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rms log file (check_x86_64_windows)
* using log directory 'R:/run/building/build_2013-02-15-08-50/RF_PKG_CHECK/PKGS/rms.Rcheck'
* using R version 2.15.2 Patched (2013-01-31 r61797)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* checking for file 'rms/DESCRIPTION' ... OK
* this is package 'rms' version '3.3-0'
* checking CRAN incoming feasibility ... WARNING
Maintainer: 'Frank E Harrell Jr '
Insufficient package version (submitted: 3.3.0, existing: 3.6.3)
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking whether package 'rms' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking DESCRIPTION meta-information ... NOTE
Non-standard license specification:
GPL version 2 or newer
Standardizable: TRUE
Standardized license specification:
GPL (>= 2)
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* loading checks for arch 'i386'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies ... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
** checking loading without being on the library search path ... OK
* loading checks for arch 'x64'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies ... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
** checking loading without being on the library search path ... OK
* checking for unstated dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
Predict: warning in match.call(expand = FALSE): partial argument match
of 'expand' to 'expand.dots'
Rq: warning in summary.rq(fit, cov = TRUE, se = se, hs = hs): partial
argument match of 'cov' to 'covariance'
bj: warning in match.call(expand = FALSE): partial argument match of
'expand' to 'expand.dots'
cph: warning in match.call(expand = FALSE): partial argument match of
'expand' to 'expand.dots'
lrm: warning in match.call(expand = FALSE): partial argument match of
'expand' to 'expand.dots'
ols: warning in match.call(expand = FALSE): partial argument match of
'expand' to 'expand.dots'
plot.nomogram: warning in axis(sides[jj], at = scaled[jj], label =
fat[jj], pos = y, cex.axis = cex.axis, tck = tck, tcl = tcl, mgp = if
(sides[jj] == 1) c(0, lmgp - 0.6, 0) else c(0, lmgp, 0), padj = if
(sides[jj] == 1) 1 else 0): partial argument match of 'label' to
'labels'
plot.summary.rms: warning in axis(3, logb(pxlim), lab = format(pxlim)):
partial argument match of 'lab' to 'labels'
plot.xmean.ordinaly: warning in match.call(expand = FALSE): partial
argument match of 'expand' to 'expand.dots'
psm: warning in match.call(expand = FALSE): partial argument match of
'expand' to 'expand.dots'
survplot.rms: warning in symbols(rep(tt, length(yp)), yp, circle =
rep(dotsize, length(yp)), inches = dotsize, add = TRUE): partial
argument match of 'circle' to 'circles'
survplot.rms: warning in labcurve(curves, curve.labels, type = ltype,
lty = lty, col = col, lwd = lwd, opts = label.curves): partial
argument match of 'col' to 'col.'
survplot.survfit: warning in symbols(rep(tt, length(yp)), yp, circle =
rep(dotsize, length(yp)), inches = dotsize, add = TRUE): partial
argument match of 'circle' to 'circles'
survplot.survfit: warning in labcurve(curves, sleva, type = "s", lty =
lty, lwd = lwd, opts = label.curves, col = col): partial argument
match of 'col' to 'col.'
Mean.cph: multiple local function definitions for 'f' with different
formal arguments
calibrate.cph: no visible binding for global variable 'pred.obs'
calibrate.default: no visible binding for global variable '.orig.cal'
calibrate.psm: no visible binding for global variable 'fixed'
calibrate.psm: no visible binding for global variable 'pred.obs'
latexrms: no visible binding for global variable 'digit'
pantext: multiple local function definitions for 'z' with different
formal arguments
plot.Predict: multiple local function definitions for 'pan' with
different formal arguments
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... WARNING
'library' or 'require' call not declared from: 'boot'
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... OK
* checking examples ...
** running examples for arch 'i386' ... ERROR
Running examples in 'rms-Ex.R' failed
The error most likely occurred in:
> ### Name: validate.cph
> ### Title: Validation of a Fitted Cox or Parametric Survival Model's
> ### Indexes of Fit
> ### Aliases: validate.cph validate.psm
> ### Keywords: models regression survival
>
> ### ** Examples
>
> n <- 1000
> set.seed(731)
> age <- 50 + 12*rnorm(n)
> label(age) <- "Age"
> sex <- factor(sample(c('Male','Female'), n, TRUE))
> cens <- 15*runif(n)
> h <- .02*exp(.04*(age-50)+.8*(sex=='Female'))
> dt <- -log(runif(n))/h
> e <- ifelse(dt <= cens,1,0)
> dt <- pmin(dt, cens)
> units(dt) <- "Year"
> S <- Surv(dt,e)
>
> f <- cph(S ~ age*sex, x=TRUE, y=TRUE)
> # Validate full model fit
> validate(f, B=10) # normally B=150
Error in if (type == "right") coxph.fit else survival:::agreg.fit :
argument is of length zero
Calls: validate -> validate.cph -> predab.resample -> fit -> coxphFit
Execution halted
** running examples for arch 'x64' ... ERROR
Running examples in 'rms-Ex.R' failed
The error most likely occurred in:
> ### Name: validate.cph
> ### Title: Validation of a Fitted Cox or Parametric Survival Model's
> ### Indexes of Fit
> ### Aliases: validate.cph validate.psm
> ### Keywords: models regression survival
>
> ### ** Examples
>
> n <- 1000
> set.seed(731)
> age <- 50 + 12*rnorm(n)
> label(age) <- "Age"
> sex <- factor(sample(c('Male','Female'), n, TRUE))
> cens <- 15*runif(n)
> h <- .02*exp(.04*(age-50)+.8*(sex=='Female'))
> dt <- -log(runif(n))/h
> e <- ifelse(dt <= cens,1,0)
> dt <- pmin(dt, cens)
> units(dt) <- "Year"
> S <- Surv(dt,e)
>
> f <- cph(S ~ age*sex, x=TRUE, y=TRUE)
> # Validate full model fit
> validate(f, B=10) # normally B=150
Error in if (type == "right") coxph.fit else survival:::agreg.fit :
argument is of length zero
Calls: validate -> validate.cph -> predab.resample -> fit -> coxphFit
Execution halted
Run time: 158.82 seconds.