CRAN Package Check Results for Package CMF

Last updated on 2020-03-07 11:48:11 CET.

Check Details

Version: 1.0
Check: R code for possible problems
Result: NOTE
    CMF: no visible global function definition for 'rnorm'
    Undefined global functions or variables:
     rnorm
    Consider adding
     importFrom("stats", "rnorm")
    to your NAMESPACE file.
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-windows-ix86+x86_64, r-devel-windows-ix86+x86_64-gcc8, r-patched-linux-x86_64, r-patched-solaris-x86, r-release-linux-x86_64, r-release-windows-ix86+x86_64, r-release-osx-x86_64, r-oldrel-windows-ix86+x86_64, r-oldrel-osx-x86_64

Version: 1.0
Check: examples
Result: ERROR
    Running examples in 'CMF-Ex.R' failed
    The error most likely occurred in:
    
    > base::assign(".ptime", proc.time(), pos = "CheckExEnv")
    > ### Name: CMF-package
    > ### Title: Collective Matrix Factorization (CMF)
    > ### Aliases: CMF-package
    > ### Keywords: package
    >
    > ### ** Examples
    >
    > require("CMF")
    > # Create data for a circular setup with three matrices and three
    > # object sets of varying sizes.
    > X <- list()
    > D <- c(10,20,30)
    > inds <- matrix(0,nrow=3,ncol=2)
    >
    > # Matrix 1 is between sets 1 and 2 and has continuous data
    > inds[1,] <- c(1,2)
    > X[[1]] <- matrix(rnorm(D[inds[1,1]]*D[inds[1,2]],0,1),nrow=D[inds[1,1]])
    >
    > # Matrix 2 is between sets 1 and 3 and has binary data
    > inds[2,] <- c(1,3)
    > X[[2]] <- matrix(round(runif(D[inds[2,1]]*D[inds[2,2]],0,1)),nrow=D[inds[2,1]])
    >
    > # Matrix 3 is between sets 2 and 3 and has count data
    > inds[3,] <- c(2,3)
    > X[[3]] <- matrix(round(runif(D[inds[3,1]]*D[inds[3,2]],0,6)),nrow=D[inds[3,1]])
    >
    > # Convert the data into the right format
    > triplets <- list()
    > for(m in 1:3) triplets[[m]] <- matrix_to_triplets(X[[m]])
    >
    > # Missing entries correspond to missing rows in the triple representation
    > # so they can be removed from training data by simply taking a subset
    > # of the rows.
    > train <- list()
    > test <- list()
    > keepForTraining <- c(100,200,300)
    > for(m in 1:3) {
    + subset <- sample(nrow(triplets[[m]]))[1:keepForTraining[m]]
    + train[[m]] <- triplets[[m]][subset,]
    + test[[m]] <- triplets[[m]][setdiff(1:nrow(triplets[[m]]),subset),]
    + }
    >
    > # Learn the model with the correct likelihoods
    > K <- 4
    > likelihood <- c("gaussian","bernoulli","poisson")
    > opts <- getCMFopts()
    > opts$iter.max <- 10 # Less iterations for faster computation
    > model <- CMF(train,inds,K,likelihood,D,test=test,opts=opts)
     ----------- FAILURE REPORT --------------
     --- failure: the condition has length > 1 ---
     --- srcref ---
    :
     --- package (from environment) ---
    CMF
     --- call from context ---
    p_check_sparsity(X[[i]], D[inds[i, 1]], D[inds[i, 2]])
     --- call from argument ---
    if (class(mat) == "matrix") {
     if (ncol(mat) != 3 | min(mat[, 1:2]) < 1 | max(mat[, 1]) >
     max_row | max(mat[, 2]) > max_col) {
     print("Matrix not in coordinate/triplet format")
     return(FALSE)
     }
     else {
     return(TRUE)
     }
    }
     --- R stacktrace ---
    where 1: p_check_sparsity(X[[i]], D[inds[i, 1]], D[inds[i, 2]])
    where 2: CMF(train, inds, K, likelihood, D, test = test, opts = opts)
    
     --- value of length: 2 type: logical ---
    [1] TRUE FALSE
     --- function from context ---
    function (mat, max_row, max_col)
    {
     if (class(mat) == "matrix") {
     if (ncol(mat) != 3 | min(mat[, 1:2]) < 1 | max(mat[,
     1]) > max_row | max(mat[, 2]) > max_col) {
     print("Matrix not in coordinate/triplet format")
     return(FALSE)
     }
     else {
     return(TRUE)
     }
     }
     print("Input not of class 'matrix'")
     return(FALSE)
    }
    <bytecode: 0x2797648>
    <environment: namespace:CMF>
     --- function search by body ---
    Function p_check_sparsity in namespace CMF has this body.
     ----------- END OF FAILURE REPORT --------------
    Error in if (class(mat) == "matrix") { : the condition has length > 1
    Calls: CMF -> p_check_sparsity
    Execution halted
Flavor: r-devel-linux-x86_64-debian-clang

Version: 1.0
Check: examples
Result: ERROR
    Running examples in ‘CMF-Ex.R’ failed
    The error most likely occurred in:
    
    > base::assign(".ptime", proc.time(), pos = "CheckExEnv")
    > ### Name: CMF-package
    > ### Title: Collective Matrix Factorization (CMF)
    > ### Aliases: CMF-package
    > ### Keywords: package
    >
    > ### ** Examples
    >
    > require("CMF")
    > # Create data for a circular setup with three matrices and three
    > # object sets of varying sizes.
    > X <- list()
    > D <- c(10,20,30)
    > inds <- matrix(0,nrow=3,ncol=2)
    >
    > # Matrix 1 is between sets 1 and 2 and has continuous data
    > inds[1,] <- c(1,2)
    > X[[1]] <- matrix(rnorm(D[inds[1,1]]*D[inds[1,2]],0,1),nrow=D[inds[1,1]])
    >
    > # Matrix 2 is between sets 1 and 3 and has binary data
    > inds[2,] <- c(1,3)
    > X[[2]] <- matrix(round(runif(D[inds[2,1]]*D[inds[2,2]],0,1)),nrow=D[inds[2,1]])
    >
    > # Matrix 3 is between sets 2 and 3 and has count data
    > inds[3,] <- c(2,3)
    > X[[3]] <- matrix(round(runif(D[inds[3,1]]*D[inds[3,2]],0,6)),nrow=D[inds[3,1]])
    >
    > # Convert the data into the right format
    > triplets <- list()
    > for(m in 1:3) triplets[[m]] <- matrix_to_triplets(X[[m]])
    >
    > # Missing entries correspond to missing rows in the triple representation
    > # so they can be removed from training data by simply taking a subset
    > # of the rows.
    > train <- list()
    > test <- list()
    > keepForTraining <- c(100,200,300)
    > for(m in 1:3) {
    + subset <- sample(nrow(triplets[[m]]))[1:keepForTraining[m]]
    + train[[m]] <- triplets[[m]][subset,]
    + test[[m]] <- triplets[[m]][setdiff(1:nrow(triplets[[m]]),subset),]
    + }
    >
    > # Learn the model with the correct likelihoods
    > K <- 4
    > likelihood <- c("gaussian","bernoulli","poisson")
    > opts <- getCMFopts()
    > opts$iter.max <- 10 # Less iterations for faster computation
    > model <- CMF(train,inds,K,likelihood,D,test=test,opts=opts)
     ----------- FAILURE REPORT --------------
     --- failure: the condition has length > 1 ---
     --- srcref ---
    :
     --- package (from environment) ---
    CMF
     --- call from context ---
    p_check_sparsity(X[[i]], D[inds[i, 1]], D[inds[i, 2]])
     --- call from argument ---
    if (class(mat) == "matrix") {
     if (ncol(mat) != 3 | min(mat[, 1:2]) < 1 | max(mat[, 1]) >
     max_row | max(mat[, 2]) > max_col) {
     print("Matrix not in coordinate/triplet format")
     return(FALSE)
     }
     else {
     return(TRUE)
     }
    }
     --- R stacktrace ---
    where 1: p_check_sparsity(X[[i]], D[inds[i, 1]], D[inds[i, 2]])
    where 2: CMF(train, inds, K, likelihood, D, test = test, opts = opts)
    
     --- value of length: 2 type: logical ---
    [1] TRUE FALSE
     --- function from context ---
    function (mat, max_row, max_col)
    {
     if (class(mat) == "matrix") {
     if (ncol(mat) != 3 | min(mat[, 1:2]) < 1 | max(mat[,
     1]) > max_row | max(mat[, 2]) > max_col) {
     print("Matrix not in coordinate/triplet format")
     return(FALSE)
     }
     else {
     return(TRUE)
     }
     }
     print("Input not of class 'matrix'")
     return(FALSE)
    }
    <bytecode: 0x5581ac6b6338>
    <environment: namespace:CMF>
     --- function search by body ---
    Function p_check_sparsity in namespace CMF has this body.
     ----------- END OF FAILURE REPORT --------------
    Error in if (class(mat) == "matrix") { : the condition has length > 1
    Calls: CMF -> p_check_sparsity
    Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc

Version: 1.0
Check: compiled code
Result: NOTE
    File ‘CMF/libs/CMF.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-fedora-clang, r-devel-linux-x86_64-fedora-gcc

Version: 1.0
Check: examples
Result: ERROR
    Running examples in ‘CMF-Ex.R’ failed
    The error most likely occurred in:
    
    > ### Name: CMF-package
    > ### Title: Collective Matrix Factorization (CMF)
    > ### Aliases: CMF-package
    > ### Keywords: package
    >
    > ### ** Examples
    >
    > require("CMF")
    > # Create data for a circular setup with three matrices and three
    > # object sets of varying sizes.
    > X <- list()
    > D <- c(10,20,30)
    > inds <- matrix(0,nrow=3,ncol=2)
    >
    > # Matrix 1 is between sets 1 and 2 and has continuous data
    > inds[1,] <- c(1,2)
    > X[[1]] <- matrix(rnorm(D[inds[1,1]]*D[inds[1,2]],0,1),nrow=D[inds[1,1]])
    >
    > # Matrix 2 is between sets 1 and 3 and has binary data
    > inds[2,] <- c(1,3)
    > X[[2]] <- matrix(round(runif(D[inds[2,1]]*D[inds[2,2]],0,1)),nrow=D[inds[2,1]])
    >
    > # Matrix 3 is between sets 2 and 3 and has count data
    > inds[3,] <- c(2,3)
    > X[[3]] <- matrix(round(runif(D[inds[3,1]]*D[inds[3,2]],0,6)),nrow=D[inds[3,1]])
    >
    > # Convert the data into the right format
    > triplets <- list()
    > for(m in 1:3) triplets[[m]] <- matrix_to_triplets(X[[m]])
    >
    > # Missing entries correspond to missing rows in the triple representation
    > # so they can be removed from training data by simply taking a subset
    > # of the rows.
    > train <- list()
    > test <- list()
    > keepForTraining <- c(100,200,300)
    > for(m in 1:3) {
    + subset <- sample(nrow(triplets[[m]]))[1:keepForTraining[m]]
    + train[[m]] <- triplets[[m]][subset,]
    + test[[m]] <- triplets[[m]][setdiff(1:nrow(triplets[[m]]),subset),]
    + }
    >
    > # Learn the model with the correct likelihoods
    > K <- 4
    > likelihood <- c("gaussian","bernoulli","poisson")
    > opts <- getCMFopts()
    > opts$iter.max <- 10 # Less iterations for faster computation
    > model <- CMF(train,inds,K,likelihood,D,test=test,opts=opts)
     ----------- FAILURE REPORT --------------
     --- failure: the condition has length > 1 ---
     --- srcref ---
    :
     --- package (from environment) ---
    CMF
     --- call from context ---
    p_check_sparsity(X[[i]], D[inds[i, 1]], D[inds[i, 2]])
     --- call from argument ---
    if (class(mat) == "matrix") {
     if (ncol(mat) != 3 | min(mat[, 1:2]) < 1 | max(mat[, 1]) >
     max_row | max(mat[, 2]) > max_col) {
     print("Matrix not in coordinate/triplet format")
     return(FALSE)
     }
     else {
     return(TRUE)
     }
    }
     --- R stacktrace ---
    where 1: p_check_sparsity(X[[i]], D[inds[i, 1]], D[inds[i, 2]])
    where 2: CMF(train, inds, K, likelihood, D, test = test, opts = opts)
    
     --- value of length: 2 type: logical ---
    [1] TRUE FALSE
     --- function from context ---
    function (mat, max_row, max_col)
    {
     if (class(mat) == "matrix") {
     if (ncol(mat) != 3 | min(mat[, 1:2]) < 1 | max(mat[,
     1]) > max_row | max(mat[, 2]) > max_col) {
     print("Matrix not in coordinate/triplet format")
     return(FALSE)
     }
     else {
     return(TRUE)
     }
     }
     print("Input not of class 'matrix'")
     return(FALSE)
    }
    <bytecode: 0x1ebb190>
    <environment: namespace:CMF>
     --- function search by body ---
    Function p_check_sparsity in namespace CMF has this body.
     ----------- END OF FAILURE REPORT --------------
    Error in if (class(mat) == "matrix") { : the condition has length > 1
    Calls: CMF -> p_check_sparsity
    Execution halted
Flavor: r-devel-linux-x86_64-fedora-clang

Version: 1.0
Check: examples
Result: ERROR
    Running examples in ‘CMF-Ex.R’ failed
    The error most likely occurred in:
    
    > ### Name: CMF-package
    > ### Title: Collective Matrix Factorization (CMF)
    > ### Aliases: CMF-package
    > ### Keywords: package
    >
    > ### ** Examples
    >
    > require("CMF")
    > # Create data for a circular setup with three matrices and three
    > # object sets of varying sizes.
    > X <- list()
    > D <- c(10,20,30)
    > inds <- matrix(0,nrow=3,ncol=2)
    >
    > # Matrix 1 is between sets 1 and 2 and has continuous data
    > inds[1,] <- c(1,2)
    > X[[1]] <- matrix(rnorm(D[inds[1,1]]*D[inds[1,2]],0,1),nrow=D[inds[1,1]])
    >
    > # Matrix 2 is between sets 1 and 3 and has binary data
    > inds[2,] <- c(1,3)
    > X[[2]] <- matrix(round(runif(D[inds[2,1]]*D[inds[2,2]],0,1)),nrow=D[inds[2,1]])
    >
    > # Matrix 3 is between sets 2 and 3 and has count data
    > inds[3,] <- c(2,3)
    > X[[3]] <- matrix(round(runif(D[inds[3,1]]*D[inds[3,2]],0,6)),nrow=D[inds[3,1]])
    >
    > # Convert the data into the right format
    > triplets <- list()
    > for(m in 1:3) triplets[[m]] <- matrix_to_triplets(X[[m]])
    >
    > # Missing entries correspond to missing rows in the triple representation
    > # so they can be removed from training data by simply taking a subset
    > # of the rows.
    > train <- list()
    > test <- list()
    > keepForTraining <- c(100,200,300)
    > for(m in 1:3) {
    + subset <- sample(nrow(triplets[[m]]))[1:keepForTraining[m]]
    + train[[m]] <- triplets[[m]][subset,]
    + test[[m]] <- triplets[[m]][setdiff(1:nrow(triplets[[m]]),subset),]
    + }
    >
    > # Learn the model with the correct likelihoods
    > K <- 4
    > likelihood <- c("gaussian","bernoulli","poisson")
    > opts <- getCMFopts()
    > opts$iter.max <- 10 # Less iterations for faster computation
    > model <- CMF(train,inds,K,likelihood,D,test=test,opts=opts)
     ----------- FAILURE REPORT --------------
     --- failure: the condition has length > 1 ---
     --- srcref ---
    :
     --- package (from environment) ---
    CMF
     --- call from context ---
    p_check_sparsity(X[[i]], D[inds[i, 1]], D[inds[i, 2]])
     --- call from argument ---
    if (class(mat) == "matrix") {
     if (ncol(mat) != 3 | min(mat[, 1:2]) < 1 | max(mat[, 1]) >
     max_row | max(mat[, 2]) > max_col) {
     print("Matrix not in coordinate/triplet format")
     return(FALSE)
     }
     else {
     return(TRUE)
     }
    }
     --- R stacktrace ---
    where 1: p_check_sparsity(X[[i]], D[inds[i, 1]], D[inds[i, 2]])
    where 2: CMF(train, inds, K, likelihood, D, test = test, opts = opts)
    
     --- value of length: 2 type: logical ---
    [1] TRUE FALSE
     --- function from context ---
    function (mat, max_row, max_col)
    {
     if (class(mat) == "matrix") {
     if (ncol(mat) != 3 | min(mat[, 1:2]) < 1 | max(mat[,
     1]) > max_row | max(mat[, 2]) > max_col) {
     print("Matrix not in coordinate/triplet format")
     return(FALSE)
     }
     else {
     return(TRUE)
     }
     }
     print("Input not of class 'matrix'")
     return(FALSE)
    }
    <bytecode: 0x241c7d0>
    <environment: namespace:CMF>
     --- function search by body ---
    Function p_check_sparsity in namespace CMF has this body.
     ----------- END OF FAILURE REPORT --------------
    Error in if (class(mat) == "matrix") { : the condition has length > 1
    Calls: CMF -> p_check_sparsity
    Execution halted
Flavor: r-devel-linux-x86_64-fedora-gcc