• using R Under development (unstable) (2012-02-06 r58287)
• using platform: i686-pc-linux-gnu (32-bit)
• using session charset: UTF-8
• checking for file ‘gnm/DESCRIPTION’ ... OK
• this is package ‘gnm’ version ‘1.0-1’
• 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 whether package ‘gnm’ can be installed ... OK
• checking installed package size ... 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 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 ... NOTE
  predict.gnm: warning in matrix(, nr = nrow(X), nc = length(terms)):
  partial argument match of 'nr' to 'nrow'
  predict.gnm: warning in matrix(, nr = nrow(X), nc = length(terms)):
  partial argument match of 'nc' to 'ncol'
  print.meanResiduals: warning in deparse(x$call, width =
  options()$width): partial argument match of 'width' to 'width.cutoff'
  print.summary.gnm: warning in print.default(x$deviance.resid, digits =
  digits, na = "", print.gap = 2): partial argument match of 'na' to
  'na.print'
  print.summary.gnm: warning in symnum(correl, abbr.col = NULL): partial
  argument match of 'abbr.col' to 'abbr.colnames'
  summary.meanResiduals: warning in deparse(object$call, width =
  options()$width): partial argument match of 'width' to 'width.cutoff'
  summary.meanResiduals: warning in print.default(q, digits = digits, na
  = "", print.gap = 2): partial argument match of 'na' to 'na.print'
• 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 sizes of PDF files under ‘inst/doc’ ... NOTE
  ‘qpdf’ made some significant size reductions:
  compacted ‘gnmOverview.pdf’ from 513Kb to 354Kb
  consider running tools::compactPDF() on these files
• checking installed files from ‘inst/doc’ ... NOTE
  The following files should probably not be installed:
  ‘fig-Effect_plots.pdf’, ‘fig-LCall.pdf’, ‘fig-LCover45.pdf’,
  ‘fig-LCqvplot.pdf’, ‘fig-deaths1921-1940.pdf’, ‘fig-profilePlot.pdf’
  
  Consider the use of a .Rinstignore file: see ‘Writing R Extensions’,
  or move the vignette sources from ‘inst/doc’ to ‘vignettes’.
• checking examples ... [20s/20s] OK
• checking for unstated dependencies in tests ... OK
• checking tests ... [30s/30s] OK
  Running ‘RC.R’ [2s/2s]
  Comparing ‘RC.Rout’ to ‘RC.Rout.save’ ... OK
  Running ‘RChomog.R’ [3s/3s]
  Comparing ‘RChomog.Rout’ to ‘RChomog.Rout.save’ ... OK
  Running ‘biplot.R’ [2s/2s]
  Comparing ‘biplot.Rout’ to ‘biplot.Rout.save’ ... OK
  Running ‘bwt.R’ [3s/3s]
  Comparing ‘bwt.Rout’ to ‘bwt.Rout.save’ ... OK
  Running ‘diagonalRef.R’ [2s/2s]
  Comparing ‘diagonalRef.Rout’ to ‘diagonalRef.Rout.save’ ... OK
  Running ‘doubleUnidiff.R’ [3s/3s]
  Comparing ‘doubleUnidiff.Rout’ to ‘doubleUnidiff.Rout.save’ ... OK
  Running ‘gammi.R’ [3s/3s]
  Comparing ‘gammi.Rout’ to ‘gammi.Rout.save’ ... OK
  Running ‘logexcess.R’ [2s/2s]
  Comparing ‘logexcess.Rout’ to ‘logexcess.Rout.save’ ... OK
  Running ‘logistic.R’ [2s/2s]
  Comparing ‘logistic.Rout’ to ‘logistic.Rout.save’ ...53c53
  < Start-up iteration 2. Deviance = 0.06637329
  ---
  > Start-up iteration 2. Deviance = 0.0663733
  Running ‘nls.R’ [2s/2s]
  Comparing ‘nls.Rout’ to ‘nls.Rout.save’ ...20c20
  < Iteration 4. Deviance = 0.00479172
  ---
  > Iteration 4. Deviance = 0.004791720
  Running ‘stereotype.R’ [2s/2s]
  Comparing ‘stereotype.Rout’ to ‘stereotype.Rout.save’ ... OK
  Running ‘unidiff.R’ [3s/3s]
  Comparing ‘unidiff.Rout’ to ‘unidiff.Rout.save’ ... OK
• checking for unstated dependencies in vignettes ... OK
• checking package vignettes in ‘inst/doc’ ... OK
• checking running R code from vignettes ... [12s/12s] OK
• checking re-building of vignette PDFs ... [14s/14s] OK
• checking PDF version of manual ... OK
  NOTE: There were 3 notes.
  See
  ‘/home/hornik/tmp/R.check/r-devel/Work/PKGS/gnm.Rcheck/00check.log’
  for details.