CRAN Package Check Results for Package NMF

Last updated on 2018-03-02 07:48:20 CET.

Check Details

Version: 0.20.6
Check: package dependencies
Result: NOTE
    Package suggested but not available for checking: ‘RcppOctave’
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-patched-linux-x86_64, r-release-linux-x86_64

Version: 0.20.6
Check: R code for possible problems
Result: NOTE
    algorithm,NMFStrategyOctave: no visible global function definition for
     ‘fstop’
    evar,ANY: no visible binding for global variable ‘Biobase’
    nmf,matrix-numeric-NMFStrategy : run.all: no visible binding for global
     variable ‘n’
    nmf,matrix-numeric-NMFStrategy : run.all: no visible binding for global
     variable ‘RNGobj’
    rss,matrix: no visible binding for global variable ‘Biobase’
    Undefined global functions or variables:
     Biobase RNGobj fstop n
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-windows-ix86+x86_64, r-patched-linux-x86_64, r-release-linux-x86_64, r-release-windows-ix86+x86_64, r-oldrel-windows-ix86+x86_64, r-oldrel-osx-x86_64

Version: 0.20.6
Check: Rd cross-references
Result: WARN
    Unknown package ‘RcppOctave’ in Rd xrefs
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-patched-linux-x86_64, r-release-linux-x86_64

Version: 0.20.6
Check: compiled code
Result: NOTE
    File ‘NMF/libs/NMF.so’:
     Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’
    
    It is good practice to register native routines and to disable symbol
    search.
    
    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-release-linux-x86_64

Version: 0.20.6
Check: package dependencies
Result: NOTE
    Packages suggested but not available for checking: ‘RcppOctave’ ‘Biobase’
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc

Version: 0.20.6
Check: R code for possible problems
Result: NOTE
    .foreach_regfun: no visible global function definition for
     ‘getS3method’
    .wrapResult: no visible global function definition for ‘exprs’
    hash_function: no visible global function definition for
     ‘capture.output’
    nmfInfo: no visible global function definition for ‘packageDescription’
    nmfReport : nmfRun: no visible global function definition for ‘str’
    print.foreach_backend: no visible global function definition for ‘str’
    setupLibPaths: no visible global function definition for
     ‘capture.output’
    setupTempDirectory: no visible global function definition for
     ‘file_test’
    staticVar: no visible global function definition for ‘capture.output’
    str_args: no visible global function definition for ‘capture.output’
    txtProgressBar : up1: no visible global function definition for
     ‘flush.console’
    txtProgressBar : up2: no visible global function definition for
     ‘flush.console’
    txtProgressBar : up3: no visible global function definition for
     ‘flush.console’
    txtProgressBar : kill: no visible global function definition for
     ‘flush.console’
    algorithm,NMFStrategyOctave: no visible global function definition for
     ‘fstop’
    evar,ANY: no visible binding for global variable ‘Biobase’
    nmf,matrix-numeric-NMFStrategy: no visible global function definition
     for ‘capture.output’
    nmf,matrix-numeric-NMFStrategy : run.all: no visible binding for global
     variable ‘n’
    nmf,matrix-numeric-NMFStrategy : run.all: no visible binding for global
     variable ‘RNGobj’
    nmf,matrix-numeric-NMFStrategy : run.all: no visible global function
     definition for ‘setTxtProgressBar’
    nmf,matrix-numeric-NMFStrategy : run.all: no visible global function
     definition for ‘file_test’
    nmfModel,formula-ANY : merge_pdata: no visible global function
     definition for ‘pData’
    nmfModel,formula-ANY: no visible global function definition for ‘exprs’
    rss,matrix: no visible binding for global variable ‘Biobase’
    seed,ANY-list-NMFSeed: no visible global function definition for
     ‘capture.output’
    show,NMFfit: no visible global function definition for ‘capture.output’
    Undefined global functions or variables:
     Biobase RNGobj capture.output exprs file_test flush.console fstop
     getS3method n pData packageDescription setTxtProgressBar str
    Consider adding
     importFrom("utils", "capture.output", "file_test", "flush.console",
     "getS3method", "packageDescription", "setTxtProgressBar",
     "str")
    to your NAMESPACE file.
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc

Version: 0.20.6
Check: Rd cross-references
Result: WARN
    Package unavailable to check Rd xrefs: ‘Biobase’
    Unknown package ‘RcppOctave’ in Rd xrefs
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc

Version: 0.20.6
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
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-release-osx-x86_64

Version: 0.20.6
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 in ExpressionSet(x) : could not find function "ExpressionSet"
    Execution halted
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-release-osx-x86_64

Version: 0.20.6
Check: re-building of vignette outputs
Result: WARN
    Error in re-building vignettes:
     ...
    Quitting from lines 385-398 (NMF-vignette.Rnw)
    Error: processing vignette 'NMF-vignette.Rnw' failed with diagnostics:
    unable to find required package 'Biobase'
    Execution halted
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc

Version: 0.20.6
Check: package dependencies
Result: NOTE
    Packages suggested but not available for checking:
     'RcppOctave' 'synchronicity'
Flavor: r-devel-windows-ix86+x86_64

Version: 0.20.6
Check: Rd cross-references
Result: WARN
    Package unavailable to check Rd xrefs: 'synchronicity'
    Unknown package 'RcppOctave' in Rd xrefs
Flavor: r-devel-windows-ix86+x86_64

Version: 0.20.6
Flags: --no-build-vignettes
Check: package dependencies
Result: NOTE
    Package suggested but not available for checking: ‘RcppOctave’
Flavor: r-patched-solaris-x86

Version: 0.20.6
Flags: --no-build-vignettes
Check: R code for possible problems
Result: NOTE
    algorithm,NMFStrategyOctave: no visible global function definition for
     ‘fstop’
    evar,ANY: no visible binding for global variable ‘Biobase’
    nmf,matrix-numeric-NMFStrategy : run.all: no visible binding for global
     variable ‘n’
    nmf,matrix-numeric-NMFStrategy : run.all: no visible binding for global
     variable ‘RNGobj’
    rss,matrix: no visible binding for global variable ‘Biobase’
    Undefined global functions or variables:
     Biobase RNGobj fstop n
Flavor: r-patched-solaris-x86

Version: 0.20.6
Flags: --no-build-vignettes
Check: Rd cross-references
Result: WARN
    Unknown package ‘RcppOctave’ in Rd xrefs
Flavor: r-patched-solaris-x86

Version: 0.20.6
Check: package dependencies
Result: NOTE
    Package suggested but not available for checking: 'synchronicity'
Flavors: r-release-windows-ix86+x86_64, r-oldrel-windows-ix86+x86_64

Version: 0.20.6
Check: Rd cross-references
Result: NOTE
    Package unavailable to check Rd xrefs: 'synchronicity'
Flavors: r-release-windows-ix86+x86_64, r-oldrel-windows-ix86+x86_64

Version: 0.20.6
Check: package dependencies
Result: NOTE
    Packages suggested but not available for checking:
     ‘RcppOctave’ ‘doMPI’ ‘devtools’ ‘Biobase’
Flavor: r-release-osx-x86_64

Version: 0.20.6
Check: R code for possible problems
Result: NOTE
    .wrapResult: no visible global function definition for ‘exprs’
    algorithm,NMFStrategyOctave: no visible global function definition for
     ‘fstop’
    evar,ANY: no visible binding for global variable ‘Biobase’
    nmf,matrix-numeric-NMFStrategy : run.all: no visible binding for global
     variable ‘n’
    nmf,matrix-numeric-NMFStrategy : run.all: no visible binding for global
     variable ‘RNGobj’
    nmfModel,formula-ANY : merge_pdata: no visible global function
     definition for ‘pData’
    nmfModel,formula-ANY: no visible global function definition for ‘exprs’
    rss,matrix: no visible binding for global variable ‘Biobase’
    Undefined global functions or variables:
     Biobase RNGobj exprs fstop n pData
Flavor: r-release-osx-x86_64

Version: 0.20.6
Check: Rd cross-references
Result: NOTE
    Packages unavailable to check Rd xrefs: ‘RcppOctave’, ‘Biobase’
Flavor: r-release-osx-x86_64

Version: 0.20.6
Check: re-building of vignette outputs
Result: WARN
    Error in re-building vignettes:
     ...
    Warning: running command 'kpsewhich framed.sty' had status 1
    Warning in test_latex_pkg("framed", system.file("misc", "framed.sty", package = "knitr")) :
     unable to find LaTeX package 'framed'; will use a copy from knitr
    Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet, :
     Running 'texi2dvi' on 'NMF-unitTests.tex' failed.
    LaTeX errors:
    ! LaTeX Error: File `vmargin.sty' not found.
    
    Type X to quit or <RETURN> to proceed,
    or enter new name. (Default extension: sty)
    
    ! Emergency stop.
    <read *>
    
    l.58 \setmargrb
     {0.75in}{0.75in}{0.75in}{0.75in}^^M
    ! ==> Fatal error occurred, no output PDF file produced!
    Calls: buildVignettes -> texi2pdf -> texi2dvi
    Execution halted
Flavor: r-release-osx-x86_64

Version: 0.20.6
Check: package dependencies
Result: NOTE
    Packages suggested but not available for checking: ‘RcppOctave’ ‘doMPI’
Flavor: r-oldrel-osx-x86_64

Version: 0.20.6
Check: Rd cross-references
Result: NOTE
    Package unavailable to check Rd xrefs: ‘RcppOctave’
Flavor: r-oldrel-osx-x86_64