[R] [survMisc]: error message in examples of comp()

[William Dunlap]

If you execute the command
  options(useFancyQuotes=FALSE)
before calling comp(s1) that error should go away.

dQuote() was being used inappropriately - its value depends on the
option "useFancyQuotes" so should really only be used for messages or
text that machines don't have to parse.

Bill Dunlap
TIBCO Software
wdunlap tibco.com


On Fri, Oct 17, 2014 at 5:34 PM, David Winsemius <dwinsemius at comcast.net> wrote:
>
> On Oct 17, 2014, at 1:39 PM, Gerrit Eichner wrote:
>
>> Hello, list members,
>>
>> I have tried to contact the maintainer of the survMisc package, but my message could not be delivered. I can't get survMisc package to work as expected or documented, respectively. Maybe one of you has an idea regarding the following problem:
>>
>> When, e.g., trying to executed the first few lines of code in the examples section of comp() (one of the package functions), i.e.,
>>
>>> data(kidney,package="KMsurv")
>>> s1 <- survfit(Surv(time=time, event=delta) ~ type, data=kidney)
>>> comp(s1)
>>
>>
>> I receive the following error message:
>>
>> Error in parse(text = t2) : <text>:1:8: unexpected input
>> 1: paste( ``
>>            ^
>
> I get the same error on a Mac in an English locale. I'm afraid the code in the offending function `.getTne` appears somewhat cobbled together. When I try to debug, I get a single row, 1920 column matrix for n1 which is numeric with all entries == 1. Object `t1` cannot be found.
>
> {
>     s <- Es <- .SD <- NULL
>     n1 <- names(dt1)
>     f1 <- function(x) paste(dQuote(paste(x, "=", sep = "")),
>         ", get(", dQuote(x), ")", sep = "")
>     t1 <- paste(sapply(n1, f1), sep = ",")
>     if (length(t1) > 1) {
>         t1[2:length(t1)] <- sub("\"", "\"_", t1[2:length(t1)],
>             fixed = TRUE)
>     }
>     t1 <- paste(t1, collapse = ",")
>     t2 <- paste("paste(", t1, ", sep='')")
>
> # next line throw the error.
>
>     p1 <- parse(text = t2)
>     q <- quote(eval(p1))
>     dt1[, `:=`("s", as.factor(eval(q, envir = .SD)))]
>     stopifnot(attr(model.response(mf), "type") == "right")
>     y <- data.table(unclass(model.response(mf, "numeric")))
>
> I'm afraid I have been o help.
>
> --
> David.
>>
>>
>> Could this be an encoding-related issue inside the code? Does somebody have an idea where to look for a solution for this problem?
>>
>> Below you'll find my survMisc version and R session info. Thanks for any support!
>>
>> Kind regards  --  Gerrit
>>
>> ---------------------------------------------------------------------
>> Dr. Gerrit Eichner                   Mathematical Institute, Room 212
>> gerrit.eichner at math.uni-giessen.de   Justus-Liebig-University Giessen
>> Tel: +49-(0)641-99-32104          Arndtstr. 2, 35392 Giessen, Germany
>> Fax: +49-(0)641-99-32109        http://www.uni-giessen.de/cms/eichner
>> ---------------------------------------------------------------------
>>
>>
>>> citation( "survMisc")
>>
>> To cite package .survMisc. in publications use:
>>
>>  Chris Dardis (2014). survMisc: Miscellaneous functions for survival
>>  data.. R package version 0.4.2.
>>  http://CRAN.R-project.org/package=survMisc
>>
>>
>>> sessionInfo()
>> R version 3.1.1 (2014-07-10)
>> Platform: x86_64-w64-mingw32/x64 (64-bit)
>>
>> locale:
>> [1] LC_COLLATE=German_Germany.1252  LC_CTYPE=German_Germany.1252
>> [3] LC_MONETARY=German_Germany.1252 LC_NUMERIC=C
>> [5] LC_TIME=German_Germany.1252
>>
>> attached base packages:
>> [1] splines   stats     graphics  grDevices utils     datasets  methods
>> [8] base
>>
>> other attached packages:
>> [1] survMisc_0.4.2   rpart_4.1-8      data.table_1.9.2 ggplot2_1.0.0
>> [5] survival_2.37-7  fortunes_1.5-2
>>
>> loaded via a namespace (and not attached):
>> [1] colorspace_1.2-4 digest_0.6.4     gam_1.09.1       grid_3.1.1
>> [5] gtable_0.1.2     km.ci_0.5-2      KMsurv_0.1-5     MASS_7.3-33
>> [9] munsell_0.4.2    plyr_1.8.1       proto_0.3-10     Rcpp_0.11.2
>> [13] reshape2_1.4     scales_0.2.4     stringr_0.6.2    tools_3.1.1
>>
>> ______________________________________________
>> R-help at r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-help
>> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
>> and provide commented, minimal, self-contained, reproducible code.
>
> David Winsemius
> Alameda, CA, USA
>
> ______________________________________________
> R-help at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.