- using R Under development (unstable) (2012-02-27 r58511)
- using platform: x86_64-pc-mingw32 (64-bit)
- using session charset: ISO8859-1
- 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 whether package 'qtlbim' can be installed ... OK
- checking installed package size ... NOTE
installed size is 6.9Mb
sub-directories of 1Mb or more:
doc 5.1Mb
- checking package directory ... OK
- checking for portable file names ... 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
- loading checks for arch 'i386'
** 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
- loading checks for arch 'x64'
** 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 'd:/RCompile/CRANpkg/local/2.15/qtlbim/man/diag.Rd':
'[base]{boxplot}'
Missing link(s) in documentation object 'd:/RCompile/CRANpkg/local/2.15/qtlbim/man/loci.Rd':
'[graphics]{jitter}' '[base]{plot}'
Missing link(s) in documentation object 'd:/RCompile/CRANpkg/local/2.15/qtlbim/man/plot.Rd':
'[base]{plot}'
Missing link(s) in documentation object 'd:/RCompile/CRANpkg/local/2.15/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 ... WARNING
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 63Kb 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 'd:/Rcompile/CRANpkg/lib/2.15/qtlbim/libs/i386/qtlbim.dll':
Found 'abort', possibly from 'abort' (C)
Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
File 'd:/Rcompile/CRANpkg/lib/2.15/qtlbim/libs/x64/qtlbim.dll':
Found 'abort', possibly from 'abort' (C)
Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
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' ... NOTE
'qpdf' made some significant size reductions:
compacted 'FIG-QBCODA.pdf' from 294Kb to 65Kb
compacted 'FIG-QBEPI.pdf' from 195Kb to 23Kb
compacted 'FIG-QBLOCI34.pdf' from 234Kb to 25Kb
compacted 'FIG-Scantwo-HyperData.pdf' from 395Kb to 48Kb
compacted 'mult.pdf' from 520Kb to 111Kb
compacted 'multmerge.pdf' from 268Kb to 69Kb
compacted 'prototype.qtl.hyper.slides.pdf' from 429Kb to 145Kb
compacted 'qtlbim.pdf' from 2356Kb to 606Kb
compacted 'slide2LOD-1.pdf' from 151Kb to 20Kb
consider running tools::compactPDF() on these files
- checking installed files from 'inst/doc' ... OK
- checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
- checking for unstated dependencies in vignettes ... OK
- checking package vignettes in 'inst/doc' ... OK
- checking running R code from vignettes ... OK
- checking re-building of vignette PDFs ... OK
- checking PDF version of manual ... OK
WARNING: There were 2 warnings.
NOTE: There were 4 notes.
See
'd:/Rcompile/CRANpkg/local/2.15/qtlbim.Rcheck/00check.log'
for details.