[Rd] That 'make check-all' problem with the survival package

Hin-Tak Leung htl10 at users.sourceforge.net
Sat May 16 07:22:47 CEST 2015

'make check-all' for current R has been showing this error in the middle
for a few months now - any thought on fixing this? I think cmprsk
should be either included in the recommended bundle, or
the survival vignette to not depend on it. Having 'make check-all' showing
glaring ERROR's for a few months seems to defeat the purpose of
doing any checking at all via 'make check-all'.

FWIW, I did look at when/how the issue was introduced, but it appeared
that svn://svn.r-forge.r-project.org/svnroot/survival is no longer being
updated, and git://github.com/cran/survival.git only shows release jumps.
Anyway, if first appears with survival 2.38-1 in February, and as the previous
2.37-7 was 13 months older, this info is of no use to anybody.
I didn't write earlier as I thought the issue would go away at some point;
but obviously this isn't the case after 3 months.

Errors in running code in vignettes:
when running code in ‘compete.Rnw’
> temp$fstat <- as.numeric(event)

> temp$msex <- with(temp, 1 * (sex == "M"))

> fgfit1 <- with(temp, crr(etime, fstat, cov1 = cbind(age, 
+     msex, mspike), failcode = 2, cencode = 1, variance = TRUE))

  When sourcing ‘compete.R’:
Error: could not find function "crr"
Execution halted

* checking re-building of vignette outputs ... NOTE
Error in re-building vignettes:
Warning in coxph(Surv(futime, death) ~ group:age2 + sex + strata(group),  :
  X matrix deemed to be singular; variable 23 24 25
Loading required package: cmprsk
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘cmprsk’

Error: processing vignette 'compete.Rnw' failed with diagnostics:
 chunk 15 (label = finegray) 
Error in eval(expr, envir, enclos) : could not find function "crr"
Execution halted

More information about the R-devel mailing list