BioC 2.9: CHECK report for survcomp on moscato1

Package: survcomp

Version: 1.4.0

Command: rm -rf survcomp.buildbin-libdir && mkdir survcomp.buildbin-libdir && D:\biocbld\bbs-2.9-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=survcomp.buildbin-libdir survcomp_1.4.0.tar.gz >survcomp-install.out 2>&1 && D:\biocbld\bbs-2.9-bioc\R\bin\R.exe CMD check --library=survcomp.buildbin-libdir --install="check:survcomp-install.out" --force-multiarch --no-vignettes --timings survcomp_1.4.0.tar.gz && mv survcomp.buildbin-libdir/* survcomp.Rcheck/ && rmdir survcomp.buildbin-libdir

StartedAt: 2012-03-24 03:05:56 -0700 (Sat, 24 Mar 2012)

EndedAt: 2012-03-24 03:06:50 -0700 (Sat, 24 Mar 2012)

EllapsedTime: 53.5 seconds

RetCode: 1

Status: ERROR

CheckDir: survcomp.Rcheck

Warnings: NA

Command output

* using log directory 'D:/biocbld/bbs-2.9-bioc/meat/survcomp.Rcheck'
* using R version 2.14.2 (2012-02-29)
* using platform: i386-pc-mingw32 (32-bit)
* using session charset: ISO8859-1
* 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 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ...
** running examples for arch 'i386' ... 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


install for i386

* installing *source* package 'survcomp' ...
** libs
gcc  -I"D:/biocbld/BBS-2˜1.9-B/R/include"          -O3 -Wall  -std=gnu99 -mtune=core2 -c concordance.index.c -o concordance.index.o
gcc -shared -s -static-libgcc -o survcomp.dll tmp.def concordance.index.o -LD:/biocbld/BBS-2˜1.9-B/R/bin/i386 -lR
installing to D:/biocbld/bbs-2.9-bioc/meat/survcomp.buildbin-libdir/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

add DLL for x64

* installing *source* package 'survcomp' ...
** libs
gcc -m64 -I"D:/biocbld/BBS-2˜1.9-B/R/include"     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c concordance.index.c -o concordance.index.o
gcc -m64 -shared -s -static-libgcc -o survcomp.dll tmp.def concordance.index.o -Ld:/RCompile/CRANpkg/extralibs64/local/lib/x64 -Ld:/RCompile/CRANpkg/extralibs64/local/lib -LD:/biocbld/BBS-2˜1.9-B/R/bin/x64 -lR
installing to D:/biocbld/bbs-2.9-bioc/meat/survcomp.buildbin-libdir/survcomp/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'survcomp' as survcomp_1.4.0.zip

* DONE (survcomp)

Summary

Command output