• using R version 2.10.0 Patched (2009-11-22 r50534)
• using session charset: UTF-8
• checking for file 'crosshybDetector/DESCRIPTION' ... OK
• checking extension type ... Package
• this is package 'crosshybDetector' version '1.0.4'
• checking package dependencies ... OK
• checking if this is a source package ... OK
• checking whether package 'crosshybDetector' can be installed ... 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 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
  crosshyb: no visible binding for global variable ‘EBLOSUM50’
• checking Rd files ... NOTE
  prepare_Rd: AAAlphabet-class.Rd:34-35: Dropping empty section \seealso
  prepare_Rd: AASequence.Rd:16-17: Dropping empty section \details
  prepare_Rd: AASequenceList-class.Rd:49-50: Dropping empty section \examples
  prepare_Rd: EPAM110.Rd:11: Dropping empty section \format
  prepare_Rd: salign-methods.Rd:38-39: Dropping empty section \examples
• checking Rd metadata ... OK
• checking Rd cross-references ... OK
• checking for missing documentation entries ... OK
• checking for code/documentation mismatches ... WARNING
  S4 class codoc mismatches from documentation object 'AASequenceList-class':
  Slots for class 'AASequenceList'
  Code: .Data info names
  Docs: .Data info
  
• checking Rd \usage sections ... OK
• checking data for non-ASCII characters ... OK
• checking line endings in C/C++/Fortran sources/headers ... OK
• checking line endings in Makefiles ... OK
• checking for portable use of $BLAS_LIBS ... OK
• checking examples ... OK
• checking PDF version of manual ... OK