘~/tmp/scratch/xvfb-run.huTVCN’ ‘~/tmp/scratch/xvfb-run.jCQvpz’   ‘~/tmp/scratch/xvfb-run.jZOLPY’ ‘~/tmp/scratch/xvfb-run.nQEULv’   ‘~/tmp/scratch/xvfb-run.o2fanp’ ‘~/tmp/scratch/xvfb-run.oi7mZg’   ‘~/tmp/scratch/xvfb-run.ozhMU4’ ‘~/tmp/scratch/xvfb-run.pFR87B’   ‘~/tmp/scratch/xvfb-run.qdtX38’ ‘~/tmp/scratch/xvfb-run.r8THKK’   ‘~/tmp/scratch/xvfb-run.sTPsp7’ ‘~/tmp/scratch/xvfb-run.uFu9v2’   ‘~/tmp/scratch/xvfb-run.uQVnfZ’ ‘~/tmp/scratch/xvfb-run.x8oud8’   ‘~/tmp/scratch/xvfb-run.xirfho’ ‘~/tmp/scratch/xvfb-run.y3p6Lt’   ‘~/tmp/scratch/xvfb-run.z58eHI’ ‘~/tmp/scratch/xvfb-run.zDOd8l’   ‘~/tmp/scratch/xvfb-run.zveUaE’   ‘/dev/shm/sm_segment.gimli1.1001.51bf0000.0’   ‘/dev/shm/sm_segment.gimli1.1001.56e60000.0’   ‘/dev/shm/sm_segment.gimli1.1001.6c710000.0’   ‘/dev/shm/sm_segment.gimli1.1001.99e00000.0’   ‘~/.cache/pocl/uncached/tempfile_31YUI5’   ‘~/.cache/pocl/uncached/tempfile_RHb5N9’   ‘~/.cache/pocl/uncached/tempfile_SDHoQi’   ‘~/.cache/pocl/uncached/tempfile_e6MKRk’   ‘~/.cache/pocl/uncached/tempfile_h7inXj’
• DONE

Status: 1 NOTE