* using log directory ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/nlme.Rcheck’
* using R Under development (unstable) (2024-04-29 r86495)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc-13 (Debian 13.2.0-23) 13.2.0
    GNU Fortran (Debian 13.2.0-23) 13.2.0
* running under: Debian GNU/Linux trixie/sid
* using session charset: UTF-8
* checking for file ‘nlme/DESCRIPTION’ ... OK
* this is package ‘nlme’ version ‘3.1-164’
* package encoding: UTF-8
* 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 'https://www.r-project.org/nosvn/R.check/r-devel-linux-x86_64-debian-gcc/nlme-00install.html' for details.
* used C compiler: ‘gcc-13 (Debian 13.2.0-23) 13.2.0’
* used Fortran compiler: ‘GNU Fortran (Debian 13.2.0-23) 13.2.0’
* 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/1s] 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 ... [55s/92s] OK
* checking Rd files ... [3s/5s] 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/1s] 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 ... [39s/56s] OK
Examples with CPU (user + system) or elapsed time > 5s
           user system elapsed
anova.lme 4.775  0.012   6.351
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ... [51s/86s] OK
  Processing ‘extras.Rin’
  Running ‘anova.gls.R’ [1s/2s]
  Running ‘augPred_lab.R’ [18s/27s]
  Running ‘augPredmissing.R’ [0s/1s]
  Running ‘coef.R’ [0s/1s]
  Comparing ‘coef.Rout’ to ‘coef.Rout.save’ ... OK
  Running ‘contrMat.R’ [0s/1s]
  Running ‘corFactor.R’ [0s/1s]
  Running ‘data.frame.R’ [0s/1s]
  Running ‘deparse.R’ [1s/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/2s]
  Running ‘lmList.R’ [1s/1s]
  Running ‘lme.R’ [3s/5s]
  Comparing ‘lme.Rout’ to ‘lme.Rout.save’ ... OK
  Running ‘missing.R’ [1s/1s]
  Comparing ‘missing.Rout’ to ‘missing.Rout.save’ ... OK
  Running ‘nlme.R’ [2s/3s]
  Running ‘nlme2.R’ [1s/2s]
  Running ‘predict.lme.R’ [1s/2s]
  Running ‘scoping.R’ [1s/1s]
  Running ‘sigma-fixed-etc.R’ [14s/22s]
  Running ‘updateLme.R’ [1s/2s]
  Running ‘varConstProp.R’ [1s/2s]
  Running ‘varIdent.R’ [0s/1s]
* checking PDF version of manual ... [25s/40s] OK
* checking HTML version of manual ... [15s/34s] OK
* checking for non-standard things in the check directory ... OK
* DONE
Status: OK