* using log directory 'd:/Rcompile/CRANpkg/local/2.15/crosshybDetector.Rcheck'
* using R version 2.15.0 (2012-03-30)
* using platform: x86_64-pc-mingw32 (64-bit)
* using session charset: ISO8859-1
* checking for file 'crosshybDetector/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'crosshybDetector' version '1.0.5'
* 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 whether package 'crosshybDetector' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for portable file names ... 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 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'
crosshybImage: warning in png(file = plotName, bg = "white", width =
  400, height = 600): partial argument match of 'file' to 'filename'
crosshybMAplot: warning in png(file = plotName, bg = "white", width =
  600, height = 600): partial argument match of 'file' to 'filename'
crosshybMCplot: warning in png(file = plotName, bg = "white", width =
  400, height = 600): partial argument match of 'file' to 'filename'
* 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:50-51: 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 ... 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 ... WARNING
  
  Note: significantly better compression could be obtained
        by using R CMD build --resave-data
                   old_size new_size compress
  crosshyb.out.rda     26Kb     19Kb       xz
  probeSeq.rda         72Kb     22Kb       xz
  raw.rda             464Kb    176Kb       xz
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... NOTE
File 'd:/Rcompile/CRANpkg/lib/2.15/crosshybDetector/libs/i386/crosshybDetector.dll':
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
    Object: 'basic.o'
  Found 'printf', possibly from 'printf' (C)
    Objects: 'align.o', 'basic.o'
  Found 'putchar', possibly from 'putchar' (C)
    Object: 'basic.o'
  Found 'puts', possibly from 'printf' (C), 'puts' (C)
    Objects: 'align.o', 'basic.o', 'callalign.o'
File 'd:/Rcompile/CRANpkg/lib/2.15/crosshybDetector/libs/x64/crosshybDetector.dll':
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
    Object: 'basic.o'
  Found 'printf', possibly from 'printf' (C)
    Objects: 'align.o', 'basic.o'
  Found 'putchar', possibly from 'putchar' (C)
    Object: 'basic.o'
  Found 'puts', possibly from 'printf' (C), 'puts' (C)
    Objects: 'align.o', 'basic.o', 'callalign.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 ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* checking PDF version of manual ... OK
WARNING: There was 1 warning.
NOTE: There were 4 notes.
See
  'd:/Rcompile/CRANpkg/local/2.15/crosshybDetector.Rcheck/00check.log'
for details.