Check results for 'GenABEL'

using R version 2.14.1 Patched (2012-02-05 r58287)
using platform: i686-pc-linux-gnu (32-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 whether package ‘GenABEL’ can be installed ... OK
checking installed package size ... NOTE
installed size is 12.6Mb
sub-directories of 1Mb or more:
data 2.3Mb
exdata 5.7Mb
libs 3.7Mb
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 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'
impute2databel: no visible binding for global variable ‘SNP’
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'
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 examples ... SKIPPED
checking PDF version of manual ... OK