Last updated on 2018-06-17 19:49:43 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 1.3.1 | 5.85 | 97.87 | 103.72 | ERROR | |
| r-devel-linux-x86_64-debian-gcc | 1.3.1 | 5.92 | 74.49 | 80.41 | ERROR | |
| r-devel-linux-x86_64-fedora-clang | 1.3.1 | 117.04 | NOTE | |||
| r-devel-linux-x86_64-fedora-gcc | 1.3.1 | 111.17 | NOTE | |||
| r-devel-windows-ix86+x86_64 | 1.3.1 | 19.00 | 105.00 | 124.00 | NOTE | |
| r-patched-linux-x86_64 | 1.3.1 | 5.74 | 80.54 | 86.28 | ERROR | |
| r-patched-solaris-x86 | 1.3.1 | 158.60 | NOTE | |||
| r-release-linux-x86_64 | 1.3.1 | 5.87 | 79.48 | 85.35 | ERROR | |
| r-release-windows-ix86+x86_64 | 1.3.1 | 20.00 | 94.00 | 114.00 | NOTE | |
| r-release-osx-x86_64 | 1.3.1 | NOTE | ||||
| r-oldrel-windows-ix86+x86_64 | 1.3.1 | 11.00 | 125.00 | 136.00 | NOTE | |
| r-oldrel-osx-x86_64 | 1.3.1 | NOTE |
Version: 1.3.1
Check: S3 generic/method consistency
Result: NOTE
Found the following apparent S3 methods exported but not registered:
AIC.haplo.ccs anova.haplo.ccs coef.haplo.ccs fitted.haplo.ccs
logLik.haplo.ccs print.haplo.ccs print.summary.haplo.ccs
residuals.haplo.ccs summary.haplo.ccs vcov.haplo.ccs
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: 1.3.1
Check: R code for possible problems
Result: NOTE
haplo.ccs: no visible global function definition for ‘terms’
haplo.ccs: no visible global function definition for ‘model.response’
haplo.ccs: no visible global function definition for ‘model.matrix’
haplo.ccs.fit: no visible global function definition for ‘glm’
haplo.ccs.fit: no visible global function definition for
‘quasibinomial’
haplo.ccs.fit: no visible binding for global variable ‘logit’
haplo.ccs.fit: no visible global function definition for ‘coef’
print.summary.haplo.ccs: no visible global function definition for ‘pt’
sandcov: no visible global function definition for ‘coef’
sandcov: no visible global function definition for ‘model.matrix’
sandcov: no visible global function definition for ‘residuals’
Undefined global functions or variables:
coef glm logit model.matrix model.response pt quasibinomial residuals
terms
Consider adding
importFrom("stats", "coef", "glm", "model.matrix", "model.response",
"pt", "quasibinomial", "residuals", "terms")
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: 1.3.1
Check: examples
Result: ERROR
Running examples in ‘haplo.ccs-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: sandcov
> ### Title: Compute Sandwich Variance-Covariance Estimates
> ### Aliases: sandcov
> ### Keywords: models regression
>
> ### ** Examples
>
>
> data(renin)
>
> ## Fit a model for covariate effects.
>
> m1 <- glm(case ~ age + factor(race) + gender, family=binomial(link=logit))
>
> ## Obtain sandwich variance-covariance matrix.
>
> id <- 1:length(case)
> v1 <- sandcov(model = m1, id = id)
>
> ## Calculate robust standard error estimates.
>
> se1 <- sqrt(diag(v1))
>
> ## Fit a model for haplotype and covariate effects.
>
> m2 <- haplo.ccs(case ~ gender + age + factor(race) + haplo(geno))
>
> ## Obtain sandwich variance-covariance matrix by one of two methods.
>
> v2 <- m2$covariance
> v2 <- vcov(m2)
Error in vcov.default(m2) :
object does not have variance-covariance matrix
Calls: vcov -> vcov.default
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