CRAN Package Check Results for Package RJaCGH

Last updated on 2014-11-26 05:47:56.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 2.0.2 4.25 41.63 45.88 ERROR
r-devel-linux-x86_64-debian-gcc 2.0.2 7.04 41.32 48.37 ERROR
r-devel-linux-x86_64-fedora-clang 2.0.2 73.64 ERROR
r-devel-linux-x86_64-fedora-gcc 2.0.2 128.58 NOTE
r-devel-osx-x86_64-clang 2.0.2 89.01 NOTE
r-devel-windows-ix86+x86_64 2.0.2 28.00 160.00 188.00 NOTE
r-patched-linux-x86_64 2.0.2 7.03 74.04 81.07 NOTE
r-patched-solaris-sparc 2.0.2 752.50 NOTE
r-patched-solaris-x86 2.0.2 168.50 NOTE
r-release-linux-ix86 2.0.2 7.58 78.65 86.23 NOTE
r-release-linux-x86_64 2.0.2 6.98 72.47 79.45 NOTE
r-release-osx-x86_64-mavericks 2.0.2 NOTE
r-release-windows-ix86+x86_64 2.0.2 27.00 162.00 189.00 NOTE
r-oldrel-windows-ix86+x86_64 2.0.2 26.00 163.00 189.00 NOTE

Memtest notes: valgrind

Check Details

Version: 2.0.2
Check: top-level files
Result: NOTE
    Non-standard files/directories found at top level:
     ‘README.RJaCGH’ ‘README.zlib’ ‘README.zlib.in.RJaCGH’
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-release-linux-x86_64

Version: 2.0.2
Check: R code for possible problems
Result: NOTE
    genomePlot: warning in layout(rbind(c(1, 2), c(3, 3)), width = c(1, 1),
     height = c(9, 2.5)): partial argument match of ‘width’ to ‘widths’
    genomePlot: warning in layout(rbind(c(1, 2), c(3, 3)), width = c(1, 1),
     height = c(9, 2.5)): partial argument match of ‘height’ to ‘heights’
    plot.pREC_S: warning in layout(matrix(c(1, 2), 1, 2), width = c(1, 7)):
     partial argument match of ‘width’ to ‘widths’
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, r-oldrel-windows-ix86+x86_64

Version: 2.0.2
Check: Rd line widths
Result: NOTE
    Rd file 'plot.RJaCGH.Rd':
     \examples lines wider than 100 characters:
     fit.Genom <- RJaCGH(y=y, Pos=Pos, Chrom=Chrom, model="Genome", burnin=100, TOT=1000, jump.parameters=jp, k.max=4)
     fit.Genom.array <- RJaCGH(y=ya, Pos=Pos, Chrom=Chrom, model="Genome", burnin=100, TOT=1000, jump.parameters=jp, k.max=4)
    
    These lines will be truncated in the PDF 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-release-linux-x86_64

Version: 2.0.2
Check: Rd \usage sections
Result: NOTE
    S3 methods shown with full name in documentation object 'plot.Q.NH':
     ‘plot.Q.NH’
    
    The \usage entries for S3 methods should use the \method markup and not
    their full name.
    See the chapter ‘Writing R documentation files’ 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, 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, r-oldrel-windows-ix86+x86_64

Version: 2.0.2
Check: examples
Result: ERROR
    Running examples in ‘RJaCGH-Ex.R’ failed
    The error most likely occurred in:
    
    > ### Name: pREC_A
    > ### Title: Probabilistic Common Regions for copy number alteration.
    > ### Aliases: pREC_A
    > ### Keywords: models
    >
    > ### ** Examples
    >
    > ## MCR for a single array:
    > y <- c(rnorm(100, 0, 1), rnorm(10, -3, 1), rnorm(20, 3, 1),
    + rnorm(100,0, 1))
    > Pos <- sample(x=1:500, size=230, replace=TRUE)
    > Pos <- cumsum(Pos)
    > Chrom <- rep(1:23, rep(10, 23))
    >
    > jp <- list(sigma.tau.mu=rep(0.05, 4), sigma.tau.sigma.2=rep(0.03, 4),
    + sigma.tau.beta=rep(0.07, 4), tau.split.mu=0.1, tau.split.beta=0.1)
    >
    > fit.genome <- RJaCGH(y=y, Pos=Pos, Chrom=Chrom, model="Genome",
    + burnin=1000, TOT=1000, jump.parameters=jp, k.max = 4)
     Doing Array array1
     Starting Reversible Jump
     Start burn-in
     End burn-in
    > pREC_A(fit.genome, p=0.8, alteration="Gain")
    
     *** caught segfault ***
    address (nil), cause 'memory not mapped'
    
    Traceback:
     1: .C("wrap_pREC", alteration = as.integer(alteration.int), numarrays = as.integer(narrays), num_sequences = as.integer(num.sequences), num_probes = as.integer(nprobes), starting_indices_sequences = as.integer(starting.indices.sequences), starting_indices_state_probs = as.integer(starting.indices.state.probs), filename = as.character(filename), threshold = as.double(p), freq_arrays = as.integer(freq.array), array_weights = as.double(array.weights), state_probs = as.double(unlist(stretchedProbsList)), numregions = as.integer(-9), total_narrays = as.integer(-9), regionsStart = as.integer(rep(-9, nprobes)), regionsEnd = as.integer(rep(-9, nprobes)), regionsProb = as.double(rep(-9.9, nprobes)), verboseC = as.integer(ifelse(verbose, 1, 0)), method_prec = as.integer(method_prec))
     2: pREC(method = "pREC_A", obj = obj, p = p, alteration = alteration, array.weights = array.weights, verbose = verbose)
     3: pREC_A(fit.genome, p = 0.8, alteration = "Gain")
    aborting ...
    Segmentation fault
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc

Version: 2.0.2
Check: examples
Result: ERROR
    Running examples in ‘RJaCGH-Ex.R’ failed
    The error most likely occurred in:
    
    > ### Name: pREC_A
    > ### Title: Probabilistic Common Regions for copy number alteration.
    > ### Aliases: pREC_A
    > ### Keywords: models
    >
    > ### ** Examples
    >
    > ## MCR for a single array:
    > y <- c(rnorm(100, 0, 1), rnorm(10, -3, 1), rnorm(20, 3, 1),
    + rnorm(100,0, 1))
    > Pos <- sample(x=1:500, size=230, replace=TRUE)
    > Pos <- cumsum(Pos)
    > Chrom <- rep(1:23, rep(10, 23))
    >
    > jp <- list(sigma.tau.mu=rep(0.05, 4), sigma.tau.sigma.2=rep(0.03, 4),
    + sigma.tau.beta=rep(0.07, 4), tau.split.mu=0.1, tau.split.beta=0.1)
    >
    > fit.genome <- RJaCGH(y=y, Pos=Pos, Chrom=Chrom, model="Genome",
    + burnin=1000, TOT=1000, jump.parameters=jp, k.max = 4)
     Doing Array array1
     Starting Reversible Jump
     Start burn-in
     End burn-in
    > pREC_A(fit.genome, p=0.8, alteration="Gain")
    
     *** caught segfault ***
    address (nil), cause 'memory not mapped'
    
    Traceback:
     1: .C("wrap_pREC", alteration = as.integer(alteration.int), numarrays = as.integer(narrays), num_sequences = as.integer(num.sequences), num_probes = as.integer(nprobes), starting_indices_sequences = as.integer(starting.indices.sequences), starting_indices_state_probs = as.integer(starting.indices.state.probs), filename = as.character(filename), threshold = as.double(p), freq_arrays = as.integer(freq.array), array_weights = as.double(array.weights), state_probs = as.double(unlist(stretchedProbsList)), numregions = as.integer(-9), total_narrays = as.integer(-9), regionsStart = as.integer(rep(-9, nprobes)), regionsEnd = as.integer(rep(-9, nprobes)), regionsProb = as.double(rep(-9.9, nprobes)), verboseC = as.integer(ifelse(verbose, 1, 0)), method_prec = as.integer(method_prec))
     2: pREC(method = "pREC_A", obj = obj, p = p, alteration = alteration, array.weights = array.weights, verbose = verbose)
     3: pREC_A(fit.genome, p = 0.8, alteration = "Gain")
    aborting ...
Flavor: r-devel-linux-x86_64-fedora-clang