• using log directory '/data/gannet/tmp/ripley/R/packages/tests-Sun/lme4.Rcheck'
• using R version 2.11.0 Under development (unstable) (2010-02-03 r51097)
• using session charset: UTF-8
• checking for file 'lme4/DESCRIPTION' ... OK
• this is package 'lme4' version '0.999375-32'
• checking package name space information ... OK
• checking package dependencies ... OK
• checking if this is a source package ... OK
• checking for executable files ... OK
• checking whether package 'lme4' can be installed ... OK
• checking package directory ... OK
• checking for portable file names ... OK
• checking for sufficient/correct file permissions ... OK
• checking DESCRIPTION meta-information ... OK
• checking top-level 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 name space can be loaded with stated dependencies ... OK
• checking whether the name space 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 data for non-ASCII characters ... 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 ... OK
• checking examples ... OK
• checking tests ...
  Running ‘extras.R’
  Running ‘lmer-1.R’
  Comparing ‘lmer-1.Rout’ to ‘lmer-1.Rout.save’ ...3a4,22
  > Matrix_NS: <environment: namespace:Matrix>
  >
  > Attaching package: 'Matrix'
  >
  >
  > The following object(s) are masked from package:stats :
  >
  > contr.helmert,
  > contr.poly,
  > contr.SAS,
  > contr.sum,
  > contr.treatment,
  > xtabs
  >
  >
  > The following object(s) are masked from package:base :
  >
  > rcond
  >
  126c145
  < 6 -1.7594786
  ---
  > 6 -1.7594785
  250c269,270
  < The following object(s) are masked from 'package:lme4':
  ---
  >
  > The following object(s) are masked from package:lme4 :
  319,320c339,342
  < [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
  < [1,] 2.190890 0 0 0 0.05974061 0.1610661 0 0 0 0.1627520
  ---
  > [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8]
  > [1,] 2.190890 2.357347 1.2607 1.310223 1.068853 0.9335019 1.010767 0.4688515
  > [,9] [,10]
  > [1,] 0.3225182 1.151649
  326,327c348,349
  < [1] 42.92570 42.92582 49.48090 49.48090 49.48090 49.38257 48.81481 49.48090
  < [9] 49.48090 49.48090
  ---
  > [1] 42.92570 42.92582 43.06062 42.68860 42.65261 42.94053 43.26243 43.06123
  > [9] 45.91098 47.31819
  337c359
  < (Intercept) 5.5 8.500135 5.820769 4.864013 7.469905 8.135526 3.896369 5.428937
  ---
  > (Intercept) 5.5 8.500135 7.22099 4.496626 8.953627 9.33549 3.471580 5.391293
  339c361
  < (Intercept) 6.655732 5.27466
  ---
  > (Intercept) 6.517353 5.294367
  345,347c367,372
  < [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
  < [1,] -2.400157 -3.8538414 0 0 0 -0.4176193 -0.6698131 0 0 0
  < [2,] 2.400157 -0.7552534 0 0 0 -0.2303590 -0.2826445 0 0 0
  ---
  > [,1] [,2] [,3] [,4] [,5] [,6] [,7]
  > [1,] -2.400157 -3.8538414 -3.9874944 -1.128572 -6.3076943 -6.685036 -1.259950
  > [2,] 2.400157 -0.7552534 0.7014855 2.503138 -0.3157271 -2.036684 2.517739
  > [,8] [,9] [,10]
  > [1,] -1.687885 -2.4715626 -0.7075876
  > [2,] 3.140762 0.4975877 0.5186987
  351c376
  < [1,] 1.581139 1.497841 1.9839 3.841709 4.029658 3.488896 4.150724 3.310712
  ---
  > [1,] 1.581139 1.497841 1.9839 2.026303 2.282117 1.977191 2.410987 2.049153
  353c378
  < [1,] 3.556495 2.718116
  ---
  > [1,] 2.160824 2.01181
  368c393
  < [1,] 2.313989 0
  ---
  > [1,] 2.313989 1.730152
  408c433
  < group (Intercept) 140.641531 11.85924
  ---
  > group (Intercept) 140.641640 11.85924
  415c440
  < (Intercept) 15.23552 8.40776 1.812
  ---
  > (Intercept) 15.23545 8.40776 1.812
  435c460
  < [1,] 7.18678711
  ---
  > [1,] 7.18679006
  443c468
  < [1] 87.58733
  ---
  > [1] 87.58735
  449c474
  < 1 0 300 900 5
  ---
  > 1 0 300 900 4
  453,454c478,479
  < (Intercept) 15.2355231
  < x 0.1855856
  ---
  > (Intercept) 15.2354526
  > x 0.1855864
  461,464c486,489
  < [1,] -8.35048135
  < [2,] 8.35048135
  < [3,] 0.08457456
  < [4,] -0.08457456
  ---
  > [1,] -8.35043630
  > [2,] 8.35043630
  > [3,] 0.08457412
  > [4,] -0.08457412
  Running ‘lmer-conv.R’
  Running ‘nlmer-conv.R’
  Running ‘nlmer.R’
  Comparing ‘nlmer.Rout’ to ‘nlmer.Rout.save’ ...28c28
  < lKa 0.227357 0.47682 NaN
  ---
  > lKa 0.227361 0.47682 NaN
  30c30
  < Residual 0.591716 0.76923
  ---
  > Residual 0.591715 0.76923
  37c37
  < lCl -3.23551 0.05235 -61.80
  ---
  > lCl -3.23552 0.05235 -61.80
  56c56
  < Subject lKa 0.227493 0.47696
  ---
  > Subject lKa 0.227495 0.47696
  58c58
  < Residual 0.591689 0.76921
  ---
  > Residual 0.591690 0.76921
  64,65c64,65
  < lKa 0.47408 0.15291 3.10
  < lCl -3.23539 0.05236 -61.79
  ---
  > lKa 0.47409 0.15291 3.10
  > lCl -3.23538 0.05236 -61.79
  OK
• checking package vignettes in 'inst/doc' ... OK
• checking PDF version of manual ... OK
  
  Time 10:06.22, 398.42 + 9.80