Re: [R] [survMisc]: error message in examples of comp()
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 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) : :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.eich...@math.uni-giessen.de Justus-Liebig-University Giessen
>> Tel: +49-(0)641-99-32104 Arndtstr. 2, 35392 Giessen, Germany
>> Fax: +49-(0)641-99-32109http://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_0.4.2plyr_1.8.1 proto_0.3-10 Rcpp_0.11.2
>> [13] reshape2_1.4 scales_0.2.4 stringr_0.6.2tools_3.1.1
>>
>> __
>> R-help@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@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.
__
R-help@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.
Re: [R] [survMisc]: error message in examples of comp()
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) : :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.eich...@math.uni-giessen.de Justus-Liebig-University Giessen
> Tel: +49-(0)641-99-32104 Arndtstr. 2, 35392 Giessen, Germany
> Fax: +49-(0)641-99-32109http://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_0.4.2plyr_1.8.1 proto_0.3-10 Rcpp_0.11.2
> [13] reshape2_1.4 scales_0.2.4 stringr_0.6.2tools_3.1.1
>
> __
> R-help@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@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.
[R] [survMisc]: error message in examples of comp()
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) : :1:8: unexpected input 1: paste( `` ^ 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.eich...@math.uni-giessen.de Justus-Liebig-University Giessen Tel: +49-(0)641-99-32104 Arndtstr. 2, 35392 Giessen, Germany Fax: +49-(0)641-99-32109http://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_0.4.2plyr_1.8.1 proto_0.3-10 Rcpp_0.11.2 [13] reshape2_1.4 scales_0.2.4 stringr_0.6.2tools_3.1.1 __ R-help@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.
