------------------------------ On Sat, May 16, 2015 2:33 PM BST Marc Schwartz wrote:
> >> On May 16, 2015, at 6:11 AM, Hin-Tak Leung <ht...@users.sourceforge.net> >> wrote: >> >> >> >> ------------------------------ >> On Sat, May 16, 2015 8:04 AM BST Uwe Ligges wrote: >> >> Not sure why this goes to R-devel. You just could have asked the >> maintainer. Terry Therneau is aware of it and promised he will fix it. >> >> >> The quickest fix is to add cmprsk to the recommended list , and that's is an >> R-devel issue. > > >Actually, the easiest solution would be for Terry to either modify relevant >code according to: > > >http://cran.r-project.org/doc/manuals/r-release/R-exts.html#Suggested-packages > >or perhaps better, as noted, to remove the need for cmprsk at all. > We shall disagree on what is "quickest" - one other option I did not mention is to back out the version upgrade to 2.38-1 in February, and ship the previous 2.37-7. I trust that Terry made the addition for good reasons. So my thoughts are geared more towards how to accommodate the new addition, rather than revert/remove it. (though I'd be happier to isolate a smaller change than a bulk 2.37-7 -> 2.38.1 upgrade and think more about that. Hence the mention of the repositories.). >The latter raises the philosophical issue as to whether or not a Recommended >package should or really needs to have any connections at all to third party >CRAN packages. It seems to me that the default R distribution of “Base” and >“Recommended” packages should be able to fully run in a stand alone manner >without any declared external connections to other non-default packages. > >The only other Recommended package that I found that has such a connection is >nlme, which has a Suggests for Frank’s Hmisc. However, based upon a grep >review of the package contents, there are only two code based references to >Hmisc that I located: > >./R/newFunc.R:264: ## e.g. Hmisc's "labelled" >./tests/augPred_lab.R:2:if(require("Hmisc")) { > >Neither of which is really needed (the first being a comment only, so benign) >and of course the latter goes against the current guidance in R-exts. The >second, within the if() code, uses the Hmisc label() function, which it seems >to me is not really needed here. > >Regards, > >Marc Schwartz > > >> >> On 16.05.2015 07:22, Hin-Tak Leung wrote: >>> '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. >>> >>> ----------------------------------------------- >>> ERROR >>> 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 >>> >>> ______________________________________________ >>> R-devel@r-project.org mailing list >>> https://stat.ethz.ch/mailman/listinfo/r-devel >>> >> >> ______________________________________________ >> R-devel@r-project.org mailing list >> https://stat.ethz.ch/mailman/listinfo/r-devel > ______________________________________________ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
