CRAN Package Check Results for Package QTLRel

Last updated on 2015-01-30 18:51:36.

Check Details

Version: 0.2-14
Check: dependencies in R code
Result: NOTE
    'library' or 'require' call to ‘qtl’ in package code.
     Please use :: or requireNamespace() instead.
     See section 'Suggested 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, r-devel-osx-x86_64-clang, r-devel-windows-ix86+x86_64

Version: 0.2-14
Check: foreign function calls
Result: NOTE
    Calls with DUP:
     .C("rgdata2", gdata = as.integer(t(gdat)), nr = as.integer(nr),
     nc = as.integer(nc), ninit = as.integer(ninit), pedigree = as.integer(t(pedd)),
     recomb = as.double(rr), xchr = as.logical(xchr), seed = as.integer(seed),
     DUP = FALSE, PACKAGE = "QTLRel")
     .C("gen_Matrix", x = as.double(t(x)), nr = as.integer(nr), nc = as.integer(nc),
     nn = as.integer(nn), ksp = as.double(t(ksp)), DD = as.double(t(DD)),
     AD = as.double(t(AD)), HH = as.double(t(HH)), MH = as.double(t(MH)),
     DUP = FALSE, PACKAGE = "QTLRel")
     .C("deltaFnc", x = as.integer(t(gdata)), nr = as.integer(nr),
     nc = as.integer(nc), deltac = as.double(t(deltac)), DUP = FALSE,
     PACKAGE = "QTLRel")
     .C("conGenoPrc", mdat = as.integer(mdat[nn, ]), n = as.integer(n),
     dist = as.double(dist), pos = as.double(pos), np = as.integer(np),
     at = as.integer(at), gr = as.integer(gr), method = as.integer(method),
     pdat = as.double(pdat), error = as.logical(err), DUP = FALSE,
     PACKAGE = "QTLRel")
     .C("ibsPrc", prdat = as.double(aperm(prdat, c(3, 2, 1))), nr = as.integer(nr),
     nc = as.integer(nc), ibsc = as.double(t(ibsc)), DUP = FALSE,
     PACKAGE = "QTLRel")
     .C("ibsFnc", gdat = as.integer(t(gdata)), nr = as.integer(nr),
     nc = as.integer(nc), ibsc = as.double(t(ibsc)), DUP = FALSE,
     PACKAGE = "QTLRel")
     .C("kinship", ped = as.integer(t(ped)), nr = as.integer(nrow(ped)),
     nc = as.integer(ncol(ped)), ksp = as.double(ksp), DUP = FALSE,
     PACKAGE = "QTLRel")
    DUP is no longer supported and will be ignored.
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

Version: 0.2-14
Check: R code for possible problems
Result: NOTE
    plotit: no visible global function definition for ‘xyplot’
    plotit : <anonymous>: no visible global function definition for
     ‘panel.xyplot’
    plotit : <anonymous>: no visible global function definition for
     ‘panel.abline’
    plotit : <anonymous>: no visible global function definition for
     ‘panel.superpose’
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, r-release-linux-ix86, r-release-linux-x86_64, r-release-osx-x86_64-mavericks, r-release-windows-ix86+x86_64

Version: 0.2-14
Check: compiled code
Result: NOTE
    File ‘QTLRel/libs/QTLRel.so’:
     Found ‘rand’, possibly from ‘rand’ (C)
     Object: ‘rgdat.o’
     Found ‘srand’, possibly from ‘srand’ (C)
     Object: ‘rgdat.o’
    
    Compiled code should not call entry points which might terminate R nor
    write to stdout/stderr instead of to the console, nor the system 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, r-patched-linux-x86_64, r-patched-solaris-sparc, r-patched-solaris-x86

Version: 0.2-14
Check: compiled code
Result: NOTE
    File ‘QTLRel/libs/QTLRel.so’:
     Found ‘_rand’, possibly from ‘rand’ (C)
     Object: ‘rgdat.o’
     Found ‘_srand’, possibly from ‘srand’ (C)
     Object: ‘rgdat.o’
    
    Compiled code should not call entry points which might terminate R nor
    write to stdout/stderr instead of to the console, nor the system RNG.
    
    See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Flavors: r-devel-osx-x86_64-clang, r-release-osx-x86_64-mavericks

Version: 0.2-14
Check: compiled code
Result: NOTE
    File 'QTLRel/libs/i386/QTLRel.dll':
     Found 'rand', possibly from 'rand' (C)
     Object: 'rgdat.o'
     Found 'srand', possibly from 'srand' (C)
     Object: 'rgdat.o'
    File 'QTLRel/libs/x64/QTLRel.dll':
     Found 'rand', possibly from 'rand' (C)
     Object: 'rgdat.o'
     Found 'srand', possibly from 'srand' (C)
     Object: 'rgdat.o'
    
    Compiled code should not call entry points which might terminate R nor
    write to stdout/stderr instead of to the console, nor the system RNG.
    
    See 'Writing portable packages' in the 'Writing R Extensions' manual.
Flavor: r-devel-windows-ix86+x86_64

Version: 0.2-14
Check: foreign function calls
Result: NOTE
    Calls with DUP != TRUE:
     .C("rgdata2", gdata = as.integer(t(gdat)), nr = as.integer(nr),
     nc = as.integer(nc), ninit = as.integer(ninit), pedigree = as.integer(t(pedd)),
     recomb = as.double(rr), xchr = as.logical(xchr), seed = as.integer(seed),
     DUP = FALSE, PACKAGE = "QTLRel")
     .C("gen_Matrix", x = as.double(t(x)), nr = as.integer(nr), nc = as.integer(nc),
     nn = as.integer(nn), ksp = as.double(t(ksp)), DD = as.double(t(DD)),
     AD = as.double(t(AD)), HH = as.double(t(HH)), MH = as.double(t(MH)),
     DUP = FALSE, PACKAGE = "QTLRel")
     .C("deltaFnc", x = as.integer(t(gdata)), nr = as.integer(nr),
     nc = as.integer(nc), deltac = as.double(t(deltac)), DUP = FALSE,
     PACKAGE = "QTLRel")
     .C("conGenoPrc", mdat = as.integer(mdat[nn, ]), n = as.integer(n),
     dist = as.double(dist), pos = as.double(pos), np = as.integer(np),
     at = as.integer(at), gr = as.integer(gr), method = as.integer(method),
     pdat = as.double(pdat), error = as.logical(err), DUP = FALSE,
     PACKAGE = "QTLRel")
     .C("ibsPrc", prdat = as.double(aperm(prdat, c(3, 2, 1))), nr = as.integer(nr),
     nc = as.integer(nc), ibsc = as.double(t(ibsc)), DUP = FALSE,
     PACKAGE = "QTLRel")
     .C("ibsFnc", gdat = as.integer(t(gdata)), nr = as.integer(nr),
     nc = as.integer(nc), ibsc = as.double(t(ibsc)), DUP = FALSE,
     PACKAGE = "QTLRel")
     .C("kinship", ped = as.integer(t(ped)), nr = as.integer(nrow(ped)),
     nc = as.integer(ncol(ped)), ksp = as.double(ksp), DUP = FALSE,
     PACKAGE = "QTLRel")
    DUP = FALSE is deprecated and will be disabled in future versions of R.
Flavors: r-patched-linux-x86_64, r-patched-solaris-sparc, r-patched-solaris-x86, r-release-linux-ix86, r-release-linux-x86_64, r-release-osx-x86_64-mavericks, r-release-windows-ix86+x86_64

Version: 0.2-14
Check: compiled code
Result: NOTE
    File ‘QTLRel/libs/QTLRel.so’:
     Found ‘rand’, possibly from ‘rand’ (C)
     Object: ‘rgdat.o’
     Found ‘srand’, possibly from ‘srand’ (C)
     Object: ‘rgdat.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-release-linux-ix86, r-release-linux-x86_64

Version: 0.2-14
Check: compiled code
Result: NOTE
    File 'QTLRel/libs/i386/QTLRel.dll':
     Found 'rand', possibly from 'rand' (C)
     Object: 'rgdat.o'
     Found 'srand', possibly from 'srand' (C)
     Object: 'rgdat.o'
    File 'QTLRel/libs/x64/QTLRel.dll':
     Found 'rand', possibly from 'rand' (C)
     Object: 'rgdat.o'
     Found 'srand', possibly from 'srand' (C)
     Object: 'rgdat.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-release-windows-ix86+x86_64