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 |
* using log directory '/Users/biocbuild/bbs-2.9-bioc/meat/survcomp.Rcheck'
* using R version 2.14.2 (2012-02-29)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* 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 sizes of PDF files under 'inst/doc' ... 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
* installing *source* package 'survcomp' ...
** libs
*** arch - i386
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -I/usr/local/include -fPIC -g -O2 -Wall -pedantic -c concordance.index.c -o concordance.index.o
gcc -arch i386 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o survcomp.so concordance.index.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.9-bioc/meat/survcomp.Rcheck/survcomp/libs/i386
** 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)