R Development Page

lme4 log file (check_x86_64_windows)

* using log directory 'R:/run/building/build_2013-02-15-08-50/RF_PKG_CHECK/PKGS/lme4.Rcheck'
* using R version 2.15.2 Patched (2013-01-31 r61797)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* checking for file 'lme4/DESCRIPTION' ... OK
* this is package 'lme4' version '0.99999911-1'
* checking CRAN incoming feasibility ... OK
Maintainer: ''
* 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 hidden files and directories ... OK
* checking whether package 'lme4' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for portable file names ... 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
* loading checks for arch 'i386'
** 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 loading without being on the library search path ... OK
* loading checks for arch 'x64'
** 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 loading without being on the library search path ... 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 ... WARNING
Codoc mismatches from documentation object 'predict.merMod':
predict.merMod
  Code: function(object, newdata = NULL, REform = NULL, terms = NULL,
                 type = c("link", "response"), allow.new.levels =
                 FALSE, na.action = na.pass, ...)
  Docs: function(object, newdata = NULL, REform = NULL, terms = NULL,
                 type = c("link", "response"), allow.new.levels =
                 FALSE, ...)
  Argument names in code not in docs:
    na.action
  Mismatches in argument names:
    Position: 7 Code: na.action Docs: ...

* 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 sizes of PDF files under 'inst/doc' ... OK
* checking installed files from 'inst/doc' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* checking for unstated dependencies in tests ... OK
* checking tests ...
** running tests for arch 'i386'
  Running 'PIRLSfail.R' [14s]
  Running 'REMLdev.R'
  Running 'bootMer.R' [16s]
  Running 'boundary.R'
  Running 'coefs.R'
  Running 'drop.R'
  Running 'drop1contrasts.R'
  Running 'elston.R' [13s]
  Running 'extras.R'
  Running 'getME.R'
  Running 'glmer-1.R' [13s]
  Running 'glmerWarn.R'
  Running 'glmmExt.R' [12s]
  Running 'is.R'
  Running 'koller-data.R'
  Running 'lmList.R'
  Running 'lmer-1.R'
  Comparing 'lmer-1.Rout' to 'lmer-1.Rout.save' ... OK
  Running 'lmer-conv.R'
  Running 'lmer.R'
  Running 'lmer2_ex.R'
  Running 'minval.R'
  Running 'nadrop.R'
  Running 'napredict.R'
  Running 'nbinom.R' [13s]
  Running 'nlmer-conv.R' [15s]
  Running 'nlmer.R' [19s]
  Comparing 'nlmer.Rout' to 'nlmer.Rout.save' ...44c44
<    5.44    0.00    5.44 
---
>   5.480   0.000   5.497 
71c71
<    2.54    0.00    2.55 
---
>   2.728   0.004   2.739 
98c98
<    1.54    0.00    1.55 
---
>   1.624   0.000   1.630 
125c125
<    0.84    0.00    0.85 
---
>   0.872   0.000   0.874 
  Running 'offset.R'
  Running 'optimizer.R'
  Running 'polytomous.R' [21s]
  Running 'prLogistic.R'
  Running 'predict.R'
  Running 'predict_basis.R'
  Running 'profile.R' [23s]
  Running 'refit.R' [14s]
  Running 'resids.R'
  Running 'respiratory.R'
  Running 'simulate.R'
  Running 'test-all.R'
  Running 'throw.R'
  Running 'varcorr.R'
  Running 'vcov-etc.R'
 OK
** running tests for arch 'x64'
  Running 'PIRLSfail.R' [13s]
  Running 'REMLdev.R'
  Running 'bootMer.R' [18s]
  Running 'boundary.R'
  Running 'coefs.R'
  Running 'drop.R'
  Running 'drop1contrasts.R'
  Running 'elston.R' [11s]
  Running 'extras.R'
  Running 'getME.R'
  Running 'glmer-1.R' [14s]
  Running 'glmerWarn.R'
  Running 'glmmExt.R' [12s]
  Running 'is.R'
  Running 'koller-data.R'
  Running 'lmList.R'
  Running 'lmer-1.R'
  Comparing 'lmer-1.Rout' to 'lmer-1.Rout.save' ... OK
  Running 'lmer-conv.R'
  Running 'lmer.R'
  Running 'lmer2_ex.R'
  Running 'minval.R'
  Running 'nadrop.R'
  Running 'napredict.R'
  Running 'nbinom.R' [13s]
  Running 'nlmer-conv.R' [16s]
  Running 'nlmer.R' [19s]
  Comparing 'nlmer.Rout' to 'nlmer.Rout.save' ...44c44
<    5.33    0.00    5.33 
---
>   5.480   0.000   5.497 
71c71
<    2.64    0.00    2.64 
---
>   2.728   0.004   2.739 
98c98
<     1.5     0.0     1.5 
---
>   1.624   0.000   1.630 
125c125
<    0.86    0.00    0.85 
---
>   0.872   0.000   0.874 
  Running 'offset.R'
  Running 'optimizer.R'
  Running 'polytomous.R' [15s]
  Running 'prLogistic.R'
  Running 'predict.R'
  Running 'predict_basis.R'
  Running 'profile.R' [25s]
  Running 'refit.R' [15s]
  Running 'resids.R'
  Running 'respiratory.R'
  Running 'simulate.R'
  Running 'test-all.R'
  Running 'throw.R'
  Running 'varcorr.R'
  Running 'vcov-etc.R'
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ...
   'PLSvGLS.Rnw' ... OK
   'Theory.Rnw' ... OK
 OK
* checking re-building of vignettes ... SKIPPED
* checking PDF version of manual ... OK

WARNING: There was 1 warning.
See
  'R:/run/building/build_2013-02-15-08-50/RF_PKG_CHECK/PKGS/lme4.Rcheck/00check.log'
for details.

Run time: 864.48 seconds.