CRAN Package Check Results for Package gtx

Last updated on 2020-02-19 10:48:55 CET.

Check Details

Version: 0.0.8
Check: dependencies in R code
Result: NOTE
    Package in Depends field not imported from: 'survival'
     These packages need to be imported from (in the NAMESPACE file)
     for when this namespace is loaded but not attached.
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: 0.0.8
Check: R code for possible problems
Result: NOTE
    abf.normal : <anonymous>: no visible global function definition for
     'dnorm'
    abf.t : <anonymous>: no visible global function definition for 'dt'
    abf.t : <anonymous>: no visible global function definition for 'dnorm'
    chi2ncp: no visible global function definition for 'qchisq'
    chi2ncp: no visible global function definition for 'pchisq'
    chi2ncp: no visible global function definition for 'uniroot'
    chi2ncp : <anonymous>: no visible global function definition for
     'pchisq'
    coeff.extract: no visible global function definition for 'coefficients'
    contrasting.rainbow: no visible global function definition for
     'rainbow'
    fitmix: no visible global function definition for 'rexp'
    fitmix: no visible global function definition for 'sd'
    fitmix.plot: no visible global function definition for 'density'
    fitmix.plot: no visible global function definition for 'plot'
    fitmix.plot: no visible global function definition for 'rug'
    fitmix.plot: no visible global function definition for 'polygon'
    fitmix.plot: no visible global function definition for 'lines'
    fitmix.plot: no visible global function definition for 'dnorm'
    fitmix.plot: no visible global function definition for 'rainbow'
    fitmix.plot : <anonymous>: no visible global function definition for
     'dnorm'
    fitmix.plot: no visible global function definition for 'legend'
    fitmix.simulate: no visible global function definition for 'rnorm'
    fitmix1: no visible global function definition for 'quantile'
    fitmix1: no visible global function definition for 'sd'
    fitmix1 : <anonymous>: no visible global function definition for
     'dnorm'
    gls.approx.logistic: no visible global function definition for
     'as.formula'
    gls.approx.logistic: no visible global function definition for
     'predict'
    gls.approx.logistic: no visible global function definition for 'glm'
    gls.approx.logistic: no visible binding for global variable
     'na.exclude'
    grs.filter.Qrs: no visible global function definition for 'pchisq'
    grs.onesnp.apply: no visible global function definition for 'update'
    grs.onesnp.apply: no visible global function definition for
     'update.formula'
    grs.onesnp.apply: no visible global function definition for 'formula'
    grs.plot: no visible global function definition for 'plot'
    grs.plot: no visible global function definition for 'qnorm'
    grs.plot: no visible global function definition for 'abline'
    grs.plot: no visible global function definition for 'lines'
    grs.plot: no visible global function definition for 'points'
    grs.summary: no visible global function definition for 'pchisq'
    hapmap.read.haplotypes: no visible global function definition for
     'read.table'
    hapmap.snpdata: no visible global function definition for 'na.omit'
    multipheno.T2: no visible global function definition for 'cor'
    multipheno.T2: no visible global function definition for 'pchisq'
    read.snpdata.impute: no visible global function definition for
     'read.table'
    read.snpdata.mach: no visible global function definition for
     'read.table'
    read.snpdata.plink: no visible global function definition for
     'read.table'
    run.blat: no visible global function definition for 'read.table'
    stepdown.moments2: no visible global function definition for 'qchisq'
    stepdown.moments2: no visible global function definition for 'pchisq'
    stepup.moments2: no visible global function definition for 'qchisq'
    stepup.moments2: no visible global function definition for 'pchisq'
    test.subsample: no visible global function definition for 'update'
    test.subsample: no visible global function definition for
     'update.formula'
    test.subsample: no visible global function definition for 'formula'
    test.subsample: no visible global function definition for 'binom.test'
    Undefined global functions or variables:
     abline as.formula binom.test coefficients cor density dnorm dt
     formula glm legend lines na.exclude na.omit pchisq plot points
     polygon predict qchisq qnorm quantile rainbow read.table rexp rnorm
     rug sd uniroot update update.formula
    Consider adding
     importFrom("grDevices", "rainbow")
     importFrom("graphics", "abline", "legend", "lines", "plot", "points",
     "polygon", "rug")
     importFrom("stats", "as.formula", "binom.test", "coefficients", "cor",
     "density", "dnorm", "dt", "formula", "glm", "na.exclude",
     "na.omit", "pchisq", "predict", "qchisq", "qnorm",
     "quantile", "rexp", "rnorm", "sd", "uniroot", "update",
     "update.formula")
     importFrom("utils", "read.table")
    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: 0.0.8
Check: examples
Result: ERROR
    Running examples in 'gtx-Ex.R' failed
    The error most likely occurred in:
    
    > base::assign(".ptime", proc.time(), pos = "CheckExEnv")
    > ### Name: combine.moments2
    > ### Title: Builds a matrix of second moments for a set of individuals, from
    > ### the matrices of second moments for all constituent subsets of
    > ### individuals.
    > ### Aliases: combine.moments2
    >
    > ### ** Examples
    >
    > data(mthfrex)
    > ## artifical example with two datasets obtained by
    > ## splitting mthfrex by the HTN variable
    >
    > xtx.hi <- make.moments2(mthfr.params, c("SBP", "SexC", "Age"),
    + as.snpdata(list(snpinfo = mthfrex$snpinfo,
    + data = subset(mthfrex$data, HTN == 1))))
    >
    > xtx.lo <- make.moments2(mthfr.params, c("SBP", "SexC", "Age"),
    + as.snpdata(list(snpinfo = mthfrex$snpinfo,
    + data = subset(mthfrex$data, HTN == 0))))
    >
    > ## make list of X'X matrices
    > xtx.list <- list(hi = xtx.hi, lo = xtx.lo)
    >
    > ## combine for outcome SBP and fixed effects for all SNPs
    > ## other variables SexC and Age will be treated as study-specific
    > fixed <- paste(mthfr.params$snp, mthfr.params$coded.allele, sep = "_")
    > xtx.comb <- combine.moments2(xtx.list, c("SBP", fixed))
    >
    > ## fit regression model
    > n.comb <- sum(diag(xtx.comb)[1:length(xtx.list)])
    > lm.moments2(xtx.comb, "SBP", c("hi_ONE", "lo_ONE", "rs4846052_T"), n = n.comb)
     ----------- FAILURE REPORT --------------
     --- failure: the condition has length > 1 ---
     --- srcref ---
    :
     --- package (from environment) ---
    gtx
     --- call from context ---
    is.moments2(xtwx)
     --- call from argument ---
    if (class(object) != "moments2") return(FALSE)
     --- R stacktrace ---
    where 1: is.moments2(xtwx)
    where 2: est.moments2(xtx, leftvar, rightvars, n, vscale = NULL)
    where 3: lm.moments2(xtx.comb, "SBP", c("hi_ONE", "lo_ONE", "rs4846052_T"),
     n = n.comb)
    
     --- value of length: 2 type: logical ---
    [1] TRUE TRUE
     --- function from context ---
    function (object)
    {
     if (class(object) != "moments2")
     return(FALSE)
     if (!is.matrix(object))
     return(FALSE)
     if (nrow(object) != ncol(object))
     return(FALSE)
     if (any(rownames(object) != colnames(object)))
     return(FALSE)
     return(TRUE)
    }
    <bytecode: 0x4fac510>
    <environment: namespace:gtx>
     --- function search by body ---
    Function is.moments2 in namespace gtx has this body.
     ----------- END OF FAILURE REPORT --------------
    Error in if (class(object) != "moments2") return(FALSE) :
     the condition has length > 1
    Calls: lm.moments2 -> est.moments2 -> is.moments2
    Execution halted
Flavor: r-devel-linux-x86_64-debian-clang

Version: 0.0.8
Check: examples
Result: ERROR
    Running examples in ‘gtx-Ex.R’ failed
    The error most likely occurred in:
    
    > base::assign(".ptime", proc.time(), pos = "CheckExEnv")
    > ### Name: combine.moments2
    > ### Title: Builds a matrix of second moments for a set of individuals, from
    > ### the matrices of second moments for all constituent subsets of
    > ### individuals.
    > ### Aliases: combine.moments2
    >
    > ### ** Examples
    >
    > data(mthfrex)
    > ## artifical example with two datasets obtained by
    > ## splitting mthfrex by the HTN variable
    >
    > xtx.hi <- make.moments2(mthfr.params, c("SBP", "SexC", "Age"),
    + as.snpdata(list(snpinfo = mthfrex$snpinfo,
    + data = subset(mthfrex$data, HTN == 1))))
    >
    > xtx.lo <- make.moments2(mthfr.params, c("SBP", "SexC", "Age"),
    + as.snpdata(list(snpinfo = mthfrex$snpinfo,
    + data = subset(mthfrex$data, HTN == 0))))
    >
    > ## make list of X'X matrices
    > xtx.list <- list(hi = xtx.hi, lo = xtx.lo)
    >
    > ## combine for outcome SBP and fixed effects for all SNPs
    > ## other variables SexC and Age will be treated as study-specific
    > fixed <- paste(mthfr.params$snp, mthfr.params$coded.allele, sep = "_")
    > xtx.comb <- combine.moments2(xtx.list, c("SBP", fixed))
    >
    > ## fit regression model
    > n.comb <- sum(diag(xtx.comb)[1:length(xtx.list)])
    > lm.moments2(xtx.comb, "SBP", c("hi_ONE", "lo_ONE", "rs4846052_T"), n = n.comb)
     ----------- FAILURE REPORT --------------
     --- failure: the condition has length > 1 ---
     --- srcref ---
    :
     --- package (from environment) ---
    gtx
     --- call from context ---
    is.moments2(xtwx)
     --- call from argument ---
    if (class(object) != "moments2") return(FALSE)
     --- R stacktrace ---
    where 1: is.moments2(xtwx)
    where 2: est.moments2(xtx, leftvar, rightvars, n, vscale = NULL)
    where 3: lm.moments2(xtx.comb, "SBP", c("hi_ONE", "lo_ONE", "rs4846052_T"),
     n = n.comb)
    
     --- value of length: 2 type: logical ---
    [1] TRUE TRUE
     --- function from context ---
    function (object)
    {
     if (class(object) != "moments2")
     return(FALSE)
     if (!is.matrix(object))
     return(FALSE)
     if (nrow(object) != ncol(object))
     return(FALSE)
     if (any(rownames(object) != colnames(object)))
     return(FALSE)
     return(TRUE)
    }
    <bytecode: 0x55a713c29b70>
    <environment: namespace:gtx>
     --- function search by body ---
    Function is.moments2 in namespace gtx has this body.
     ----------- END OF FAILURE REPORT --------------
    Error in if (class(object) != "moments2") return(FALSE) :
     the condition has length > 1
    Calls: lm.moments2 -> est.moments2 -> is.moments2
    Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc

Version: 0.0.8
Check: examples
Result: ERROR
    Running examples in ‘gtx-Ex.R’ failed
    The error most likely occurred in:
    
    > ### Name: combine.moments2
    > ### Title: Builds a matrix of second moments for a set of individuals, from
    > ### the matrices of second moments for all constituent subsets of
    > ### individuals.
    > ### Aliases: combine.moments2
    >
    > ### ** Examples
    >
    > data(mthfrex)
    > ## artifical example with two datasets obtained by
    > ## splitting mthfrex by the HTN variable
    >
    > xtx.hi <- make.moments2(mthfr.params, c("SBP", "SexC", "Age"),
    + as.snpdata(list(snpinfo = mthfrex$snpinfo,
    + data = subset(mthfrex$data, HTN == 1))))
    >
    > xtx.lo <- make.moments2(mthfr.params, c("SBP", "SexC", "Age"),
    + as.snpdata(list(snpinfo = mthfrex$snpinfo,
    + data = subset(mthfrex$data, HTN == 0))))
    >
    > ## make list of X'X matrices
    > xtx.list <- list(hi = xtx.hi, lo = xtx.lo)
    >
    > ## combine for outcome SBP and fixed effects for all SNPs
    > ## other variables SexC and Age will be treated as study-specific
    > fixed <- paste(mthfr.params$snp, mthfr.params$coded.allele, sep = "_")
    > xtx.comb <- combine.moments2(xtx.list, c("SBP", fixed))
    >
    > ## fit regression model
    > n.comb <- sum(diag(xtx.comb)[1:length(xtx.list)])
    > lm.moments2(xtx.comb, "SBP", c("hi_ONE", "lo_ONE", "rs4846052_T"), n = n.comb)
     ----------- FAILURE REPORT --------------
     --- failure: the condition has length > 1 ---
     --- srcref ---
    :
     --- package (from environment) ---
    gtx
     --- call from context ---
    is.moments2(xtwx)
     --- call from argument ---
    if (class(object) != "moments2") return(FALSE)
     --- R stacktrace ---
    where 1: is.moments2(xtwx)
    where 2: est.moments2(xtx, leftvar, rightvars, n, vscale = NULL)
    where 3: lm.moments2(xtx.comb, "SBP", c("hi_ONE", "lo_ONE", "rs4846052_T"),
     n = n.comb)
    
     --- value of length: 2 type: logical ---
    [1] TRUE TRUE
     --- function from context ---
    function (object)
    {
     if (class(object) != "moments2")
     return(FALSE)
     if (!is.matrix(object))
     return(FALSE)
     if (nrow(object) != ncol(object))
     return(FALSE)
     if (any(rownames(object) != colnames(object)))
     return(FALSE)
     return(TRUE)
    }
    <bytecode: 0x4b492a8>
    <environment: namespace:gtx>
     --- function search by body ---
    Function is.moments2 in namespace gtx has this body.
     ----------- END OF FAILURE REPORT --------------
    Error in if (class(object) != "moments2") return(FALSE) :
     the condition has length > 1
    Calls: lm.moments2 -> est.moments2 -> is.moments2
    Execution halted
Flavor: r-devel-linux-x86_64-fedora-clang

Version: 0.0.8
Check: examples
Result: ERROR
    Running examples in ‘gtx-Ex.R’ failed
    The error most likely occurred in:
    
    > ### Name: combine.moments2
    > ### Title: Builds a matrix of second moments for a set of individuals, from
    > ### the matrices of second moments for all constituent subsets of
    > ### individuals.
    > ### Aliases: combine.moments2
    >
    > ### ** Examples
    >
    > data(mthfrex)
    > ## artifical example with two datasets obtained by
    > ## splitting mthfrex by the HTN variable
    >
    > xtx.hi <- make.moments2(mthfr.params, c("SBP", "SexC", "Age"),
    + as.snpdata(list(snpinfo = mthfrex$snpinfo,
    + data = subset(mthfrex$data, HTN == 1))))
    >
    > xtx.lo <- make.moments2(mthfr.params, c("SBP", "SexC", "Age"),
    + as.snpdata(list(snpinfo = mthfrex$snpinfo,
    + data = subset(mthfrex$data, HTN == 0))))
    >
    > ## make list of X'X matrices
    > xtx.list <- list(hi = xtx.hi, lo = xtx.lo)
    >
    > ## combine for outcome SBP and fixed effects for all SNPs
    > ## other variables SexC and Age will be treated as study-specific
    > fixed <- paste(mthfr.params$snp, mthfr.params$coded.allele, sep = "_")
    > xtx.comb <- combine.moments2(xtx.list, c("SBP", fixed))
    >
    > ## fit regression model
    > n.comb <- sum(diag(xtx.comb)[1:length(xtx.list)])
    > lm.moments2(xtx.comb, "SBP", c("hi_ONE", "lo_ONE", "rs4846052_T"), n = n.comb)
     ----------- FAILURE REPORT --------------
     --- failure: the condition has length > 1 ---
     --- srcref ---
    :
     --- package (from environment) ---
    gtx
     --- call from context ---
    is.moments2(xtwx)
     --- call from argument ---
    if (class(object) != "moments2") return(FALSE)
     --- R stacktrace ---
    where 1: is.moments2(xtwx)
    where 2: est.moments2(xtx, leftvar, rightvars, n, vscale = NULL)
    where 3: lm.moments2(xtx.comb, "SBP", c("hi_ONE", "lo_ONE", "rs4846052_T"),
     n = n.comb)
    
     --- value of length: 2 type: logical ---
    [1] TRUE TRUE
     --- function from context ---
    function (object)
    {
     if (class(object) != "moments2")
     return(FALSE)
     if (!is.matrix(object))
     return(FALSE)
     if (nrow(object) != ncol(object))
     return(FALSE)
     if (any(rownames(object) != colnames(object)))
     return(FALSE)
     return(TRUE)
    }
    <bytecode: 0x64e03c8>
    <environment: namespace:gtx>
     --- function search by body ---
    Function is.moments2 in namespace gtx has this body.
     ----------- END OF FAILURE REPORT --------------
    Error in if (class(object) != "moments2") return(FALSE) :
     the condition has length > 1
    Calls: lm.moments2 -> est.moments2 -> is.moments2
    Execution halted
Flavor: r-devel-linux-x86_64-fedora-gcc

Version: 0.0.8
Check: re-building of vignette outputs
Result: WARN
    Error(s) in re-building vignettes:
    --- re-building 'ashg2012.Rnw' using Sweave
    Loading required package: survival
    Warning in system(paste(shQuote(texi2dvi), if (quiet) "--quiet" else "", :
     running command '"D:\compiler\texmf\miktex\bin\texify.exe" --quiet --pdf "ashg2012.tex" --max-iterations=20 -I "D:/RCompile/recent/R-3.6.2/share/texmf/tex/latex" -I "D:/RCompile/recent/R-3.6.2/share/texmf/bibtex/bst"' had status 1
    Error: processing vignette 'ashg2012.Rnw' failed with diagnostics:
    running 'texi2dvi' on 'ashg2012.tex' failed
    
    LaTeX errors:
    ! LaTeX Error: File `D:/RCompile/recent/R-36\unhbox\voidb@x \penalty \@M \ {}1.
    2/share/texmf/tex/latex/Sweave.sty' not found.
    
    Type X to quit or <RETURN> to proceed,
    or enter new name. (Default extension: sty)
    
    --- failed re-building 'ashg2012.Rnw'
    
    SUMMARY: processing the following file failed:
     'ashg2012.Rnw'
    
    Error: Vignette re-building failed.
    Execution halted
Flavor: r-release-windows-ix86+x86_64

Version: 0.0.8
Check: re-building of vignette outputs
Result: WARN
    Error in re-building vignettes:
     ...
    Loading required package: survival
    Warning in system(paste(shQuote(texi2dvi), if (quiet) "--quiet" else "", :
     running command '"D:\compiler\texmf\miktex\bin\texify.exe" --quiet --pdf "ashg2012.tex" --max-iterations=20 -I "D:/RCompile/recent/R-3.5.3/share/texmf/tex/latex" -I "D:/RCompile/recent/R-3.5.3/share/texmf/bibtex/bst"' had status 1
    Error: running 'texi2dvi' on 'ashg2012.tex' failed
    
    LaTeX errors:
    ! LaTeX Error: File `D:/RCompile/recent/R-35\unhbox\voidb@x \penalty \@M \ {}1.
    3/share/texmf/tex/latex/Sweave.sty' not found.
    
    Type X to quit or <RETURN> to proceed,
    or enter new name. (Default extension: sty)
    Execution halted
Flavor: r-oldrel-windows-ix86+x86_64