R devel - May 2015 - That 'make check-all' problem with the survival package

------------------------------
On Sat, May 16, 2015 2:33 PM BST Marc Schwartz wrote:
>
>> On May 16, 2015, at 6:11 AM, Hin-Tak Leung <htl10 at
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
>>> 
>>> ______________________________________________
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>>> 
>> 
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