• using R Under development (unstable) (2012-02-09 r58309)
• using platform: x86_64-unknown-linux-gnu (64-bit)
• using session charset: UTF-8
• checking for file ‘hyperSpec/DESCRIPTION’ ... OK
• checking extension type ... Package
• this is package ‘hyperSpec’ version ‘0.98-20110927’
• 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 ‘hyperSpec’ can be installed ... [8s/24s] 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
  Warning: local assignments to syntactic functions: ~
• 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 ... NOTE
  S3 methods shown with full name in documentation object 'dot-DollarNames-dot-hyperSpec':
  ‘.DollarNames.hyperSpec’
  
  S3 methods shown with full name in documentation object 'seq':
  ‘seq.hyperSpec’
  
  The \usage entries for S3 methods should use the \method markup and not
  their full name.
  See the chapter ‘Writing R documentation files’ in the ‘Writing R
  Extensions’ manual.
• 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 R/sysdata.rda ... OK
• checking sizes of PDF files under ‘inst/doc’ ... NOTE
  ‘gs’ made some significant size reductions:
  compacted ‘plotting.pdf’ from 1172Kb to 756Kb
  consider running tools::compactPDF(gs_quality = "ebook") on these files
• checking installed files from ‘inst/doc’ ... NOTE
  The following files should probably not be installed:
  ‘Makefile’
  
  Consider the use of a .Rinstignore file: see ‘Writing R Extensions’,
  or move the vignette sources from ‘inst/doc’ to ‘vignettes’.
• checking examples ... [63s/184s] WARNING
  Found the following significant warnings:
  
  Warning: sd(<matrix>) is deprecated.
  Warning: sd(<matrix>) is deprecated.
  Warning: sd(<matrix>) is deprecated.
  Warning: sd(<matrix>) is deprecated.
  Warning: sd(<matrix>) is deprecated.
  Warning: sd(<matrix>) is deprecated.
  Deprecated functions may be defunct as soon as of the next release of
  R.
  See ?Deprecated.
• checking for unstated dependencies in vignettes ... OK
• checking package vignettes in ‘inst/doc’ ... OK
• checking running R code from vignettes ... [74s/224s] OK
• checking re-building of vignette PDFs ... NOTE
  Error in re-building vignettes:
  ...
  <to be read again>
  \par
  l.1383 ...the spectra are filled with \Rcode{NA}.}
  
  ! Argument of \@caption has an extra }.
  <inserted text>
  \par
  l.1580 ...ghtly changed by interpolations (blue).}
  
  ! Paragraph ended before \@caption was complete.
  <to be read again>
  \par
  l.1580 ...ghtly changed by interpolations (blue).}
  
  ! Argument of \@caption has an extra }.
  <inserted text>
  \par
  l.2141 ... map: \Rcode{plotmap (scores [, , 3])}.}
  
  Execution halted
  make[1]: *** [introduction.pdf] Error 1
  make[1]: Leaving directory `/data/gannet/tmp/ripley/R/packages/tests-devel/hyperSpec.Rcheck/vign_test/hyperSpec/inst/doc'
  Error in buildVignettes(dir = "/data/gannet/tmp/ripley/R/packages/tests-devel/hyperSpec.Rcheck/vign_test/hyperSpec") :
  running 'make' failed
  Execution halted
  
• checking PDF version of manual ... OK
  WARNING: There was 1 warning.
  NOTE: There were 5 notes.
  See
  ‘/data/gannet/tmp/ripley/R/packages/tests-devel/hyperSpec.Rcheck/00check.log’
  for details.