CRAN Package Check Results for Package skatMeta

Last updated on 2016-09-29 08:12:47.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 1.4.3 4.28 52.32 56.60 WARN
r-devel-linux-x86_64-debian-gcc 1.4.3 4.11 50.32 54.43 WARN
r-devel-linux-x86_64-fedora-clang 1.4.3 115.57 WARN
r-devel-linux-x86_64-fedora-gcc 1.4.3 94.59 WARN
r-devel-macos-x86_64-clang 1.4.3 89.90 WARN
r-devel-windows-ix86+x86_64 1.4.3 22.00 150.00 172.00 WARN
r-patched-linux-x86_64 1.4.3 3.70 52.60 56.30 WARN
r-patched-solaris-sparc 1.4.3 734.90 WARN
r-patched-solaris-x86 1.4.3 143.90 WARN
r-release-linux-x86_64 1.4.3 3.84 53.43 57.28 WARN
r-release-osx-x86_64-mavericks 1.4.3 NOTE
r-release-windows-ix86+x86_64 1.4.3 21.00 113.00 134.00 WARN
r-oldrel-windows-ix86+x86_64 1.4.3 29.00 253.00 282.00 NOTE

Check Details

Version: 1.4.3
Check: dependencies in R code
Result: NOTE
    'library' or 'require' calls to packages already attached by Depends:
     ‘coxme’ ‘survival’
     Please remove these calls from your code.
    Packages in Depends field not imported from:
     ‘CompQuadForm’ ‘Matrix’ ‘coxme’ ‘survival’
     These packages need to be imported from (in the NAMESPACE file)
     for when this namespace is loaded but not attached.
    ':::' call which should be '::': ‘coxme:::lmekin’
     See the note in ?`:::` about the use of this operator.
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-macos-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: 1.4.3
Check: R code for possible problems
Result: NOTE
    burdenMeta: no visible global function definition for ‘na.omit’
    burdenMeta: no visible global function definition for ‘txtProgressBar’
    burdenMeta: no visible global function definition for ‘pchisq’
    burdenMeta: no visible global function definition for
     ‘setTxtProgressBar’
    check_format_skat: no visible global function definition for
     ‘residuals’
    pchisqsum2: no visible global function definition for ‘davies’
    pchisqsum2: no visible global function definition for ‘farebrother’
    pchisqsum2: no visible global function definition for ‘liu’
    saddle: no visible global function definition for ‘pchisq’
    saddle: no visible global function definition for ‘uniroot’
    saddle: no visible global function definition for ‘pnorm’
    singlesnpMeta: no visible global function definition for ‘na.omit’
    singlesnpMeta: no visible global function definition for
     ‘txtProgressBar’
    singlesnpMeta: no visible global function definition for ‘pchisq’
    singlesnpMeta: no visible global function definition for
     ‘setTxtProgressBar’
    skatCohort: no visible global function definition for ‘gaussian’
    skatCohort: no visible global function definition for ‘glm’
    skatCohort: no visible global function definition for ‘residuals’
    skatCohort: no visible global function definition for ‘model.matrix’
    skatCohort: no visible global function definition for ‘txtProgressBar’
    skatCohort : <anonymous>: no visible global function definition for
     ‘setTxtProgressBar’
    skatCohort : <anonymous>: no visible global function definition for
     ‘na.omit’
    skatCohort: no visible global function definition for ‘var’
    skatCohortAdj: no visible global function definition for ‘gaussian’
    skatCohortAdj: no visible global function definition for ‘update’
    skatCoxCohort: no visible global function definition for ‘coxph’
    skatCoxCohort: no visible global function definition for ‘model.matrix’
    skatCoxCohort: no visible global function definition for ‘model.frame’
    skatCoxCohort: no visible global function definition for ‘coef’
    skatCoxCohort: no visible global function definition for
     ‘txtProgressBar’
    skatCoxCohort : <anonymous>: no visible global function definition for
     ‘setTxtProgressBar’
    skatCoxCohort : <anonymous>: no visible global function definition for
     ‘coxph.control’
    skatCoxCohort : <anonymous>: no visible global function definition for
     ‘coef’
    skatCoxCohort : <anonymous>: no visible global function definition for
     ‘na.omit’
    skatCoxCohort : <anonymous>: no visible binding for global variable
     ‘var’
    skatFamCohort: no visible global function definition for ‘Matrix’
    skatFamCohort: no visible global function definition for
     ‘forceSymmetric’
    skatFamCohort: no visible global function definition for ‘update’
    skatFamCohort: no visible global function definition for ‘Diagonal’
    skatFamCohort: no visible global function definition for ‘model.matrix’
    skatFamCohort: no visible global function definition for ‘lm’
    skatFamCohort: no visible global function definition for
     ‘txtProgressBar’
    skatFamCohort : <anonymous>: no visible global function definition for
     ‘setTxtProgressBar’
    skatFamCohort : <anonymous>: no visible global function definition for
     ‘na.omit’
    skatFamCohortAdj: no visible global function definition for ‘update’
    skatMeta : <anonymous>: no visible global function definition for
     ‘dbeta’
    skatMeta: no visible global function definition for ‘na.omit’
    skatMeta: no visible global function definition for ‘txtProgressBar’
    skatMeta: no visible global function definition for ‘setTxtProgressBar’
    skatOMeta : <anonymous>: no visible global function definition for
     ‘dbeta’
    skatOMeta: no visible global function definition for ‘na.omit’
    skatOMeta: no visible global function definition for ‘txtProgressBar’
    skatOMeta: no visible global function definition for ‘pchisq’
    skatOMeta: no visible global function definition for
     ‘setTxtProgressBar’
    skatO_getp: no visible global function definition for ‘qchisq’
    skatO_getp: no visible global function definition for ‘uniroot’
    skatO_getp : integrand: no visible global function definition for
     ‘dchisq’
    skatO_getp: no visible global function definition for ‘integrate’
    Undefined global functions or variables:
     Diagonal Matrix coef coxph coxph.control davies dbeta dchisq
     farebrother forceSymmetric gaussian glm integrate liu lm model.frame
     model.matrix na.omit pchisq pnorm qchisq residuals setTxtProgressBar
     txtProgressBar uniroot update var
    Consider adding
     importFrom("stats", "coef", "dbeta", "dchisq", "gaussian", "glm",
     "integrate", "lm", "model.frame", "model.matrix", "na.omit",
     "pchisq", "pnorm", "qchisq", "residuals", "uniroot",
     "update", "var")
     importFrom("utils", "setTxtProgressBar", "txtProgressBar")
    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-macos-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: 1.4.3
Check: files in ‘vignettes’
Result: NOTE
    The following files look like leftovers/mistakes:
     ‘skatMeta.bbl’
    Please remove them from your package.
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-macos-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: 1.4.3
Check: re-building of vignette outputs
Result: WARN
    Error in re-building vignettes:
     ...
    Attaching package: ‘bdsmatrix’
    
    The following object is masked from ‘package:base’:
    
     backsolve
    
    Loading required package: CompQuadForm
    Note: method with signature ‘CsparseMatrix#Matrix#missing#replValue’ chosen for function ‘[<-’,
     target signature ‘dsCMatrix#lsyMatrix#missing#numeric’.
     "Matrix#ldenseMatrix#missing#replValue" would also be valid
    Warning in (1 - rho) * Q.skat :
     Recycling array of length 1 in vector-array arithmetic is deprecated.
     Use c() or as.vector() instead.
    
    Warning in rho * Q.burden :
     Recycling array of length 1 in vector-array arithmetic is deprecated.
     Use c() or as.vector() instead.
    
    Warning in davies(q = Q, lambda = lambda, delta = delta, acc = acc) :
     Consider playing with 'lim' or 'acc'.
    
    Error: processing vignette ‘skatMeta.Rnw’ failed with diagnostics:
     chunk 9
    Error in ps[i] <- tmpP$p : replacement has length zero
    Execution halted
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-windows-ix86+x86_64

Version: 1.4.3
Check: re-building of vignette outputs
Result: WARN
    Error in re-building vignettes:
     ...
    Loading required package: Matrix
    Loading required package: coxme
    Loading required package: survival
    Loading required package: bdsmatrix
    
    Attaching package: ‘bdsmatrix’
    
    The following object is masked from ‘package:base’:
    
     backsolve
    
    Loading required package: CompQuadForm
    Note: method with signature ‘CsparseMatrix#Matrix#missing#replValue’ chosen for function ‘[<-’,
     target signature ‘dsCMatrix#lsyMatrix#missing#numeric’.
     "Matrix#ldenseMatrix#missing#replValue" would also be valid
    Warning in (1 - rho) * Q.skat :
     Recycling array of length 1 in vector-array arithmetic is deprecated.
     Use c() or as.vector() instead.
    
    Warning in rho * Q.burden :
     Recycling array of length 1 in vector-array arithmetic is deprecated.
     Use c() or as.vector() instead.
    
    Warning in davies(q = Q, lambda = lambda, delta = delta, acc = acc) :
     Consider playing with 'lim' or 'acc'.
    
    Error: processing vignette 'skatMeta.Rnw' failed with diagnostics:
     chunk 9
    Error in ps[i] <- tmpP$p : replacement has length zero
    Execution halted
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc

Version: 1.4.3
Check: re-building of vignette outputs
Result: WARN
    Error in re-building vignettes:
     ...
    Attaching package: ‘bdsmatrix’
    
    The following object is masked from ‘package:base’:
    
     backsolve
    
    Loading required package: CompQuadForm
    Note: method with signature ‘CsparseMatrix#Matrix#missing#replValue’ chosen for function ‘[<-’,
     target signature ‘dsCMatrix#lsyMatrix#missing#numeric’.
     "Matrix#ldenseMatrix#missing#replValue" would also be valid
    Warning in (1 - rho) * Q.skat :
     Recycling array of length 1 in vector-array arithmetic is deprecated.
     Use c() or as.vector() instead.
    
    Warning in rho * Q.burden :
     Recycling array of length 1 in vector-array arithmetic is deprecated.
     Use c() or as.vector() instead.
    
    Warning in davies(q = Q, lambda = lambda, delta = delta, acc = acc) :
     Consider playing with 'lim' or 'acc'.
    
    Error: processing vignette 'skatMeta.Rnw' failed with diagnostics:
     chunk 9
    Error in ps[i] <- tmpP$p : replacement has length zero
    Execution halted
Flavor: r-devel-macos-x86_64-clang

Version: 1.4.3
Check: re-building of vignette outputs
Result: WARN
    Error in re-building vignettes:
     ...
    Loading required package: Matrix
    Loading required package: coxme
    Loading required package: survival
    Loading required package: bdsmatrix
    
    Attaching package: ‘bdsmatrix’
    
    The following object is masked from ‘package:base’:
    
     backsolve
    
    Loading required package: CompQuadForm
    Note: method with signature ‘CsparseMatrix#Matrix#missing#replValue’ chosen for function ‘[<-’,
     target signature ‘dsCMatrix#lsyMatrix#missing#numeric’.
     "Matrix#ldenseMatrix#missing#replValue" would also be valid
    Warning in davies(q = Q, lambda = lambda, delta = delta, acc = acc) :
     Consider playing with 'lim' or 'acc'.
    
    Error: processing vignette ‘skatMeta.Rnw’ failed with diagnostics:
     chunk 9
    Error in ps[i] <- tmpP$p : replacement has length zero
    Execution halted
Flavors: r-patched-linux-x86_64, r-patched-solaris-sparc, r-patched-solaris-x86, r-release-linux-x86_64, r-release-windows-ix86+x86_64

Version: 1.4.3
Check: R code for possible problems
Result: NOTE
    pchisqsum2: no visible global function definition for 'davies'
    pchisqsum2: no visible global function definition for 'farebrother'
    pchisqsum2: no visible global function definition for 'liu'
    skatCoxCohort: no visible global function definition for 'coxph'
    skatCoxCohort : <anonymous>: no visible global function definition for
     'coxph.control'
    skatFamCohort: no visible global function definition for 'Matrix'
    skatFamCohort: no visible global function definition for
     'forceSymmetric'
    skatFamCohort: no visible global function definition for 'Diagonal'
Flavor: r-oldrel-windows-ix86+x86_64