• using R Under development (unstable) (2012-05-19 r59366)
• using platform: x86_64-unknown-linux-gnu (64-bit)
• using session charset: UTF-8
• checking for file ‘bayesSurv/DESCRIPTION’ ... OK
• this is package ‘bayesSurv’ version ‘0.6-2’
• checking package dependencies ... OK
• checking if this is a source package ... OK
• checking if there is a namespace ... WARNING
  As from R 2.14.0 all packages need a namespace.
  One will be generated on installation, but it is better to handcraft a
  NAMESPACE file: R CMD build will produce a suitable starting point.
  CRAN requires a NAMESPACE file for all submissions.
• checking for executable files ... OK
• checking whether package ‘bayesSurv’ can be installed ... WARNING
  Found the following significant warnings:
  arms.cpp:154:21: warning: ISO C++ forbids variable length array ‘xinit’ [-Wvla]
  See ‘/home/hornik/tmp/R.check/r-devel/Work/PKGS/bayesSurv.Rcheck/00install.out’ for details.
• checking installed package size ... NOTE
  installed size is 11.7Mb
  sub-directories of 1Mb or more:
  data 4.9Mb
  doc 1.9Mb
  libs 4.4Mb
• 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 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 ... NOTE
  File ‘bayesSurv/R/zzz.R’:
  .First.lib calls:
  require(survival)
  require(coda)
  require(smoothSurv)
  
  Package startup functions should not change the search path.
  See section ‘Good practice’ in ?.onAttach.
  
  files2coda: warning in read.table(file = paste(dir, "/", files[i], sep
  = ""), header = header, nrow = 1): partial argument match of 'nrow'
  to 'nrows'
• 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 ... WARNING
  File ‘/home/hornik/tmp/R.check/r-devel/Work/build/Packages/bayesSurv/libs/bayesSurv.so’:
  Found ‘_ZSt4cerr’, possibly from ‘std::cerr’ (C++)
  Objects: ‘AK_BLAS_LAPACK.o’, ‘ARS2.o’, ‘GMRF.o’, ‘GMRF_Gspline.o’,
  ‘GMRF_Gspline_Util.o’, ‘Gspline.o’, ‘Gspline_update_Intcpt.o’,
  ‘Gspline_update_Scale.o’, ‘Gspline_update_a.o’,
  ‘Gspline_update_gamma.o’, ‘Gspline_update_lambda.o’,
  ‘Gspline_update_sigma.o’, ‘MHblocks.o’, ‘MHproposal.o’,
  ‘Mvtdist3.o’, ‘arrays2Mat.o’, ‘bayesBisurvreg.o’,
  ‘bayesDensity.o’, ‘bayesGspline.o’, ‘bayesHistogram.o’,
  ‘bayessurvreg1.o’, ‘bayessurvreg2.o’, ‘bblocks.o’,
  ‘birthDeath.o’, ‘cholesky.o’, ‘classBetaGamma.o’,
  ‘classBetaGammaExtend.o’, ‘classCovMatrix.o’,
  ‘classCovMatrixExtend.o’, ‘classRandomEff.o’,
  ‘classRandomEff_rhoNorm.o’, ‘covMatrix.o’, ‘in_output.o’,
  ‘in_output_GS.o’, ‘logLikelihood.o’, ‘marginal_bayesGspline.o’,
  ‘miscellaneous.o’, ‘moodyRing.o’, ‘mvtdist.o’, ‘openFile.o’,
  ‘predictMisc.o’, ‘predictive.o’, ‘predictive_GS.o’, ‘qrdecomp.o’,
  ‘quantile.o’, ‘random.o’, ‘regresResidual_GS.o’, ‘rhoNorm.o’,
  ‘sampledKendallTau.o’, ‘splitCombine.o’, ‘structRandomEff32.o’,
  ‘updateAlloc.o’, ‘updateCovMatRandom.o’, ‘updateData.o’,
  ‘updateRandom.o’, ‘updateRegres.o’, ‘update_Alloc_GS.o’,
  ‘update_Data_GS.o’
  Found ‘_ZSt4cout’, possibly from ‘std::cout’ (C++)
  Objects: ‘MHblocks.o’, ‘bblocks.o’, ‘covMatrix.o’
  Found ‘exit’, possibly from ‘exit’ (C)
  Object: ‘arms.o’
  
  Compiled code should not call functions which might terminate R nor
  write to stdout/stderr instead of to the console.
  
  See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
• checking sizes of PDF files under ‘inst/doc’ ... OK
• checking installed files from ‘inst/doc’ ... OK
• checking examples ... [5s/5s] OK
• checking PDF version of manual ... OK
  WARNING: There were 3 warnings.
  NOTE: There were 2 notes.
  See
  ‘/home/hornik/tmp/R.check/r-devel/Work/PKGS/bayesSurv.Rcheck/00check.log’
  for details.