• using R Under development (unstable) (2012-08-11 r60235)
• using platform: x86_64-unknown-linux-gnu (64-bit)
• using session charset: UTF-8
• checking for file ‘caspar/DESCRIPTION’ ... OK
• checking extension type ... Package
• this is package ‘caspar’ version ‘1.0’
• checking package dependencies ... OK
• checking if this is a source package ... OK
• checking if there is a namespace ... NOTE
  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 for hidden files and directories ... OK
• checking whether package ‘caspar’ 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 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 ‘caspar/R/zzz.r’:
  .First.lib calls:
  require(mvtnorm)
  
  Package startup functions should not change the search path.
  See section ‘Good practice’ in ?.onAttach.
  
  caspar.engine: warning in matrix(0, nr = p, nc = p): partial argument
  match of 'nr' to 'nrow'
  caspar.engine: warning in matrix(0, nr = p, nc = p): partial argument
  match of 'nc' to 'ncol'
  caspar.grid: warning in matrix(0, nr = length(kp.vec), nc =
  length(mix.vec)): partial argument match of 'nr' to 'nrow'
  caspar.grid: warning in matrix(0, nr = length(kp.vec), nc =
  length(mix.vec)): partial argument match of 'nc' to 'ncol'
  caspar.grid: warning in matrix(0, nr = p, nc = p): partial argument
  match of 'nr' to 'nrow'
  caspar.grid: warning in matrix(0, nr = p, nc = p): partial argument
  match of 'nc' to 'ncol'
  simulateCasparData: warning in matrix(rnorm(n * p), nr = n, nc = p):
  partial argument match of 'nr' to 'nrow'
  simulateCasparData: warning in matrix(rnorm(n * p), nr = n, nc = p):
  partial argument match of 'nc' to 'ncol'
  simulateCasparData: warning in matrix(cor, nr = sz, nc = sz): partial
  argument match of 'nr' to 'nrow'
  simulateCasparData: warning in matrix(cor, nr = sz, nc = sz): partial
  argument match of 'nc' to 'ncol'
  demo.hiv: no visible binding for global variable ‘HIVDAT1APV’
  demo.hiv: no visible binding for global variable ‘HIVDAT2ATV’
  demo.hiv: no visible binding for global variable ‘HIVDAT3IDV’
  demo.hiv: no visible binding for global variable ‘HIVDAT4LPV’
  demo.hiv: no visible binding for global variable ‘HIVDAT5NFV’
  demo.hiv: no visible binding for global variable ‘HIVDAT6RTV’
  demo.hiv: no visible binding for global variable ‘HIVDAT7SQV’
• checking Rd files ... NOTE
  prepare_Rd: caspar-package.Rd:36-37: Dropping empty section \seealso
  prepare_Rd: caspar-package.Rd:38-39: Dropping empty section \examples
  prepare_Rd: caspar.engine.Rd:53-55: Dropping empty section \details
  prepare_Rd: caspar.engine.Rd:56-62: Dropping empty section \value
  prepare_Rd: caspar.engine.Rd:69-71: Dropping empty section \note
  prepare_Rd: caspar.engine.Rd:66-68: Dropping empty section \author
  prepare_Rd: caspar.engine.Rd:63-65: Dropping empty section \references
  prepare_Rd: caspar.engine.Rd:75-77: Dropping empty section \seealso
  prepare_Rd: caspar.engine.Rd:78-79: Dropping empty section \examples
  prepare_Rd: caspar.grid.Rd:44-46: Dropping empty section \details
  prepare_Rd: caspar.grid.Rd:47-53: Dropping empty section \value
  prepare_Rd: caspar.grid.Rd:60-62: Dropping empty section \note
  prepare_Rd: caspar.grid.Rd:57-59: Dropping empty section \author
  prepare_Rd: caspar.grid.Rd:54-56: Dropping empty section \references
  prepare_Rd: caspar.grid.Rd:66-68: Dropping empty section \seealso
  prepare_Rd: caspar.grid.Rd:69-70: Dropping empty section \examples
  prepare_Rd: caspar.main.Rd:65-67: Dropping empty section \note
  prepare_Rd: caspar.main.Rd:62-64: Dropping empty section \author
  prepare_Rd: caspar.main.Rd:59-61: Dropping empty section \references
  prepare_Rd: caspar.main.Rd:71-73: Dropping empty section \seealso
  prepare_Rd: casparCV.Rd:49-51: Dropping empty section \details
  prepare_Rd: casparCV.Rd:52-58: Dropping empty section \value
  prepare_Rd: casparCV.Rd:65-67: Dropping empty section \note
  prepare_Rd: casparCV.Rd:62-64: Dropping empty section \author
  prepare_Rd: casparCV.Rd:59-61: Dropping empty section \references
  prepare_Rd: casparCV.Rd:71-73: Dropping empty section \seealso
  prepare_Rd: casparCV.Rd:74-75: Dropping empty section \examples
  prepare_Rd: col2cov.Rd:23-25: Dropping empty section \details
  prepare_Rd: col2cov.Rd:26-32: Dropping empty section \value
  prepare_Rd: col2cov.Rd:39-41: Dropping empty section \note
  prepare_Rd: col2cov.Rd:36-38: Dropping empty section \author
  prepare_Rd: col2cov.Rd:33-35: Dropping empty section \references
  prepare_Rd: col2cov.Rd:45-47: Dropping empty section \seealso
  prepare_Rd: col2cov.Rd:48-49: Dropping empty section \examples
  prepare_Rd: cov2grid.Rd:23-25: Dropping empty section \details
  prepare_Rd: cov2grid.Rd:26-32: Dropping empty section \value
  prepare_Rd: cov2grid.Rd:39-41: Dropping empty section \note
  prepare_Rd: cov2grid.Rd:36-38: Dropping empty section \author
  prepare_Rd: cov2grid.Rd:33-35: Dropping empty section \references
  prepare_Rd: cov2grid.Rd:45-47: Dropping empty section \seealso
  prepare_Rd: cov2grid.Rd:48-49: Dropping empty section \examples
  prepare_Rd: demo.caspar.Rd:15-17: Dropping empty section \details
  prepare_Rd: demo.caspar.Rd:18-24: Dropping empty section \value
  prepare_Rd: demo.caspar.Rd:31-33: Dropping empty section \note
  prepare_Rd: demo.caspar.Rd:28-30: Dropping empty section \author
  prepare_Rd: demo.caspar.Rd:25-27: Dropping empty section \references
  prepare_Rd: demo.caspar.Rd:37-39: Dropping empty section \seealso
  prepare_Rd: demo.hiv.Rd:39-41: Dropping empty section \note
  prepare_Rd: demo.hiv.Rd:36-38: Dropping empty section \author
  prepare_Rd: demo.hiv.Rd:33-35: Dropping empty section \references
  prepare_Rd: demo.hiv.Rd:45-47: Dropping empty section \seealso
  prepare_Rd: simulateCasparData.Rd:53-55: Dropping empty section \details
  prepare_Rd: simulateCasparData.Rd:56-62: Dropping empty section \value
  prepare_Rd: simulateCasparData.Rd:69-71: Dropping empty section \note
  prepare_Rd: simulateCasparData.Rd:66-68: Dropping empty section \author
  prepare_Rd: simulateCasparData.Rd:63-65: Dropping empty section \references
  prepare_Rd: simulateCasparData.Rd:75-77: Dropping empty section \seealso
• 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 ... NOTE
  File ‘/home/hornik/tmp/R.check/r-devel/Work/build/Packages/caspar/libs/caspar.so’:
  Found ‘printf’, possibly from ‘printf’ (C)
  Object: ‘caspar-i-cv-dmat.o’
  Found ‘putchar’, possibly from ‘putchar’ (C)
  Object: ‘caspar-i-cv-dmat.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 examples ... [15s/15s] OK
• checking PDF version of manual ... OK
  NOTE: There were 4 notes.
  See
  ‘/home/hornik/tmp/R.check/r-devel/Work/PKGS/caspar.Rcheck/00check.log’
  for details.