CRAN Package Check Results for Package NMF

Last updated on 2014-04-17 06:46:54.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 0.20.5 7.86 433.24 441.10 OK
r-devel-linux-x86_64-debian-gcc 0.20.5 8.61 428.22 436.84 OK
r-devel-linux-x86_64-fedora-clang 0.20.5 1064.44 NOTE
r-devel-linux-x86_64-fedora-gcc 0.20.5 1028.48 OK
r-devel-macosx-x86_64-clang 0.20.5 684.01 NOTE
r-devel-macosx-x86_64-gcc 0.20.5 ERROR
r-devel-windows-ix86+x86_64 0.20.5 23.00 197.00 220.00 NOTE --no-vignettes
r-patched-linux-x86_64 0.20.5 8.45 423.40 431.85 OK
r-patched-solaris-sparc 0.20.5 1276.00 NOTE --no-tests --no-vignettes
r-patched-solaris-x86 0.20.5 791.60 NOTE --no-build-vignettes
r-release-linux-ix86 0.20.5 18.00 742.00 760.00 OK
r-release-linux-x86_64 0.20.5 8.78 426.51 435.28 OK
r-release-macosx-x86_64 0.20.5 ERROR
r-release-windows-ix86+x86_64 0.20.5 27.00 209.00 236.00 NOTE --no-vignettes
r-oldrel-windows-ix86+x86_64 0.20.5 26.00 216.00 242.00 NOTE --no-vignettes

Check Details

Version: 0.20.5
Check: package dependencies
Result: NOTE
    Package suggested but not available for checking: ‘RcppOctave’
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-macosx-x86_64-clang

Version: 0.20.5
Check: Rd cross-references
Result: NOTE
    Package unavailable to check Rd xrefs: ‘RcppOctave’
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-macosx-x86_64-clang

Version: 0.20.5
Check: package dependencies
Result: ERROR
    Packages required but not available: ‘pkgmaker’ ‘rngtools’ ‘ggplot2’
    
    Packages suggested but not available for checking:
     ‘RcppOctave’ ‘doMPI’ ‘devtools’ ‘knitr’ ‘Biobase’
    
    Files named as vignettes but with no recognized vignette engine:
     ‘inst/doc/NMF-unitTests.Rnw’
     ‘inst/doc/NMF-vignette.Rnw’
     ‘inst/doc/heatmaps.Rnw’
    (Is a VignetteBuilder field missing?)
    
    See the information on DESCRIPTION files in the chapter ‘Creating R
    packages’ of the ‘Writing R Extensions’ manual.
Flavor: r-devel-macosx-x86_64-gcc

Version: 0.20.5
Flags: --no-vignettes
Check: package dependencies
Result: NOTE
    Packages suggested but not available for checking:
     'RcppOctave' 'doMPI' 'bigmemory' 'synchronicity'
Flavors: r-devel-windows-ix86+x86_64, r-release-windows-ix86+x86_64, r-oldrel-windows-ix86+x86_64

Version: 0.20.5
Flags: --no-vignettes
Check: Rd cross-references
Result: NOTE
    Packages unavailable to check Rd xrefs: 'RcppOctave', 'synchronicity'
Flavors: r-devel-windows-ix86+x86_64, r-release-windows-ix86+x86_64, r-oldrel-windows-ix86+x86_64

Version: 0.20.5
Flags: --no-tests --no-vignettes
Check: package dependencies
Result: NOTE
    Package suggested but not available for checking: ‘RcppOctave’
Flavor: r-patched-solaris-sparc

Version: 0.20.5
Flags: --no-tests --no-vignettes
Check: Rd cross-references
Result: NOTE
    Package unavailable to check Rd xrefs: ‘RcppOctave’
Flavor: r-patched-solaris-sparc

Version: 0.20.5
Flags: --no-build-vignettes
Check: package dependencies
Result: NOTE
    Package suggested but not available for checking: ‘RcppOctave’
Flavor: r-patched-solaris-x86

Version: 0.20.5
Flags: --no-build-vignettes
Check: Rd cross-references
Result: NOTE
    Package unavailable to check Rd xrefs: ‘RcppOctave’
Flavor: r-patched-solaris-x86

Version: 0.20.5
Check: package dependencies
Result: NOTE
    Packages suggested but not available for checking: ‘RcppOctave’ ‘Biobase’
Flavor: r-release-macosx-x86_64

Version: 0.20.5
Check: R code for possible problems
Result: NOTE
    .wrapResult: no visible global function definition for ‘exprs’
Flavor: r-release-macosx-x86_64

Version: 0.20.5
Check: Rd cross-references
Result: NOTE
    Packages unavailable to check Rd xrefs: ‘RcppOctave’, ‘Biobase’
Flavor: r-release-macosx-x86_64

Version: 0.20.5
Check: data for non-ASCII characters
Result: NOTE
     Error in .requirePackage(package) :
     unable to find required package 'Biobase'
     Calls: <Anonymous> ... .extendsForS3 -> extends -> getClassDef -> .requirePackage
     Execution halted
Flavor: r-release-macosx-x86_64

Version: 0.20.5
Check: examples
Result: ERROR
    Running examples in ‘NMF-Ex.R’ failed
    The error most likely occurred in:
    
    > ### Name: nmfModel
    > ### Title: Factory Methods NMF Models
    > ### Aliases: nmfModel nmfModel,data.frame,data.frame-method
    > ### nmfModel,formula,ANY-method nmfModel,matrix,ANY-method
    > ### nmfModel,matrix,matrix-method nmfModel-methods
    > ### nmfModel,missing,ANY-method nmfModel,missing,missing-method
    > ### nmfModel,NULL,ANY-method nmfModel,numeric,matrix-method
    > ### nmfModel,numeric,missing-method nmfModel,numeric,numeric-method
    > ### nmfModels
    > ### Keywords: methods
    >
    > ### ** Examples
    >
    > ## Don't show:
    > # roxygen generated flag
    > options(R_CHECK_RUNNING_EXAMPLES_=TRUE)
    > ## End Don't show
    >
    > #----------
    > # nmfModel,numeric,numeric-method
    > #----------
    > # data
    > n <- 20; r <- 3; p <- 10
    > V <- rmatrix(n, p) # some target matrix
    >
    > # create a r-ranked NMF model with a given target dimensions n x p as a 2-length vector
    > nmfModel(r, c(n,p)) # directly
    <Object of class:NMFstd>
    features: 20
    basis/rank: 3
    samples: 10
    > nmfModel(r, dim(V)) # or from an existing matrix <=> nmfModel(r, V)
    <Object of class:NMFstd>
    features: 20
    basis/rank: 3
    samples: 10
    > # or alternatively passing each dimension separately
    > nmfModel(r, n, p)
    <Object of class:NMFstd>
    features: 20
    basis/rank: 3
    samples: 10
    >
    > # trying to create a NMF object based on incompatible matrices generates an error
    > w <- rmatrix(n, r)
    > h <- rmatrix(r+1, p)
    > try( new('NMFstd', W=w, H=h) )
    Error in validObject(.Object) :
     invalid class “NMFstd” object: Dimensions of W and H are not compatible [ncol(W)= 3 != nrow(H)= 4 ]
    > try( nmfModel(w, h) )
    Error in .local(rank, target, ...) :
     nmfModel - Invalid number of columns in the basis matrix [3]: it should match the number of rows in the mixture coefficient matrix [4]
    > try( nmfModel(r+1, W=w, H=h) )
    Error in .local(rank, target, ...) :
     nmfModel - Objective rank [4] is greater than the number of columns in W [3]
    > # The factory method can be force the model to match some target dimensions
    > # but warnings are thrown
    > nmfModel(r, W=w, H=h)
    Warning in .local(rank, target, ...) :
     nmfModel - Objective rank [3] is lower than the number of rows in H [4]: only the first 3 rows of H will be used
    <Object of class:NMFstd>
    features: 20
    basis/rank: 3
    samples: 10
    > nmfModel(r, n-1, W=w, H=h)
    Warning in .local(rank, target, ...) :
     nmfModel - Number of rows in target is lower than the number of rows in W [20]: only the first 19 rows of W will be used
    Warning in .local(rank, target, ...) :
     nmfModel - Objective rank [3] is lower than the number of rows in H [4]: only the first 3 rows of H will be used
    <Object of class:NMFstd>
    features: 19
    basis/rank: 3
    samples: 10
    >
    > #----------
    > # nmfModel,numeric,missing-method
    > #----------
    > ## Empty model of given rank
    > nmfModel(3)
    <Object of class:NMFstd>
    features: 0
    basis/rank: 3
    samples: 0
    >
    > #----------
    > # nmfModel,missing,ANY-method
    > #----------
    > nmfModel(target=10) #square
    <Object of class:NMFstd>
    features: 10
    basis/rank: 0
    samples: 10
    > nmfModel(target=c(10, 5))
    <Object of class:NMFstd>
    features: 10
    basis/rank: 0
    samples: 5
    >
    > #----------
    > # nmfModel,missing,missing-method
    > #----------
    > # Build an empty NMF model
    > nmfModel()
    <Object of class:NMFstd>
    features: 0
    basis/rank: 0
    samples: 0
    >
    > # create a NMF object based on one random matrix: the missing matrix is deduced
    > # Note this only works when using factory method NMF
    > n <- 50; r <- 3;
    > w <- rmatrix(n, r)
    > nmfModel(W=w)
    <Object of class:NMFstd>
    features: 50
    basis/rank: 3
    samples: 0
    >
    > # create a NMF object based on random (compatible) matrices
    > p <- 20
    > h <- rmatrix(r, p)
    > nmfModel(H=h)
    <Object of class:NMFstd>
    features: 0
    basis/rank: 3
    samples: 20
    >
    > # specifies two compatible matrices
    > nmfModel(W=w, H=h)
    <Object of class:NMFstd>
    features: 50
    basis/rank: 3
    samples: 20
    > # error if not compatible
    > try( nmfModel(W=w, H=h[-1,]) )
    Error in .local(rank, target, ...) :
     nmfModel - Invalid number of columns in the basis matrix [3]: it should match the number of rows in the mixture coefficient matrix [2]
    >
    > #----------
    > # nmfModel,numeric,matrix-method
    > #----------
    > # create a r-ranked NMF model compatible with a given target matrix
    > obj <- nmfModel(r, V)
    > all(is.na(basis(obj)))
    [1] TRUE
    >
    > #----------
    > # nmfModel,matrix,matrix-method
    > #----------
    > ## From two existing factors
    >
    > # allows a convenient call without argument names
    > w <- rmatrix(n, 3); h <- rmatrix(3, p)
    > nmfModel(w, h)
    <Object of class:NMFstd>
    features: 50
    basis/rank: 3
    samples: 20
    >
    > # Specify the type of NMF model (e.g. 'NMFns' for non-smooth NMF)
    > mod <- nmfModel(w, h, model='NMFns')
    > mod
    <Object of class:NMFns>
    features: 50
    basis/rank: 3
    samples: 20
    theta: 0.5
    >
    > # One can use such an NMF model as a seed when fitting a target matrix with nmf()
    > V <- rmatrix(mod)
    > res <- nmf(V, mod)
    > nmf.equal(res, nmf(V, mod))
    [1] TRUE
    >
    > # NB: when called only with such a seed, the rank and the NMF algorithm
    > # are selected based on the input NMF model.
    > # e.g. here rank was 3 and the algorithm "nsNMF" is used, because it is the default
    > # algorithm to fit "NMFns" models (See ?nmf).
    >
    > #----------
    > # nmfModel,matrix,ANY-method
    > #----------
    > ## swapped arguments `rank` and `target`
    > V <- rmatrix(20, 10)
    > nmfModel(V) # equivalent to nmfModel(target=V)
    <Object of class:NMFstd>
    features: 20
    basis/rank: 0
    samples: 10
    > nmfModel(V, 3) # equivalent to nmfModel(3, V)
    <Object of class:NMFstd>
    features: 20
    basis/rank: 3
    samples: 10
    >
    > #----------
    > # nmfModel,formula,ANY-method
    > #----------
    > # empty 3-rank model
    > nmfModel(~ 3)
    <Object of class:NMFstd>
    features: 0
    basis/rank: 3
    samples: 0
    >
    > # 3-rank model that fits a given data matrix
    > x <- rmatrix(20,10)
    > nmfModel(x ~ 3)
    <Object of class:NMFstd>
    features: 20
    basis/rank: 3
    samples: 10
    >
    > # add fixed coefficient term defined by a factor
    > gr <- gl(2, 5)
    > nmfModel(x ~ 3 + gr)
    <Object of class:NMFstd>
    features: 20
    basis/rank: 5
    samples: 10
    fixed coef [2]:
     gr = <1, 2>
    >
    > # add fixed coefficient term defined by a numeric covariate
    > nmfModel(x ~ 3 + gr + b, data=list(b=runif(10)))
    <Object of class:NMFstd>
    features: 20
    basis/rank: 6
    samples: 10
    fixed coef [3]:
     gr = <1, 2>
     b = 0.0101301828399301, 0.21454192395322, ..., 0.767450851621106
    >
    > # 3-rank model that fits a given ExpressionSet (with fixed coef terms)
    > e <- ExpressionSet(x)
    Error: could not find function "ExpressionSet"
    Execution halted
Flavor: r-release-macosx-x86_64