CRAN Package Check Results for Package MDR

Last updated on 2016-05-26 21:49:32.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-gcc 1.2 0.83 25.34 26.17 NOTE
r-devel-linux-x86_64-fedora-clang 1.2 51.39 NOTE
r-devel-linux-x86_64-fedora-gcc 1.2 48.54 NOTE
r-devel-osx-x86_64-clang 1.2 55.87 NOTE
r-devel-windows-ix86+x86_64 1.2 4.00 52.00 56.00 NOTE
r-patched-linux-x86_64 1.2 0.87 24.72 25.59 NOTE
r-patched-solaris-sparc 1.2 388.50 NOTE
r-patched-solaris-x86 1.2 62.40 NOTE
r-release-linux-x86_64 1.2 0.83 24.64 25.47 NOTE
r-release-osx-x86_64-mavericks 1.2 NOTE
r-release-windows-ix86+x86_64 1.2 5.00 48.00 53.00 NOTE
r-oldrel-windows-ix86+x86_64 1.2 3.00 76.00 79.00 NOTE

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-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-x86_64, r-release-osx-x86_64-mavericks, r-release-windows-ix86+x86_64, r-oldrel-windows-ix86+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-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-osx-x86_64-clang, r-patched-linux-x86_64, r-patched-solaris-sparc, 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-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-x86_64, r-release-osx-x86_64-mavericks, r-release-windows-ix86+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-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