• using R version 3.0.1 (2013-05-16)
• using platform: i686-pc-linux-gnu (32-bit)
• using session charset: UTF-8
• checking for file ‘nlme/DESCRIPTION’ ... OK
• this is package ‘nlme’ version ‘3.1-109’
• 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
• checking installed package size ... OK
• checking package 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 R files for non-ASCII characters ... OK
• checking R files for syntax errors ... OK
• checking whether the package can be loaded ... OK
• checking whether the package can be loaded with stated dependencies ... OK
• checking whether the package can be unloaded cleanly ... OK
• checking whether the namespace can be loaded with stated dependencies ... OK
• checking whether the namespace can be unloaded cleanly ... OK
• checking for unstated 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 ... OK
• checking Rd files ... OK
• checking Rd metadata ... 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 ... 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 for portable compilation flags in Makevars ... OK
• checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
• checking compiled code ... OK
• checking examples ... [53s/53s] OK
• checking for unstated dependencies in tests ... OK
• checking tests ... [16s/17s] OK
  Running ‘anova.gls.R’ [1s/1s]
  Running ‘augPred_lab.R’ [1s/1s]
  Running ‘augPredmissing.R’ [1s/1s]
  Running ‘coef.R’ [1s/1s]
  Running ‘contrMat.R’ [1s/1s]
  Running ‘data.frame.R’ [0s/0s]
  Running ‘deparse.R’ [1s/1s]
  Running ‘getData.R’ [1s/1s]
  Running ‘gls.R’ [1s/1s]
  Running ‘lmList.R’ [1s/1s]
  Running ‘lme.R’ [5s/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’ [1s/1s]
  Comparing ‘nlme.Rout’ to ‘nlme.Rout.save’ ...18c18
  < 311 109.98574 -8.558543 -3.362518
  ---
  > 311 109.98575 -8.558543 -3.362518
  25c25
  < 303 105.71793 -8.906081 -3.222957
  ---
  > 303 105.71792 -8.906081 -3.222957
  Running ‘predict.lme.R’ [1s/1s]
  Running ‘update.R’ [1s/1s]
  Running ‘updateLme.R’ [1s/1s]
  Running ‘varIdent.R’ [0s/0s]
• checking PDF version of manual ... OK