CRAN Package Check Results for Package MDR

Last updated on 2018-06-17 19:49:47 CEST.

Check Details

Version: 1.2
Check: top-level files
Result: NOTE
    File
     LICENCE
    is not mentioned in the DESCRIPTION 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-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: 1.2
Check: S3 generic/method consistency
Result: NOTE
    Found the following apparent S3 methods exported but not registered:
     plot.mdr predict.mdr summary.mdr
    See section ‘Registering S3 methods’ 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-x86, r-release-linux-x86_64

Version: 1.2
Check: R code for possible problems
Result: NOTE
    mdr.3WS: no visible global function definition for ‘combn’
    mdr.cv: no visible global function definition for ‘combn’
    permute.mdr : mdr.lrt: no visible global function definition for
     ‘combn’
    permute.mdr : mdr.lrt: no visible global function definition for ‘glm’
    permute.mdr : mdr.lrt: no visible global function definition for
     ‘as.formula’
    permute.mdr : mdr.lrt: no visible global function definition for
     ‘binomial’
    permute.mdr : mdr.lrt: no visible binding for global variable ‘logit’
    plot.mdr: no visible global function definition for ‘formula’
    Undefined global functions or variables:
     as.formula binomial combn formula glm logit
    Consider adding
     importFrom("stats", "as.formula", "binomial", "formula", "glm")
     importFrom("utils", "combn")
    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-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: 1.2
Check: Rd line widths
Result: NOTE
    Rd file 'boot.error.Rd':
     \examples lines wider than 100 characters:
     #this runs mdr with 5-fold cross-validation on a subset of the sample data, considering all pairwise combinations (K=2)
     #calculates bootstrap estimate from b=100 bootstrap samples of the sample data for the previously fit MDR object 'fit', assuming the po ... [TRUNCATED]
    
    Rd file 'mdr.3WS.Rd':
     \usage lines wider than 90 characters:
     mdr.3WS(data, K, x = NULL, proportion = NULL, ratio = NULL, equal = "HR", genotype = c(0, 1, 2))
     \examples lines wider than 100 characters:
     fit<-mdr.3WS(data=mdr1[,1:11], K=3, x = NULL, proportion = NULL, ratio = NULL, equal = "HR", genotype = c(0, 1, 2)) #fit MDR with 3WS t ... [TRUNCATED]
     plot(fit, data=mdr1) #create contingency plot of best MDR model; may need to expand the plot window for large values of K
    
    Rd file 'mdr.Rd':
     \examples lines wider than 100 characters:
     #define matrix of all two-way combinations of 15 SNPs; this 105 by 2 matrix defines the 105 combinations of two-way interactions to con ... [TRUNCATED]
     #this runs mdr on the sample data, considering the two-way combinations in 'loci', saving the top 5 models, and defining the threshold ... [TRUNCATED]
    
    Rd file 'mdr.ca.adj.Rd':
     \examples lines wider than 100 characters:
     #this runs mdr with 5-fold cross-validation on a subset of the sample data, considering all pairwise combinations (K=2)
     #calculates adjusted CA estimate from the sample data for the previously fit MDR object 'fit', assuming the population prevalence is 10 ... [TRUNCATED]
    
    Rd file 'mdr.cv.Rd':
     \examples lines wider than 100 characters:
     fit<-mdr.cv(data=mdr1[,1:11], K=2, cv=5, ratio = NULL, equal = "HR", genotype = c(0, 1, 2)) #fit MDR with 5-fold cross-validation to a ... [TRUNCATED]
     plot(fit, data=mdr1) #create contingency plot of best MDR model; may need to expand the plot window for large values of K
    
    Rd file 'mdr.hr.Rd':
     \examples lines wider than 100 characters:
     #define matrix of all two-way combinations of 15 SNPs; this 105 by 2 matrix defines the 105 combinations of two-way interactions to con ... [TRUNCATED]
     #this runs mdr on the training data, considering the two-way combinations in 'loci', saving the top model, and defining the threshold a ... [TRUNCATED]
    
    Rd file 'permute.mdr.Rd':
     \usage lines wider than 90 characters:
     permute.mdr(accuracy, loci, N.permute, method = c("CV", "3WS", "none"), data, cv, K, x = NULL, proportion = NULL, ratio = NULL, equal = ... [TRUNCATED]
     \examples lines wider than 100 characters:
     perm<-permute.mdr(accuracy=acc, loci=loc, N.permute=10, method="3WS",data=mdr1[,1:11], K=2, LRT=TRUE)
    
    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: 1.2
Check: examples
Result: ERROR
    Running examples in ‘MDR-Ex.R’ failed
    The error most likely occurred in:
    
    > base::assign(".ptime", proc.time(), pos = "CheckExEnv")
    > ### Name: mdr.3WS
    > ### Title: A function to perform MDR on a dataset using the three-way split
    > ### for internal validation.
    > ### Aliases: mdr.3WS
    >
    > ### ** Examples
    >
    > #load test data
    > data(mdr1)
    >
    > fit<-mdr.3WS(data=mdr1[,1:11], K=3, x = NULL, proportion = NULL, ratio = NULL, equal = "HR", genotype = c(0, 1, 2)) #fit MDR with 3WS to a subset of the sample data, allowing for 1 to 3-way interactions
    >
    > print(fit) #view the fitted mdr object
    $`final model`
    [1] 2 4 9
    
    $`final model accuracy`
    [1] 77.75974
    
    $`top models`
    $`top models`[[1]]
    [1] 9
    
    $`top models`[[2]]
    [1] 4 9
    
    $`top models`[[3]]
    [1] 2 4 9
    
    
    $`top model accuracies`
     training accuracy testing accuracy prediction accuracy
    [1,] 64.26282 62.44498 59.25325
    [2,] 68.75000 68.10724 68.34416
    [3,] 75.48077 74.06963 77.75974
    
    $`high-risk/low-risk`
     [1] 0 0 0 0 0 0 0 1 NA 0 0 0 1 1 1 1 1 0 0 1 0 1 1 1 1
    [26] 1 1
    
    $genotypes
    [1] 0 1 2
    
    $`validation method`
    [1] "3WS"
    
    attr(,"class")
    [1] "mdr"
    >
    > summary(fit) #create summary table of best MDR model
     Length Class Mode
    final model 3 -none- numeric
    final model accuracy 1 -none- numeric
    top models 3 -none- list
    top model accuracies 9 -none- numeric
    high-risk/low-risk 27 -none- numeric
    genotypes 3 -none- numeric
    validation method 1 -none- character
    >
    > plot(fit, data=mdr1) #create contingency plot of best MDR model; may need to expand the plot window for large values of K
    Error in xy.coords(x, y, xlabel, ylabel, log) :
     'x' is a list, but does not have components 'x' and 'y'
    Calls: plot -> plot.default -> xy.coords
    Execution halted
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