• using R Under development (unstable) (2013-04-22 r62639)
• using platform: x86_64-unknown-linux-gnu (64-bit)
• using session charset: UTF-8
• checking for file ‘GWAF/DESCRIPTION’ ... OK
• checking extension type ... Package
• this is package ‘GWAF’ version ‘2.0’
• 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 for portable file names ... OK
• checking for sufficient/correct file permissions ... OK
• checking whether package ‘GWAF’ can be installed ... OK
• checking installed package size ... OK
• checking package directory ... 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 ... NOTE
  Foreign function call with ‘PACKAGE’ argument in a different package:
  .C("coxph_wtest", ..., PACKAGE = "survival")
  See the chapter ‘System and foreign language interfaces’ of the
  ‘Writing R Extensions’ manual.
• checking R code for possible problems ... NOTE
  autohint: no visible binding for global variable ‘spousid’
  geepack.quant.batch: no visible binding for global variable ‘famid’
  geepack.quant.batch.imputed: no visible binding for global variable
  ‘famid’
  lmepack.batch: no visible binding for global variable ‘kmat’
  lmepack.batch.imputed: no visible binding for global variable ‘kmat’
  lmepack.int.batch: no visible binding for global variable ‘kmat’
  lmepack.int.batch.imputed: no visible binding for global variable
  ‘kmat’
  min,bdsmatrix: no visible binding for global variable ‘rmat’
  
  Found the following assignments to the global environment:
  File ‘GWAF/R/align.pedigree.R’:
  assign("spouselist", spouselist, envir = as.environment(sys.frame()))
  File ‘GWAF/R/alignped1.R’:
  assign("spouselist", spouselist[, !toss, drop = F], envir = as.environment(sys.frame()))
  File ‘GWAF/R/geepack.quant.R’:
  assign("phen", phen, envir = .GlobalEnv, inherits = T)
  assign("test.dat", test.dat, envir = .GlobalEnv, inherits = T)
  assign("i", i, envir = .GlobalEnv, inherits = T)
  assign("x.covar", x.covar, envir = .GlobalEnv, inherits = T)
  assign("test2.dat", test2.dat, envir = .GlobalEnv, inherits = T)
  assign("snp.i", snp.i, envir = .GlobalEnv, inherits = T)
  assign("snp.i", snp.i, envir = .GlobalEnv, inherits = T)
  assign("snp.i", snp.i, envir = .GlobalEnv, inherits = T)
  File ‘GWAF/R/geepack.quant.imputed.R’:
  assign("phen", phen, envir = .GlobalEnv, inherits = T)
  assign("test.dat", test.dat, envir = .GlobalEnv, inherits = T)
  assign("i", i, envir = .GlobalEnv, inherits = T)
  assign("x.covar", x.covar, envir = .GlobalEnv, inherits = T)
  assign("test2.dat", test2.dat, envir = .GlobalEnv, inherits = T)
  File ‘GWAF/R/geepack.quant.int.R’:
  assign("phen", phen, envir = .GlobalEnv, inherits = T)
  assign("cov.int", cov.int, envir = .GlobalEnv, inherits = T)
  File ‘GWAF/R/geepack.quant.int.imputed.R’:
  assign("phen", phen, envir = .GlobalEnv, inherits = T)
  assign("cov.int", cov.int, envir = .GlobalEnv, inherits = T)
  File ‘GWAF/R/lme.R’:
  assign("phen", phen, envir = .GlobalEnv, inherits = T)
  assign("test.dat", test.dat, envir = .GlobalEnv, inherits = T)
  assign("i", i, envir = .GlobalEnv, inherits = T)
  assign("x.covar", x.covar, envir = .GlobalEnv, inherits = T)
  assign("test2.dat", test2.dat, envir = .GlobalEnv, inherits = T)
  assign("id", id, envir = .GlobalEnv, inherits = T)
  assign("snp.i", snp.i, envir = .GlobalEnv, inherits = T)
  assign("snp.i", snp.i, envir = .GlobalEnv, inherits = T)
  assign("snp.i", snp.i, envir = .GlobalEnv, inherits = T)
  File ‘GWAF/R/lme.imputed.R’:
  assign("phen", phen, envir = .GlobalEnv, inherits = T)
  assign("test.dat", test.dat, envir = .GlobalEnv, inherits = T)
  assign("xcovar", xcovar, envir = .GlobalEnv, inherits = T)
  assign("test1.dat", test1.dat, envir = .GlobalEnv, inherits = T)
  assign("id", id, envir = .GlobalEnv, inherits = T)
  assign("i", i, envir = .GlobalEnv, inherits = T)
  assign("x.covar", x.covar, envir = .GlobalEnv, inherits = T)
  assign("test2.dat", test2.dat, envir = .GlobalEnv, inherits = T)
  File ‘GWAF/R/lme.int.R’:
  assign("phen", phen, envir = .GlobalEnv, inherits = T)
  assign("cov.int", cov.int, envir = .GlobalEnv, inherits = T)
  assign("test2.dat", test2.dat, envir = .GlobalEnv, inherits = T)
  assign("x.covar", x.covar, envir = .GlobalEnv, inherits = T)
  assign("bin", bin, envir = .GlobalEnv, inherits = T)
  assign("id", id, envir = .GlobalEnv, inherits = T)
  assign("snp", snp, envir = .GlobalEnv, inherits = T)
  assign("x.int", x.int, envir = .GlobalEnv, inherits = T)
  File ‘GWAF/R/lme.int.imputed.R’:
  assign("phen", phen, envir = .GlobalEnv, inherits = T)
  assign("cov.int", cov.int, envir = .GlobalEnv, inherits = T)
  assign("test2.dat", test2.dat, envir = .GlobalEnv, inherits = T)
  assign("x.covar", x.covar, envir = .GlobalEnv, inherits = T)
  assign("id", id, envir = .GlobalEnv, inherits = T)
  assign("snp", snp, envir = .GlobalEnv, inherits = T)
  assign("bin", bin, envir = .GlobalEnv, inherits = T)
  assign("x.int", x.int, envir = .GlobalEnv, inherits = T)
• 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 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 ... OK
• checking sizes of PDF files under ‘inst/doc’ ... OK
• checking installed files from ‘inst/doc’ ... OK
• checking examples ... OK
• checking PDF version of manual ... OK
  NOTE: There were 2 notes.
  See
  ‘/data/blackswan/ripley/R/packages/tests-devel/GWAF.Rcheck/00check.log’
  for details.