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Package 483/514HostnameOS / ArchBUILDCHECKBUILD BIN
survcomp 1.4.0
Benjamin Haibe-Kains , Markus Schroeder
Snapshot Date: 2012-03-23 18:21:46 -0700 (Fri, 23 Mar 2012)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_9/madman/Rpacks/survcomp
Last Changed Rev: 59920 / Revision: 64395
Last Changed Date: 2011-10-31 15:59:03 -0700 (Mon, 31 Oct 2011)
wilson2 Linux (openSUSE 11.4) / x86_64  OK [ ERROR ]
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  ERROR  OK 
pitt Mac OS X Leopard (10.5.8) / i386  OK  ERROR  OK 

Summary

Package: survcomp
Version: 1.4.0
Command: /home/biocbuild/bbs-2.9-bioc/R/bin/R CMD check --no-vignettes --timings survcomp_1.4.0.tar.gz
StartedAt: 2012-03-24 02:59:53 -0700 (Sat, 24 Mar 2012)
EndedAt: 2012-03-24 03:00:23 -0700 (Sat, 24 Mar 2012)
EllapsedTime: 30.0 seconds
RetCode: 1
Status:  ERROR 
CheckDir: survcomp.Rcheck
Warnings: NA

Command output

* using log directory ‘/loc/home/biocbuild/bbs-2.9-bioc/meat/survcomp.Rcheck’
* using R version 2.14.2 (2012-02-29)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘survcomp/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘survcomp’ version ‘1.4.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking whether package ‘survcomp’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking for unstated dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... OK
* checking examples ... ERROR
Running examples in ‘survcomp-Ex.R’ failed
The error most likely occurred in:

> assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: ibsc.comp
> ### Title: Function to compare two IBSCs
> ### Aliases: ibsc.comp
> ### Keywords: survival htest
> 
> ### ** Examples
> 
> set.seed(12345)
> age <- rnorm(30, 50, 10)
> size <- rexp(30,1)
> stime <- rexp(30)
> cens <- runif(30,.5,2)
> sevent <- as.numeric(stime <= cens)
> stime <- pmin(stime, cens)
> ##Brier scores
> ##size
> dd <- data.frame("time"=stime, "event"=sevent, "score"=size)
> bsc1 <- sbrier.score2proba(data.tr=dd, data.ts=dd, method="cox")
Error in sbrier(obj = Surv(surv.time.ts, surv.event.ts), pred = mypred,  : 
  could not find function "prodlim"
Calls: sbrier.score2proba -> sbrier
Execution halted

survcomp.Rcheck/00install.out:

* installing *source* package ‘survcomp’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c concordance.index.c -o concordance.index.o
gcc -std=gnu99 -shared -L/usr/local/lib64 -o survcomp.so concordance.index.o -L/home/biocbuild/bbs-2.9-bioc/R/lib -lR
installing to /loc/home/biocbuild/bbs-2.9-bioc/meat/survcomp.Rcheck/survcomp/libs
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices ...
*** tangling vignette sources ...
   ‘survcomp.Rnw’ 
** testing if installed package can be loaded

* DONE (survcomp)

survcomp.Rcheck/survcomp-Ex.timings:

nameusersystemelapsed
D.index0.0320.0040.034
breastCancerData1.1160.0401.160
censor.time0.0000.0000.001
cindex.comp0.0080.0000.005
cindex.comp.meta0.0040.0000.006
combine.est0.0000.0000.001
combine.test0.0000.0000.001
concordance.index0.0040.0000.004
cvpl0.3480.0080.356
dindex.comp0.0120.0000.014
dindex.comp.meta0.0320.0000.033
fisherz000
forestplot.surv000
getsurv20.0040.0000.006
hazard.ratio0.0160.0000.014
hr.comp0.0120.0040.014
hr.comp.meta0.0280.0000.028
hr.comp20.0080.0000.009
iauc.comp0.6840.0160.698