Last updated on 2014-10-10 15:49:16.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 2.0.7 | 5.97 | 113.92 | 119.88 | NOTE | |
| r-devel-linux-x86_64-debian-gcc | 2.0.7 | 8.23 | 113.04 | 121.28 | NOTE | |
| r-devel-linux-x86_64-fedora-clang | 2.0.7 | 268.31 | NOTE | |||
| r-devel-linux-x86_64-fedora-gcc | 2.0.7 | 261.92 | NOTE | |||
| r-devel-osx-x86_64-clang | 2.0.7 | 177.16 | NOTE | |||
| r-devel-windows-ix86+x86_64 | 2.0.7 | 28.00 | 195.00 | 223.00 | NOTE | |
| r-patched-linux-x86_64 | 2.0.7 | 8.44 | 139.92 | 148.36 | NOTE | |
| r-patched-solaris-sparc | 2.0.7 | 1483.10 | NOTE | |||
| r-patched-solaris-x86 | 2.0.7 | 290.30 | NOTE | |||
| r-release-linux-ix86 | 2.0.7 | 9.83 | 150.80 | 160.63 | NOTE | |
| r-release-linux-x86_64 | 2.0.7 | 8.47 | 132.29 | 140.76 | NOTE | |
| r-release-osx-x86_64-mavericks | 2.0.7 | NOTE | ||||
| r-release-osx-x86_64-snowleopard | 2.0.7 | NOTE | ||||
| r-release-windows-ix86+x86_64 | 2.0.7 | 29.00 | 200.00 | 229.00 | NOTE | |
| r-oldrel-windows-ix86+x86_64 | 2.0.7 | 30.00 | 206.00 | 236.00 | NOTE |
Version: 2.0.7
Check: dependencies in R code
Result: NOTE
'library' or 'require' calls to packages already attached by Depends:
‘MASS’ ‘coda’ ‘lattice’ ‘tools’
Please remove these calls from your code.
Packages in Depends field not imported from:
‘MASS’ ‘coda’ ‘lattice’ ‘qtl’ ‘tools’
These packages need to be imported from (in the NAMESPACE file)
for when this namespace is loaded but not attached.
See the information on DESCRIPTION files in the chapter ‘Creating R
packages’ of the ‘Writing R Extensions’ manual.
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-osx-x86_64-clang, r-devel-windows-ix86+x86_64, r-patched-linux-x86_64, r-patched-solaris-sparc, r-patched-solaris-x86
Version: 2.0.7
Check: R code for possible problems
Result: NOTE
make.main: no visible global function definition for ‘nchr’
make.main: no visible global function definition for ‘drop.markers’
make.main: no visible global function definition for ‘nind’
make.main: no visible global function definition for ‘nmar’
plot.qb.close: no visible global function definition for ‘bwplot’
plot.qb.condloci: no visible global function definition for
‘densityplot’
plot.qb.covar: no visible global function definition for
‘trellis.par.set’
plot.qb.covar: no visible global function definition for ‘col.whitebg’
plot.qb.covar: no visible global function definition for ‘xyplot’
plot.qb.covar : <anonymous>: no visible global function definition for
‘panel.abline’
plot.qb.covar : <anonymous>: no visible global function definition for
‘panel.xyplot’
plot.qb.epistasis: no visible global function definition for
‘trellis.par.set’
plot.qb.epistasis: no visible global function definition for
‘col.whitebg’
plot.qb.epistasis: no visible global function definition for ‘bwplot’
plot.qb.epistasis : <anonymous>: no visible global function definition
for ‘panel.abline’
plot.qb.epistasis : <anonymous>: no visible global function definition
for ‘panel.stripplot’
plot.qb.epistasis : <anonymous>: no visible global function definition
for ‘panel.bwplot’
plot.qb.epistasis : <anonymous>: no visible global function definition
for ‘panel.lines’
plot.qb.meancomp: no visible global function definition for
‘trellis.par.set’
plot.qb.meancomp: no visible global function definition for
‘col.whitebg’
plot.qb.meancomp: no visible global function definition for ‘splom’
plot.qb.meancomp : <anonymous>: no visible global function definition
for ‘panel.abline’
plot.qb.meancomp : <anonymous>: no visible global function definition
for ‘panel.splom’
plot.qb.meancomp : <anonymous>: no visible global function definition
for ‘panel.xyplot’
plot.qb.meancomp : <anonymous>: no visible global function definition
for ‘diag.panel.splom’
plot.qb.meancomp: no visible global function definition for
‘densityplot’
plot.qb.multloci: no visible global function definition for
‘trellis.par.set’
plot.qb.multloci: no visible global function definition for
‘col.whitebg’
plot.qb.multloci : mydensityplot: no visible global function definition
for ‘densityplot’
plot.qb.multloci : mydensityplot : <anonymous>: no visible global
function definition for ‘trellis.par.get’
plot.qb.multloci : mydensityplot : <anonymous>: no visible global
function definition for ‘current.panel.limits’
plot.qb.multloci : mydensityplot : <anonymous>: no visible global
function definition for ‘panel.lines’
plot.qb.multloci : mydensityplot : <anonymous>: no visible global
function definition for ‘panel.xyplot’
plot.qb.multloci : mydensityplot : <anonymous>: no visible global
function definition for ‘panel.abline’
plot.qb.multloci : mydensityplot : <anonymous>: no visible global
function definition for ‘panel.rug’
plot.qb.multloci : mydensityplot : <anonymous>: no visible global
function definition for ‘panel.superpose’
plot.qb.multloci: no visible global function definition for
‘densityplot’
plot.qb.multloci : <anonymous>: no visible global function definition
for ‘panel.densityplot’
plot.qb.multloci : <anonymous>: no visible global function definition
for ‘panel.rug’
plot.qb.multloci: no visible global function definition for ‘barchart’
plot.qb.multloci: no visible global function definition for ‘xyplot’
plot.qb.multloci : <anonymous>: no visible global function definition
for ‘panel.abline’
plot.qb.multloci : <anonymous>: no visible global function definition
for ‘panel.points’
plot.qb.multloci : <anonymous>: no visible global function definition
for ‘panel.superpose’
plot.qb.multloci : <anonymous> : <anonymous>: no visible global
function definition for ‘panel.lines’
plot.qb.scantwo: no visible global function definition for ‘qtlversion’
plot.qb.slicetwo: no visible global function definition for
‘find.marker’
plot.qb.slicetwo: no visible global function definition for ‘sim.geno’
plot.qb.slicetwo: no visible global function definition for
‘effectplot’
plot.qb.varcomp: no visible global function definition for
‘trellis.par.set’
plot.qb.varcomp: no visible global function definition for
‘col.whitebg’
plot.qb.varcomp: no visible global function definition for ‘splom’
plot.qb.varcomp : <anonymous>: no visible global function definition
for ‘panel.abline’
plot.qb.varcomp : <anonymous>: no visible global function definition
for ‘panel.splom’
plot.qb.varcomp : <anonymous>: no visible global function definition
for ‘panel.xyplot’
plot.qb.varcomp : <anonymous>: no visible global function definition
for ‘diag.panel.splom’
plot.qb.varcomp: no visible global function definition for
‘densityplot’
pull.grid: no visible global function definition for ‘pull.map’
pull.loci : tmpfn: no visible global function definition for
‘create.map’
qb.chrom: no visible global function definition for ‘pull.map’
qb.coda: no visible global function definition for ‘mcmc’
qb.condloci: no visible global function definition for ‘lda’
qb.confound: no visible global function definition for ‘nind’
qb.data: no visible global function definition for ‘find.pheno’
qb.data: no visible global function definition for ‘nind’
qb.epimodes : chrsplit: no visible global function definition for ‘lda’
qb.genoprob: no visible binding for global variable ‘calc.genoprob’
qb.genoprob: no visible global function definition for ‘pull.map’
qb.genoprob: no visible global function definition for ‘jittermap’
qb.genoprob: no visible global function definition for ‘calc.genoprob’
qb.genoprob.defaults: no visible binding for global variable
‘calc.genoprob’
qb.hpdone: no visible global function definition for ‘pull.map’
qb.humanGenoProb: no visible global function definition for ‘nchr’
qb.humanGenoProb: no visible global function definition for ‘nind’
qb.humanGenoProb: no visible global function definition for ‘nmar’
qb.legacy: no visible global function definition for ‘clean’
qb.loci: no visible global function definition for ‘pull.map’
qb.mainmodes : chrsplit: no visible global function definition for
‘lda’
qb.mcmc: no visible global function definition for ‘nind’
qb.mcmc: no visible global function definition for ‘nchr’
qb.model: no visible global function definition for ‘nchr’
qb.multloci: no visible global function definition for ‘pull.map’
qb.outbredF2: no visible global function definition for ‘read.cross’
qb.pairloci: no visible global function definition for ‘pull.map’
qb.pairs: no visible global function definition for ‘pull.map’
qb.pattern: no visible global function definition for ‘pull.map’
qb.recover: no visible global function definition for ‘find.pheno’
qb.reorder: no visible global function definition for ‘pull.map’
qb.save: no visible global function definition for ‘clean’
qb.scantwo: no visible global function definition for ‘pull.map’
qb.sim.cross: no visible global function definition for ‘mvrnorm’
qb.sweave: no visible global function definition for ‘clean’
qb.valid.phenoData: no visible global function definition for ‘nind’
select.cc: no visible global function definition for ‘nchr’
select.cc: no visible global function definition for ‘nind’
step.fitqtl: no visible global function definition for ‘qtlversion’
step.fitqtl : myfitqtl: no visible global function definition for
‘fitqtl’
subset.qb: no visible global function definition for ‘pull.map’
summary.qb.scantwo: no visible global function definition for
‘qtlversion’
Found the following assignments to the global environment:
File ‘qtlbim/R/sweave.R’:
assign(".qb.name", .qb.name, ".GlobalEnv")
assign(".qb.cross", cross, ".GlobalEnv")
assign(".qb.pheno", pheno.col, ".GlobalEnv")
assign(".qb.niter", n.iter, ".GlobalEnv")
assign(".qb.draws", n.draws, ".GlobalEnv")
assign(".qb.threshold", c(upper = upper.threshold), ".GlobalEnv")
assign(".qb.scan.type", scan.type, ".GlobalEnv")
assign(".qb.hpd.level", hpd.level, ".GlobalEnv")
assign(".qb.PDFDir", PDFDir, ".GlobalEnv")
assign(".qb.SweaveFile", SweaveFile, ".GlobalEnv")
assign(".qb.SweaveExtra", SweaveExtra, ".GlobalEnv")
assign(".qb.remove", remove.qb, ".GlobalEnv")
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-osx-x86_64-clang
Version: 2.0.7
Check: compiled code
Result: NOTE
File ‘qtlbim/libs/qtlbim.so’:
Found ‘rand’, possibly from ‘rand’ (C)
Objects: ‘MultipleTraitsMCMC.o’, ‘SingleTraitMCMC.o’, ‘StatUtils.o’
Found ‘srand’, possibly from ‘srand’ (C)
Objects: ‘MultipleTraitsMCMC.o’, ‘SingleTraitMCMC.o’
Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor the C RNG.
See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc
Version: 2.0.7
Check: R code for possible problems
Result: NOTE
make.main: no visible global function definition for ‘nchr’
make.main: no visible global function definition for ‘drop.markers’
make.main: no visible global function definition for ‘nind’
make.main: no visible global function definition for ‘nmar’
plot.qb.close: no visible global function definition for ‘bwplot’
plot.qb.condloci: no visible global function definition for
‘densityplot’
plot.qb.covar: no visible global function definition for
‘trellis.par.set’
plot.qb.covar: no visible global function definition for ‘col.whitebg’
plot.qb.covar: no visible global function definition for ‘xyplot’
plot.qb.covar : <anonymous>: no visible global function definition for
‘panel.abline’
plot.qb.covar : <anonymous>: no visible global function definition for
‘panel.xyplot’
plot.qb.epistasis: no visible global function definition for
‘trellis.par.set’
plot.qb.epistasis: no visible global function definition for
‘col.whitebg’
plot.qb.epistasis: no visible global function definition for ‘bwplot’
plot.qb.epistasis : <anonymous>: no visible global function definition
for ‘panel.abline’
plot.qb.epistasis : <anonymous>: no visible global function definition
for ‘panel.stripplot’
plot.qb.epistasis : <anonymous>: no visible global function definition
for ‘panel.bwplot’
plot.qb.epistasis : <anonymous>: no visible global function definition
for ‘panel.lines’
plot.qb.meancomp: no visible global function definition for
‘trellis.par.set’
plot.qb.meancomp: no visible global function definition for
‘col.whitebg’
plot.qb.meancomp: no visible global function definition for ‘splom’
plot.qb.meancomp : <anonymous>: no visible global function definition
for ‘panel.abline’
plot.qb.meancomp : <anonymous>: no visible global function definition
for ‘panel.splom’
plot.qb.meancomp : <anonymous>: no visible global function definition
for ‘panel.xyplot’
plot.qb.meancomp : <anonymous>: no visible global function definition
for ‘diag.panel.splom’
plot.qb.meancomp: no visible global function definition for
‘densityplot’
plot.qb.multloci: no visible global function definition for
‘trellis.par.set’
plot.qb.multloci: no visible global function definition for
‘col.whitebg’
plot.qb.multloci : mydensityplot: no visible global function definition
for ‘densityplot’
plot.qb.multloci : mydensityplot : <anonymous>: no visible global
function definition for ‘trellis.par.get’
plot.qb.multloci : mydensityplot : <anonymous>: no visible global
function definition for ‘current.panel.limits’
plot.qb.multloci : mydensityplot : <anonymous>: no visible global
function definition for ‘panel.lines’
plot.qb.multloci : mydensityplot : <anonymous>: no visible global
function definition for ‘panel.xyplot’
plot.qb.multloci : mydensityplot : <anonymous>: no visible global
function definition for ‘panel.abline’
plot.qb.multloci : mydensityplot : <anonymous>: no visible global
function definition for ‘panel.rug’
plot.qb.multloci : mydensityplot : <anonymous>: no visible global
function definition for ‘panel.superpose’
plot.qb.multloci: no visible global function definition for
‘densityplot’
plot.qb.multloci : <anonymous>: no visible global function definition
for ‘panel.densityplot’
plot.qb.multloci : <anonymous>: no visible global function definition
for ‘panel.rug’
plot.qb.multloci: no visible global function definition for ‘barchart’
plot.qb.multloci: no visible global function definition for ‘xyplot’
plot.qb.multloci : <anonymous>: no visible global function definition
for ‘panel.abline’
plot.qb.multloci : <anonymous>: no visible global function definition
for ‘panel.points’
plot.qb.multloci : <anonymous>: no visible global function definition
for ‘panel.superpose’
plot.qb.multloci : <anonymous> : <anonymous>: no visible global
function definition for ‘panel.lines’
plot.qb.scantwo: no visible global function definition for ‘qtlversion’
plot.qb.slicetwo: no visible global function definition for
‘find.marker’
plot.qb.slicetwo: no visible global function definition for ‘sim.geno’
plot.qb.slicetwo: no visible global function definition for
‘effectplot’
plot.qb.varcomp: no visible global function definition for
‘trellis.par.set’
plot.qb.varcomp: no visible global function definition for
‘col.whitebg’
plot.qb.varcomp: no visible global function definition for ‘splom’
plot.qb.varcomp : <anonymous>: no visible global function definition
for ‘panel.abline’
plot.qb.varcomp : <anonymous>: no visible global function definition
for ‘panel.splom’
plot.qb.varcomp : <anonymous>: no visible global function definition
for ‘panel.xyplot’
plot.qb.varcomp : <anonymous>: no visible global function definition
for ‘diag.panel.splom’
plot.qb.varcomp: no visible global function definition for
‘densityplot’
pull.grid: no visible global function definition for ‘pull.map’
pull.loci : tmpfn: no visible global function definition for
‘create.map’
qb.chrom: no visible global function definition for ‘pull.map’
qb.coda: no visible global function definition for ‘mcmc’
qb.condloci: no visible global function definition for ‘lda’
qb.confound: no visible global function definition for ‘nind’
qb.data: no visible global function definition for ‘find.pheno’
qb.data: no visible global function definition for ‘nind’
qb.epimodes : chrsplit: no visible global function definition for ‘lda’
qb.genoprob: no visible binding for global variable ‘calc.genoprob’
qb.genoprob: no visible global function definition for ‘pull.map’
qb.genoprob: no visible global function definition for ‘jittermap’
qb.genoprob: no visible global function definition for ‘calc.genoprob’
qb.genoprob.defaults: no visible binding for global variable
‘calc.genoprob’
qb.hpdone: no visible global function definition for ‘pull.map’
qb.humanGenoProb: no visible global function definition for ‘nchr’
qb.humanGenoProb: no visible global function definition for ‘nind’
qb.humanGenoProb: no visible global function definition for ‘nmar’
qb.legacy: no visible global function definition for ‘clean’
qb.loci: no visible global function definition for ‘pull.map’
qb.mainmodes : chrsplit: no visible global function definition for
‘lda’
qb.mcmc: no visible global function definition for ‘nind’
qb.mcmc: no visible global function definition for ‘nchr’
qb.model: no visible global function definition for ‘nchr’
qb.multloci: no visible global function definition for ‘pull.map’
qb.outbredF2: no visible global function definition for ‘read.cross’
qb.pairloci: no visible global function definition for ‘pull.map’
qb.pairs: no visible global function definition for ‘pull.map’
qb.pattern: no visible global function definition for ‘pull.map’
qb.recover: no visible global function definition for ‘find.pheno’
qb.reorder: no visible global function definition for ‘pull.map’
qb.save: no visible global function definition for ‘clean’
qb.scantwo: no visible global function definition for ‘pull.map’
qb.sim.cross: no visible global function definition for ‘mvrnorm’
qb.sweave: no visible global function definition for ‘clean’
qb.valid.phenoData: no visible global function definition for ‘nind’
select.cc: no visible global function definition for ‘nchr’
select.cc: no visible global function definition for ‘nind’
step.fitqtl: no visible global function definition for ‘qtlversion’
step.fitqtl : myfitqtl: no visible global function definition for
‘fitqtl’
subset.qb: no visible global function definition for ‘pull.map’
summary.qb.scantwo: no visible global function definition for
‘qtlversion’
Flavors: r-devel-linux-x86_64-fedora-gcc, r-devel-windows-ix86+x86_64
Version: 2.0.7
Check: compiled code
Result: NOTE
File ‘qtlbim/libs/qtlbim.so’:
Found ‘_rand’, possibly from ‘rand’ (C)
Objects: ‘MultipleTraitsMCMC.o’, ‘SingleTraitMCMC.o’, ‘StatUtils.o’
Found ‘_srand’, possibly from ‘srand’ (C)
Objects: ‘MultipleTraitsMCMC.o’, ‘SingleTraitMCMC.o’
Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor the C RNG.
See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Flavor: r-devel-osx-x86_64-clang
Version: 2.0.7
Check: compiled code
Result: NOTE
File 'qtlbim/libs/i386/qtlbim.dll':
Found 'rand', possibly from 'rand' (C)
Objects: 'MultipleTraitsMCMC.o', 'SingleTraitMCMC.o', 'StatUtils.o'
Found 'srand', possibly from 'srand' (C)
Objects: 'MultipleTraitsMCMC.o', 'SingleTraitMCMC.o'
File 'qtlbim/libs/x64/qtlbim.dll':
Found 'rand', possibly from 'rand' (C)
Objects: 'MultipleTraitsMCMC.o', 'SingleTraitMCMC.o', 'StatUtils.o'
Found 'srand', possibly from 'srand' (C)
Objects: 'MultipleTraitsMCMC.o', 'SingleTraitMCMC.o'
Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor the C RNG.
See 'Writing portable packages' in the 'Writing R Extensions' manual.
Flavor: r-devel-windows-ix86+x86_64
Version: 2.0.7
Check: R code for possible problems
Result: NOTE
Found the following assignments to the global environment:
File ‘qtlbim/R/sweave.R’:
assign(".qb.name", .qb.name, ".GlobalEnv")
assign(".qb.cross", cross, ".GlobalEnv")
assign(".qb.pheno", pheno.col, ".GlobalEnv")
assign(".qb.niter", n.iter, ".GlobalEnv")
assign(".qb.draws", n.draws, ".GlobalEnv")
assign(".qb.threshold", c(upper = upper.threshold), ".GlobalEnv")
assign(".qb.scan.type", scan.type, ".GlobalEnv")
assign(".qb.hpd.level", hpd.level, ".GlobalEnv")
assign(".qb.PDFDir", PDFDir, ".GlobalEnv")
assign(".qb.SweaveFile", SweaveFile, ".GlobalEnv")
assign(".qb.SweaveExtra", SweaveExtra, ".GlobalEnv")
assign(".qb.remove", remove.qb, ".GlobalEnv")
Flavors: r-patched-linux-x86_64, r-release-linux-ix86, r-release-linux-x86_64
Version: 2.0.7
Check: dependencies in R code
Result: NOTE
'library' or 'require' calls to packages already attached by Depends:
‘MASS’ ‘coda’ ‘lattice’ ‘tools’
Please remove these calls from your code.
Packages in Depends field not imported from:
‘MASS’ ‘coda’ ‘lattice’ ‘qtl’
These packages need to be imported from (in the NAMESPACE file)
for when this namespace is loaded but not attached.
See the information on DESCRIPTION files in the chapter ‘Creating R
packages’ of the ‘Writing R Extensions’ manual.
Flavors: r-release-linux-ix86, r-release-linux-x86_64, r-release-osx-x86_64-mavericks, r-release-windows-ix86+x86_64, r-oldrel-windows-ix86+x86_64
Version: 2.0.7
Check: dependencies in R code
Result: NOTE
'library' or 'require' calls to packages already attached by Depends:
'MASS' 'coda' 'lattice' 'tools'
Please remove these calls from your code.
See the information on DESCRIPTION files in the chapter 'Creating R
packages' of the 'Writing R Extensions' manual.
Flavor: r-release-osx-x86_64-snowleopard