Check results for 'qtlbim'

using R version 2.14.1 (2011-12-22)
using platform: i686-pc-linux-gnu (32-bit)
using session charset: UTF-8
using option ‘--no-vignettes’
checking for file ‘qtlbim/DESCRIPTION’ ... OK
this is package ‘qtlbim’ version ‘1.9.4’
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 ‘qtlbim’ can be installed ... 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 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
File ‘qtlbim/R/zzz.R’:
.onLoad calls:
require("qtl")

Package startup functions should not change the search path.
See section ‘Good practice’ in ?.onAttach.

qb.hpdone: warning in qb.scanone(qbObject, ..., type = "posterior"):
partial argument match of 'type' to 'type.scan'
qb.hpdone: warning in qb.scanone(qbObject, type = profile, chr = chr,
...): partial argument match of 'type' to 'type.scan'
qb.hpdone: warning in qb.scanone(qbObject, type = "cellmean", chr =
chr, ...): partial argument match of 'type' to 'type.scan'
qb.hpdone: warning in qb.scanone(qbObject, type = "estimate", scan =
"main", aggregate = FALSE, chr = chr, ...): partial argument match of
'type' to 'type.scan'
qb.inter.pleiotropy: warning in qb.get(qbObject, "mainloci", pheno =
i): partial argument match of 'pheno' to 'pheno.col'
qb.pleiotropy: warning in qb.get(qbObject, "mainloci", pheno = i):
partial argument match of 'pheno' to 'pheno.col'
qb.sim.cross: warning in sample(1:2, n.ind, repl = TRUE): partial
argument match of 'repl' to 'replace'
qb.sim.cross: warning in sample(0:1, n.ind, repl = TRUE, prob = c(1 -
r[j], r[j])): partial argument match of 'repl' to 'replace'
qb.sim.cross: warning in sample(1:3, n.ind, repl = TRUE, prob = c(1, 2,
1)): partial argument match of 'repl' to 'replace'
qb.sim.cross: warning in sample(1:3, sum(data[, j] == 1), repl = TRUE,
prob = c(rbar[j] * rbar[j], 2 * r[j] * rbar[j], r[j] * r[j])):
partial argument match of 'repl' to 'replace'
qb.sim.cross: warning in sample(1:3, sum(data[, j] == 2), repl = TRUE,
prob = c(r[j] * rbar[j], rbar[j] * rbar[j] + r[j] * r[j], r[j] *
rbar[j])): partial argument match of 'repl' to 'replace'
qb.sim.cross: warning in sample(1:3, sum(data[, j] == 3), repl = TRUE,
prob = c(r[j] * r[j], 2 * r[j] * rbar[j], rbar[j] * rbar[j])):
partial argument match of 'repl' to 'replace'
qb.sim.cross: warning in sample(c(0, 1), n.ind, repl = TRUE): partial
argument match of 'repl' to 'replace'
qb.sim.cross: warning in sample(0:4, n.ind, repl = TRUE): partial
argument match of 'repl' to 'replace'
qb.sim.cross: warning in sample(c(1, NA), n.ind * ncol(geno[[i]]$data),
repl = TRUE, prob = c(1 - missing.geno, missing.geno)): partial
argument match of 'repl' to 'replace'
qb.sim.cross: warning in sample(c(1, NA), n.ind, repl = TRUE, prob =
c(1 - missing.pheno, missing.pheno)): partial argument match of
'repl' to 'replace'
qb.smoothsame: no visible binding for global variable ‘smoothpair’
qb.smoothtwo: multiple local function definitions for ‘smoothpair’ with
different formal arguments
checking Rd files ... OK
checking Rd metadata ... OK
checking Rd cross-references ... WARNING
Unknown package(s) ‘code’ in Rd xrefs
Missing link(s) in documentation object ‘/home/hornik/tmp/R.check/r-release/Work/PKGS/qtlbim/man/diag.Rd’:
‘[base]{boxplot}’

Missing link(s) in documentation object ‘/home/hornik/tmp/R.check/r-release/Work/PKGS/qtlbim/man/loci.Rd’:
‘[graphics]{jitter}’ ‘[base]{plot}’

Missing link(s) in documentation object ‘/home/hornik/tmp/R.check/r-release/Work/PKGS/qtlbim/man/plot.Rd’:
‘[base]{plot}’

Missing link(s) in documentation object ‘/home/hornik/tmp/R.check/r-release/Work/PKGS/qtlbim/man/qb-internal.Rd’:
‘[base]{data}’

See the information in section ‘Cross-references’ of the ‘Writing R
Extensions’ manual.
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 ... NOTE

Note: significantly better compression could be obtained
by using R CMD build --resave-data
old_size new_size compress
Bnapus.RData 18Kb 12Kb bzip2
fisch.RData 14Kb 9Kb bzip2
qbExample.RData 262Kb 180Kb xz
qbHyper.RData 543Kb 350Kb xz
qbSimEpi.RData 94Kb 64Kb xz
qbSimMain.RData 79Kb 54Kb 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 ... NOTE
File ‘/home/hornik/tmp/R.check/r-release/Work/build/Packages/qtlbim/libs/qtlbim.so’:
Found ‘exit’, possibly from ‘exit’ (C)

Compiled code should not call functions which might terminate R nor
write to stdout/stderr instead of to the console. The detected symbols
are linked into the code but might come from libraries and not actually
be called.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
checking sizes of PDF files under ‘inst/doc’ ... OK
checking examples ... OK
checking for unstated dependencies in vignettes ... OK
checking package vignettes in ‘inst/doc’ ... OK
checking running R code from vignettes ... SKIPPED
checking re-building of vignettes ... SKIPPED
checking PDF version of manual ... OK
WARNING: There was 1 warning, see
‘/home/hornik/tmp/R.check/r-release/Work/PKGS/qtlbim.Rcheck/00check.log’
for details