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GWASBinTests log file (check_x86_64_linux)

Fri Feb 15 10:46:15 2013: Checking package GWASBinTests (SVN revision 7) ...
* using log directory ‘/mnt/building/build_2013-02-15-08-50/RF_PKG_CHECK/PKGS/GWASBinTests.Rcheck’
* using R version 2.15.2 Patched (2013-02-13 r61942)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* checking for file ‘GWASBinTests/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘GWASBinTests’ version ‘0.1’
* checking CRAN incoming feasibility ... NOTE
Maintainer: ‘Karl Forner ’
New submission
* 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 for hidden files and directories ... OK
* checking whether package ‘GWASBinTests’ can be installed ... [67s/132s] OK
* checking installed package size ... NOTE
  installed size is  8.1Mb
  sub-directories of 1Mb or more:
    extdata   1.2Mb
    libs      6.3Mb
* 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 for left-over 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 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
readGws : load: warning in load.gwaa.data(phe = paste(basename,
  GENABEL_PHENOTYPES_SUFFIX, sep = ""), gen = paste(basename,
  GENABEL_GENOTYPES_SUFFIX, sep = "")): partial argument match of 'phe'
  to 'phenofile'
readGws : load: warning in load.gwaa.data(phe = paste(basename,
  GENABEL_PHENOTYPES_SUFFIX, sep = ""), gen = paste(basename,
  GENABEL_GENOTYPES_SUFFIX, sep = "")): partial argument match of 'gen'
  to 'genofile'
* 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 ... 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 ‘/mnt/building/build_2013-02-15-08-50/RF_PKG_CHECK/PKGS/GWASBinTests.Rcheck/GWASBinTests/libs/GWASBinTests.so’:
  Found ‘_ZSt4cerr’, possibly from ‘std::cerr’ (C++)
    Objects: ‘libsrc/bins.o’, ‘libsrc/divariate_table.o’,
      ‘libsrc/genabel.o’, ‘libsrc/nnbc_engine.o’
  Found ‘_ZSt4cout’, possibly from ‘std::cout’ (C++)
    Object: ‘libsrc/nnbc_engine.o’
  Found ‘stderr’, possibly from ‘stderr’ (C)
    Objects: ‘libsrc/genotype_error_model.o’, ‘libsrc/misc.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 ... [61s/85s] OK
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘run_runit.R’ [107s/196s]
 [107s/197s] OK
* checking PDF version of manual ... OK

NOTE: There were 4 notes.
See
  ‘/mnt/building/build_2013-02-15-08-50/RF_PKG_CHECK/PKGS/GWASBinTests.Rcheck/00check.log’
for details.

Run time: 551.64 seconds.