• using R Under development (unstable) (2012-08-11 r60235)
• using platform: x86_64-unknown-linux-gnu (64-bit)
• using session charset: UTF-8
• using options ‘--no-examples --no-tests --no-vignettes’
• checking for file ‘GenABEL/DESCRIPTION’ ... OK
• checking extension type ... Package
• this is package ‘GenABEL’ version ‘1.7-0’
• 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 whether package ‘GenABEL’ can be installed ... OK
• checking installed package size ... NOTE
  installed size is 14.2Mb
  sub-directories of 1Mb or more:
  data 2.3Mb
  exdata 5.7Mb
  libs 5.3Mb
• 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 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
  HWE.show: warning in pchisq(chi2, 1, lower = F): partial argument match
  of 'lower' to 'lower.tail'
  arrange_probabel_phe: warning in read.table(phedata, head = T, strings
  = F): partial argument match of 'head' to 'header'
  arrange_probabel_phe: warning in read.table(phedata, head = T, strings
  = F): partial argument match of 'strings' to 'stringsAsFactors'
  blurGenotype: warning in apply(g, MAR = 2, FUN = getNondegenerate,
  delta = delta): partial argument match of 'MAR' to 'MARGIN'
  ccfast: warning in estlambda(chi2.1df, plot = FALSE, prop = propPs):
  partial argument match of 'prop' to 'proportion'
  ccfast: warning in pchisq(chi2.1df, 1, lower = F): partial argument
  match of 'lower' to 'lower.tail'
  ccfast: warning in pchisq(chi2.2df, actdf, lower = F): partial argument
  match of 'lower' to 'lower.tail'
  ccfast: warning in pchisq(chi2.c1df, 1, lower = F): partial argument
  match of 'lower' to 'lower.tail'
  check.marker.internal: warning in pchisq(Zhet, 1, lower = F): partial
  argument match of 'lower' to 'lower.tail'
  check.marker.internal: warning in sort(out$Pex.nohwe, dec = FALSE, ind
  = TRUE): partial argument match of 'dec' to 'decreasing'
  check.trait: warning in pchisq((tra[j] - muj) * (tra[j] - muj) * rvarj,
  1, lower = F): partial argument match of 'lower' to 'lower.tail'
  check.trait: warning in qvaluebh95(Pv, fdr = fdrate): partial argument
  match of 'fdr' to 'fdrate'
  convert.snp.mach: warning in convert.snp.ped(pedf = pedfile, mapf =
  mapfile, outf = outfile, format = "mach", wslash = T, strand =
  strand, ...): partial argument match of 'pedf' to 'pedfile'
  convert.snp.mach: warning in convert.snp.ped(pedf = pedfile, mapf =
  mapfile, outf = outfile, format = "mach", wslash = T, strand =
  strand, ...): partial argument match of 'mapf' to 'mapfile'
  convert.snp.mach: warning in convert.snp.ped(pedf = pedfile, mapf =
  mapfile, outf = outfile, format = "mach", wslash = T, strand =
  strand, ...): partial argument match of 'outf' to 'outfile'
  convert.snp.mach: warning in read.table(file = infofile, head = T):
  partial argument match of 'head' to 'header'
  convert.snp.mach: warning in grep(x = header, pat = "version"): partial
  argument match of 'pat' to 'pattern'
  convert.snp.mach: warning in save.snp.data(a, genof = outfile, human =
  FALSE): partial argument match of 'genof' to 'genofile'
  convert.snp.text: warning in grep(x = header, pat = "version"): partial
  argument match of 'pat' to 'pattern'
  descriptives.marker: warning in catable(maf, cat = mafc, digits =
  digits): partial argument match of 'cat' to 'categories'
  descriptives.marker: warning in catable(hwe, cat = hwec, cumulative =
  TRUE, digits = digits): partial argument match of 'cat' to
  'categories'
  descriptives.marker: warning in catable(ill, cat = idcc, digits =
  digits): partial argument match of 'cat' to 'categories'
  descriptives.marker: warning in catable(cll, cat = snpc, digits =
  digits): partial argument match of 'cat' to 'categories'
  dump.piece: warning in write.table(x, file = pedfile, col.n = FALSE,
  row.n = FALSE, quote = FALSE, append = append, sep = " "): partial
  argument match of 'row.n' to 'row.names'
  dump.piece: warning in write.table(x, file = pedfile, col.n = FALSE,
  row.n = FALSE, quote = FALSE, append = append, sep = " "): partial
  argument match of 'col.n' to 'col.names'
  egscore: warning in estlambda(chi2.1df, plot = FALSE, prop = propPs):
  partial argument match of 'prop' to 'proportion'
  egscore: warning in pchisq(chi2.1df, 1, lower = F): partial argument
  match of 'lower' to 'lower.tail'
  egscore: warning in pchisq(chi2.2df, actdf, lower = F): partial
  argument match of 'lower' to 'lower.tail'
  egscore: warning in pchisq(chi2.c1df, 1, lower = F): partial argument
  match of 'lower' to 'lower.tail'
  egscore.old: warning in estlambda(chi2.1df, plot = FALSE, prop =
  propPs): partial argument match of 'prop' to 'proportion'
  egscore.old: warning in pchisq(chi2.1df, 1, lower = F): partial
  argument match of 'lower' to 'lower.tail'
  egscore.old: warning in pchisq(chi2.2df, actdf, lower = F): partial
  argument match of 'lower' to 'lower.tail'
  egscore.old: warning in pchisq(chi2.c1df, 1, lower = F): partial
  argument match of 'lower' to 'lower.tail'
  estlambda: warning in qchisq(data, 1, low = FALSE): partial argument
  match of 'low' to 'lower.tail'
  export.merlin: warning in write.table(inf, file = datafile, col.n =
  FALSE, row.n = FALSE, quote = FALSE): partial argument match of
  'row.n' to 'row.names'
  export.merlin: warning in write.table(inf, file = datafile, col.n =
  FALSE, row.n = FALSE, quote = FALSE): partial argument match of
  'col.n' to 'col.names'
  export.merlin: warning in write.table(map, file = mapfile, col.n =
  TRUE, row.n = FALSE, quote = FALSE): partial argument match of
  'row.n' to 'row.names'
  export.merlin: warning in write.table(map, file = mapfile, col.n =
  TRUE, row.n = FALSE, quote = FALSE): partial argument match of
  'col.n' to 'col.names'
  export.merlin: warning in write.table(map, file = mapfile, col.n =
  FALSE, row.n = FALSE, quote = FALSE): partial argument match of
  'row.n' to 'row.names'
  export.merlin: warning in write.table(map, file = mapfile, col.n =
  FALSE, row.n = FALSE, quote = FALSE): partial argument match of
  'col.n' to 'col.names'
  export.merlin: warning in write.table(map, file = paste(mapfile,
  ".ext", sep = ""), col.n = TRUE, row.n = FALSE, quote = FALSE):
  partial argument match of 'row.n' to 'row.names'
  export.merlin: warning in write.table(map, file = paste(mapfile,
  ".ext", sep = ""), col.n = TRUE, row.n = FALSE, quote = FALSE):
  partial argument match of 'col.n' to 'col.names'
  findRelatives: warning in apply(out, MAR = 1, FUN = function(x) {:
  partial argument match of 'MAR' to 'MARGIN'
  findRelatives: warning in return(which.max(x)): partial argument match
  of 'MAR' to 'MARGIN'
  findRelatives: warning in }): partial argument match of 'MAR' to
  'MARGIN'
  findRelatives: warning in return(max(x)): partial argument match of
  'MAR' to 'MARGIN'
  findRelatives: warning in x[order(x, decreasing = TRUE)[2]]: partial
  argument match of 'MAR' to 'MARGIN'
  findRelatives: warning in apply(tmp, MAR = 1, FUN = function(x) {:
  partial argument match of 'MAR' to 'MARGIN'
  findRelatives: warning in return(all(is.na(x))): partial argument match
  of 'MAR' to 'MARGIN'
  generateOffspring: warning in apply(g1g2, MAR = 2, FUN = genSOG):
  partial argument match of 'MAR' to 'MARGIN'
  getLogLikelihoodGivenRelation: warning in apply(x, FUN = sum, MAR = 2):
  partial argument match of 'MAR' to 'MARGIN'
  grammar: warning in estlambda(chi2.1df, plot = FALSE, prop = propPs):
  partial argument match of 'prop' to 'proportion'
  grammar: warning in pchisq(chi2.1df, 1, lower = F): partial argument
  match of 'lower' to 'lower.tail'
  grammar: warning in pchisq(chi2.c1df, 1, lower = F): partial argument
  match of 'lower' to 'lower.tail'
  load.gwaa.data: warning in grep(x = header, pat = "version"): partial
  argument match of 'pat' to 'pattern'
  mlreg: warning in pchisq(chi2.1df, 1, lower = F): partial argument
  match of 'lower' to 'lower.tail'
  mlreg: warning in estlambda(chi2.1df, plot = F, prop = propPs): partial
  argument match of 'prop' to 'proportion'
  mlreg: warning in pchisq(chi2.1df/lambda$est, 1, lower = F): partial
  argument match of 'lower' to 'lower.tail'
  mlreg.p: warning in pchisq(chi2.1df, 1, lower = F): partial argument
  match of 'lower' to 'lower.tail'
  mmscore: warning in estlambda(chi2.1df, plot = FALSE, prop = propPs):
  partial argument match of 'prop' to 'proportion'
  mmscore: warning in pchisq(chi2.1df, 1, lower = F): partial argument
  match of 'lower' to 'lower.tail'
  mmscore: warning in pchisq(chi2.c1df, 1, lower = F): partial argument
  match of 'lower' to 'lower.tail'
  npsubtreated: warning in sort.int(x1$y.obs, dec = T, index = T):
  partial argument match of 'dec' to 'decreasing'
  npsubtreated: warning in sort.int(x1$y.obs, dec = T, index = T):
  partial argument match of 'index' to 'index.return'
  polygenic: warning in eigen(ginv(relmat), symm = TRUE): partial
  argument match of 'symm' to 'symmetric'
  polygenic: warning in eigen(relmat, symm = TRUE): partial argument
  match of 'symm' to 'symmetric'
  polygenic_hglm: warning in determinant(t(desmat) %*% out$InvSigma %*%
  desmat, log = TRUE): partial argument match of 'log' to 'logarithm'
  qtscore: warning in estlambda(chi2.1df, plot = FALSE, prop = propPs):
  partial argument match of 'prop' to 'proportion'
  qtscore: warning in estlambda(z0 * z0, plot = FALSE, prop = propPs):
  partial argument match of 'prop' to 'proportion'
  qtscore: warning in estlambda(z2 * z2, plot = FALSE, prop = propPs):
  partial argument match of 'prop' to 'proportion'
  qtscore: warning in pchisq(chi2.1df, 1, lower = F): partial argument
  match of 'lower' to 'lower.tail'
  qtscore: warning in pchisq(chi2.2df, actdf, lower = F): partial
  argument match of 'lower' to 'lower.tail'
  reconstructNPs : marIs.na: warning in apply(matr, MAR = MAR, FUN =
  function(x) {: partial argument match of 'MAR' to 'MARGIN'
  reconstructNPs : marIs.na: warning in any(is.na(x)): partial argument
  match of 'MAR' to 'MARGIN'
  reconstructNPs : marIs.na: warning in }): partial argument match of
  'MAR' to 'MARGIN'
  summary.snp.data: warning in pchisq(res[, 9], 1, lower = F): partial
  argument match of 'lower' to 'lower.tail'
  summary.snp.data: warning in pchisq(resX[(nsnps(oX) * 8 + 1):(nsnps(oX)
  * 9)], 1, lower = F): partial argument match of 'lower' to
  'lower.tail'
  summary.snp.data_old: warning in pchisq(res[, 9], 1, lower = F):
  partial argument match of 'lower' to 'lower.tail'
  summary.snp.data_old: warning in pchisq(resX[(oX@nsnps * 8 +
  1):(oX@nsnps * 9)], 1, lower = F): partial argument match of 'lower'
  to 'lower.tail'
  impute2databel: no visible binding for global variable ‘SNP’
• 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 ... OK
• checking installed files from ‘inst/doc’ ... OK
• checking examples ... SKIPPED
• checking PDF version of manual ... OK
  NOTE: There were 2 notes.
  See
  ‘/home/hornik/tmp/R.check/r-devel/Work/PKGS/GenABEL.Rcheck/00check.log’
  for details.