• using R Under development (unstable) (2012-05-22 r59404)
• using platform: x86_64-unknown-linux-gnu (64-bit)
• using session charset: UTF-8
• 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 ... 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 ‘crosshybDetector’ can be installed ... [6s/10s] 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
  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'
  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: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 ... WARNING
  File ‘/data/gannet/tmp/ripley/R/packages/tests-devel/crosshybDetector.Rcheck/crosshybDetector/libs/crosshybDetector.so’:
  Found ‘exit’, possibly from ‘exit’ (C)
  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 ... [9s/11s] OK
• checking PDF version of manual ... OK
  WARNING: There were 3 warnings.
  NOTE: There were 2 notes.
  See
  ‘/data/gannet/tmp/ripley/R/packages/tests-devel/crosshybDetector.Rcheck/00check.log’
  for details.