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and subject line Bug#331080: fixed in boot 1.2.23-2
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Date: Fri, 30 Sep 2005 13:34:55 -0700
From: Matt Kraai <[EMAIL PROTECTED]>
To: [EMAIL PROTECTED]
Subject: FTBFS: Error checking examples
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Package: boot
Version: 1.2.23-1
Severity: serious
boot fails to build:
> * checking examples ... ERROR
> Running examples in boot-Ex.R failed.
> The error most likely occurred in:
>=20
> > ### * censboot
> >=20
> > flush(stderr()); flush(stdout())
> >=20
> > ### Name: censboot
> > ### Title: Bootstrap for Censored Data
> > ### Aliases: censboot cens.return
> > ### Keywords: survival
> >=20
> > ### ** Examples
> >=20
> > data(aml, package=3D"boot")
> > library(survival)
> Loading required package: splines
>=20
> Attaching package: 'survival'
>=20
>=20
> The following object(s) are masked _by_ .GlobalEnv :
>=20
> aml=20
>=20
>=20
> The following object(s) are masked from package:boot :
>=20
> aml=20
>=20
> > # Example 3.9 of Davison and Hinkley (1997) does a bootstrap on some
> > # remission times for patients with a type of leukaemia. The patients
> > # were divided into those who received maintenance chemotherapy and=20
> > # those who did not. Here we are interested in the median remission=20
> > # time for the two groups.
> > aml.fun <- function(data) {
> + surv <- survfit(Surv(time, cens)~group, data=3Ddata)
> + out <- NULL
> + st <- 1
> + for (s in 1:length(surv$strata)) {
> + inds <- st:(st+surv$strata[s]-1)
> + md <- min(surv$time[inds[1-surv$surv[inds]>=3D0.5]])
> + st <- st+surv$strata[s]
> + out <- c(out,md)
> + }
> + out
> + }
> > aml.case <- censboot(aml,aml.fun,R=3D499,strata=3Daml$group)
> Warning: no finite arguments to min; returning Inf
> Warning: no finite arguments to min; returning Inf
> Warning: no finite arguments to min; returning Inf
> Warning: no finite arguments to min; returning Inf
> Warning: no finite arguments to min; returning Inf
> Warning: no finite arguments to min; returning Inf
> Warning: no finite arguments to min; returning Inf
> Warning: no finite arguments to min; returning Inf
> Warning: no finite arguments to min; returning Inf
> Warning: no finite arguments to min; returning Inf
> Warning: no finite arguments to min; returning Inf
> Warning: no finite arguments to min; returning Inf
> Warning: no finite arguments to min; returning Inf
> Warning: no finite arguments to min; returning Inf
> Warning: no finite arguments to min; returning Inf
> Warning: no finite arguments to min; returning Inf
> Warning: no finite arguments to min; returning Inf
> Warning: no finite arguments to min; returning Inf
> Warning: no finite arguments to min; returning Inf
> Warning: no finite arguments to min; returning Inf
> Warning: no finite arguments to min; returning Inf
> Warning: no finite arguments to min; returning Inf
> Warning: no finite arguments to min; returning Inf
> Warning: no finite arguments to min; returning Inf
> Warning: no finite arguments to min; returning Inf
> Warning: no finite arguments to min; returning Inf
> >=20
> > # Now we will look at the same statistic using the conditional=20
> > # bootstrap and the weird bootstrap. For the conditional bootstrap=20
> > # the survival distribution is stratified but the censoring=20
> > # distribution is not.=20
> >=20
> > aml.s1 <- survfit(Surv(time,cens)~group, data=3Daml)
> > aml.s2 <- survfit(Surv(time-0.001*cens,1-cens)~1, data=3Daml)
> > aml.cond <- censboot(aml,aml.fun,R=3D499,strata=3Daml$group,
> + F.surv=3Daml.s1,G.surv=3Daml.s2,sim=3D"cond")
> Warning: no finite arguments to min; returning Inf
> Warning: no finite arguments to min; returning Inf
> Warning: no finite arguments to min; returning Inf
> Warning: no finite arguments to min; returning Inf
> Warning: no finite arguments to min; returning Inf
> Warning: no finite arguments to min; returning Inf
> Warning: no finite arguments to min; returning Inf
> Warning: no finite arguments to min; returning Inf
> Warning: no finite arguments to min; returning Inf
> Warning: no finite arguments to min; returning Inf
> Warning: no finite arguments to min; returning Inf
> Warning: no finite arguments to min; returning Inf
> Warning: no finite arguments to min; returning Inf
> Warning: no finite arguments to min; returning Inf
> Warning: no finite arguments to min; returning Inf
> Warning: no finite arguments to min; returning Inf
> Warning: no finite arguments to min; returning Inf
> Warning: no finite arguments to min; returning Inf
> Warning: no finite arguments to min; returning Inf
> Warning: no finite arguments to min; returning Inf
> Warning: no finite arguments to min; returning Inf
> Warning: no finite arguments to min; returning Inf
> Warning: no finite arguments to min; returning Inf
> Warning: no finite arguments to min; returning Inf
> Warning: no finite arguments to min; returning Inf
> Warning: no finite arguments to min; returning Inf
> Warning: no finite arguments to min; returning Inf
> Warning: no finite arguments to min; returning Inf
> >=20
> > # For the weird bootstrap we must redefine our function slightly since
> > # the data will not contain the group number.
> > aml.fun1 <- function(data,str) {
> + surv <- survfit(Surv(data[,1],data[,2])~str)
> + out <- NULL
> + st <- 1
> + for (s in 1:length(surv$strata)) {
> + inds <- st:(st+surv$strata[s]-1)
> + md <- min(surv$time[inds[1-surv$surv[inds]>=3D0.5]])
> + st <- st+surv$strata[s]
> + out <- c(out,md)
> + }
> + }
> > aml.wei <- censboot(cbind(aml$time,aml$cens),aml.fun1,R=3D499,
> + strata=3Daml$group, F.surv=3Daml.s1,sim=3D"weird")
> Warning: no finite arguments to min; returning Inf
> Warning: no finite arguments to min; returning Inf
> Warning: no finite arguments to min; returning Inf
> Warning: no finite arguments to min; returning Inf
> Warning: no finite arguments to min; returning Inf
> Warning: no finite arguments to min; returning Inf
> Warning: no finite arguments to min; returning Inf
> Warning: no finite arguments to min; returning Inf
> >=20
> > # Now for an example where a cox regression model has been fitted
> > # the data we will look at the melanoma data of Example 7.6 from=20
> > # Davison and Hinkley (1997). The fitted model assumes that there
> > # is a different survival distribution for the ulcerated and=20
> > # non-ulcerated groups but that the thickness of the tumour has a
> > # common effect. We will also assume that the censoring distribution
> > # is different in different age groups. The statistic of interest
> > # is the linear predictor. This is returned as the values at a
> > # number of equally spaced points in the range of interest.
> > data(melanoma, package=3D"boot")
> > library(splines)# for ns
> > mel.cox <- coxph(Surv(time,status=3D=3D1)~ns(thickness,df=3D4)+strata(u=
lcer),
> + data=3Dmelanoma)
> > mel.surv <- survfit(mel.cox)
> > agec <- cut(melanoma$age,c(0,39,49,59,69,100))
> > mel.cens <- survfit(Surv(time-0.001*(status=3D=3D1),status!=3D1)~
> + strata(agec),data=3Dmelanoma)
> > mel.fun <- function(d) {=20
> + t1 <- ns(d$thickness,df=3D4)
> + cox <- coxph(Surv(d$time,d$status=3D=3D1) ~ t1+strata(d$ulcer))
> + eta <- unique(cox$linear.predictors)
> + u <- unique(d$thickness)
> + sp <- smooth.spline(u,eta,df=3D20)
> + th <- seq(from=3D0.25,to=3D10,by=3D0.25)
> + predict(sp,th)$y
> + }
> > mel.str<-cbind(melanoma$ulcer,agec)
> > # this is slow!
> > mel.mod <- censboot(melanoma,mel.fun,R=3D999,F.surv=3Dmel.surv,
> + G.surv=3Dmel.cens,cox=3Dmel.cox,strata=3Dmel.str,sim=3D"model")
> Error in xy.coords(x, y) : 'x' and 'y' lengths differ
> Execution halted
--=20
Matt
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Received: (at 331080-close) by bugs.debian.org; 2 Oct 2005 04:09:16 +0000
>From [EMAIL PROTECTED] Sat Oct 01 21:09:16 2005
Return-path: <[EMAIL PROTECTED]>
Received: from katie by spohr.debian.org with local (Exim 3.36 1 (Debian))
id 1ELv38-0003Ix-00; Sat, 01 Oct 2005 21:02:06 -0700
From: Dirk Eddelbuettel <[EMAIL PROTECTED]>
To: [EMAIL PROTECTED]
X-Katie: $Revision: 1.56 $
Subject: Bug#331080: fixed in boot 1.2.23-2
Message-Id: <[EMAIL PROTECTED]>
Sender: Archive Administrator <[EMAIL PROTECTED]>
Date: Sat, 01 Oct 2005 21:02:06 -0700
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autolearn=no version=2.60-bugs.debian.org_2005_01_02
Source: boot
Source-Version: 1.2.23-2
We believe that the bug you reported is fixed in the latest version of
boot, which is due to be installed in the Debian FTP archive:
boot_1.2.23-2.diff.gz
to pool/main/b/boot/boot_1.2.23-2.diff.gz
boot_1.2.23-2.dsc
to pool/main/b/boot/boot_1.2.23-2.dsc
r-cran-boot_1.2.23-2_all.deb
to pool/main/b/boot/r-cran-boot_1.2.23-2_all.deb
A summary of the changes between this version and the previous one is
attached.
Thank you for reporting the bug, which will now be closed. If you
have further comments please address them to [EMAIL PROTECTED],
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Dirk Eddelbuettel <[EMAIL PROTECTED]> (supplier of updated boot package)
(This message was generated automatically at their request; if you
believe that there is a problem with it please contact the archive
administrators by mailing [EMAIL PROTECTED])
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA1
Format: 1.7
Date: Sat, 1 Oct 2005 22:13:51 -0500
Source: boot
Binary: r-cran-boot
Architecture: source all
Version: 1.2.23-2
Distribution: unstable
Urgency: low
Maintainer: Dirk Eddelbuettel <[EMAIL PROTECTED]>
Changed-By: Dirk Eddelbuettel <[EMAIL PROTECTED]>
Description:
r-cran-boot - GNU R package for bootstrapping functions from Davison and Hinkle
Closes: 331080
Changes:
boot (1.2.23-2) unstable; urgency=low
.
* debian/rules: Disable R CMD check for the time being (Closes: #331080)
* debian/post{inst,rm}: No longer need to call /usr/bin/R for html index
Files:
4c9a3c71a60d4cf7856ded770c58ce43 625 math optional boot_1.2.23-2.dsc
f974a4cdf35e89f772494a36c565e285 2811 math optional boot_1.2.23-2.diff.gz
133385b0c4d122b4d087e292ea23f92e 442710 math optional
r-cran-boot_1.2.23-2_all.deb
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