CRAN Package Check Results for Package shrink

Last updated on 2014-04-24 09:49:11.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 1.1 0.65 13.83 14.48 OK
r-devel-linux-x86_64-debian-gcc 1.1 0.60 14.10 14.71 OK
r-devel-linux-x86_64-fedora-clang 1.1 28.10 OK
r-devel-linux-x86_64-fedora-gcc 1.1 27.24 OK
r-devel-osx-x86_64-clang 1.1 29.42 OK
r-devel-osx-x86_64-gcc 1.1 ERROR
r-devel-windows-ix86+x86_64 1.1 2.00 20.00 22.00 OK
r-patched-linux-x86_64 1.1 0.60 13.80 14.40 OK
r-patched-solaris-sparc 1.1 160.70 OK
r-patched-solaris-x86 1.1 39.50 OK
r-release-linux-ix86 1.1 1.00 28.00 29.00 OK
r-release-linux-x86_64 1.1 0.60 13.63 14.23 OK
r-release-osx-x86_64-mavericks 1.1 WARN
r-release-windows-ix86+x86_64 1.1 2.00 21.00 23.00 OK
r-oldrel-windows-ix86+x86_64 1.1 2.00 21.00 23.00 OK

Check Details

Version: 1.1
Check: package dependencies
Result: NOTE
    Package suggested but not available for checking: ‘rms’
Flavor: r-devel-osx-x86_64-gcc

Version: 1.1
Check: examples
Result: ERROR
    Running examples in ‘shrink-Ex.R’ failed
    The error most likely occurred in:
    
    > ### Name: shrink
    > ### Title: Global, Parameterwise, and Joint Shrinkage of Regression
    > ### Coefficients
    > ### Aliases: shrink
    > ### Keywords: models regression survival nonlinear
    >
    > ### ** Examples
    >
    > # Example with mfp (family = cox)
    > library("mfp")
    Loading required package: survival
    Loading required package: splines
    > data("GBSG")
    > fit1 <- mfp(Surv(rfst, cens) ~ fp(age, df = 4, select = 0.05) +
    + fp(prm, df = 4, select = 0.05), family = cox, data = GBSG)
    >
    > shrink(fit1, type = "global", method = "dfbeta")
    Shrinkage Factors (type=global, method=dfbeta):
    [1] 0.9237358
    
    Shrunken Regression Coefficients:
     prm.1 age.1 age.2
    -0.1986325 0.3759619 -4.5820305
    >
    > dfbeta.pw <- shrink(fit1, type = "parameterwise", method = "dfbeta")
    > dfbeta.pw
    Shrinkage Factors (type=parameterwise, method=dfbeta):
     prm.1 age.1 age.2
    0.9592653 0.7615833 0.7114137
    
    Postfit:
    Call:
    coxph(formula = Surv(time, status) ~ prm.1 + age.1 + age.2, data = data.frame(modx),
     x = TRUE)
    
    
     coef exp(coef) se(coef) z p
    prm.1 -0.206 0.8136 0.0296 -6.97 3.1e-12
    age.1 0.310 1.3634 0.1015 3.05 2.3e-03
    age.2 -3.529 0.0293 1.4921 -2.37 1.8e-02
    
    Likelihood ratio test=58.9 on 3 df, p=1.04e-12 n= 686, number of events= 299
    > cov2cor(dfbeta.pw$vcov.shrinkage)
     prm.1 age.1 age.2
    prm.1 1.0000000 0.015627 0.0291499
    age.1 0.0156270 1.000000 0.9685090
    age.2 0.0291499 0.968509 1.0000000
    > sqrt(diag(dfbeta.pw$vcov.shrinkage))
     prm.1 age.1 age.2
    0.1375348 0.2494794 0.3008002
    >
    > shrink(fit1, type = "parameterwise", method = "dfbeta",
    + join = list(c("age.1", "age.2")))
    Shrinkage Factors (type=parameterwise, method=dfbeta):
     prm.1 age.1 age.2
    0.9639732 0.8318633 0.8318633
    
    Shrunken Regression Coefficients:
     prm.1 age.1 age.2
    -0.2072848 0.3385696 -4.1263128
    >
    > #shrink(fit1, type = "global", method = "jackknife")
    > #shrink(fit1, type = "parameterwise", method = "jackknife")
    > #shrink(fit1, type = "parameterwise", method = "jackknife",
    > # join = list(c("age.1", "age.2")))
    >
    >
    > # Example with rcs
    > library("rms")
    Error in library("rms") : there is no package called ‘rms’
    Execution halted
Flavor: r-devel-osx-x86_64-gcc

Version: 1.1
Check: PDF version of manual
Result: WARNING
    LaTeX errors when creating PDF version.
    This typically indicates Rd problems.
    LaTeX errors found:
    ! LaTeX Error: File `upquote.sty' not found.
    
    Type X to quit or <RETURN> to proceed,
    or enter new name. (Default extension: sty)
    
    2b75dc99/Rd2.tex:8: ==> Fatal error occurred, no output PDF file produced!
Flavor: r-release-osx-x86_64-mavericks