Package: genoset

Version: 1.11.14

Command: /home/biocbuild/bbs-2.12-bioc/R/bin/R CMD check --no-vignettes --timings genoset_1.11.14.tar.gz

StartedAt: 2013-01-16 02:56:23 -0800 (Wed, 16 Jan 2013)

EndedAt: 2013-01-16 02:59:31 -0800 (Wed, 16 Jan 2013)

EllapsedTime: 187.6 seconds

RetCode: 1

Status:  ERROR

CheckDir: genoset.Rcheck

Warnings: NA

* using log directory ‘/loc/home/biocbuild/bbs-2.12-bioc/meat/genoset.Rcheck’
* using R Under development (unstable) (2012-12-17 r61365)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘genoset/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘genoset’ version ‘1.11.14’
* 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 for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘genoset’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over 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 installed files from ‘inst/doc’ ... OK
* checking examples ... WARNING
Found the following significant warnings:

  Warning: %in% between a GRanges and a RangedData object is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘prove.R’
 ERROR
Running the tests in ‘tests/prove.R’ failed.
Last 13 lines of output:
  
     test_cbs.R 
       test_runCBS 
       test_segs2Rle 
  
     test_genoset-class.R 
       test_subset_w_granges 
  
  
  Error in BiocGenerics:::testPackage("genoset") : 
    unit tests failed for package genoset
  Calls: <Anonymous> -> <Anonymous>
  Execution halted

* installing *source* package ‘genoset’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c genoset.c -o genoset.o
gcc -std=gnu99 -shared -L/usr/local/lib64 -o genoset.so genoset.o -L/home/biocbuild/bbs-2.12-bioc/R/lib -lR
installing to /loc/home/biocbuild/bbs-2.12-bioc/meat/genoset.Rcheck/genoset/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
   ‘genoset.Rnw’ 
** testing if installed package can be loaded

* DONE (genoset)

name	user	system	elapsed
BAFSet-class	0.192	0.004	0.198
BAFSet	0.248	0.000	0.247
BAFSet.to.ExpressionSets	0.152	0.008	0.161
CNSet-class	0.072	0.000	0.073
CNSet	0.128	0.004	0.132
GenoSet-class	0.072	0.000	0.070
GenoSet	0.112	0.004	0.117
baf	0.024	0.016	0.043
baf2mbaf	0.276	0.000	0.277
boundingIndices	0.004	0.000	0.006
boundingIndices2	0.008	0.000	0.007
chr-methods	0.112	0.000	0.110
chrIndices-methods	0.024	0.000	0.024
chrInfo	0.032	0.000	0.031
chrNames	0.200	0.000	0.198
chrOrder	0.000	0.008	0.008
cn	0.028	0.012	0.038
colMeans	0.016	0.000	0.015
featureNames	0.064	0.000	0.064
gcCorrect	0.016	0.000	0.016
genoPlot-methods	0.072	0.008	0.081
genoPos-methods	0.036	0.000	0.037
genomeAxis	0.052	0.000	0.049
genoset-methods	0.360	0.016	0.374
initGenoSet	0.124	0.000	0.125
isGenomeOrder-methods	0.024	0.000	0.025
locData-methods	0.024	0.000	0.028
lrr	0.044	0.004	0.046
modeCenter	0.012	0.004	0.015
pos	0.356	0.000	0.359
rangeSampleMeans	0.068	0.000	0.068
readGenoSet	0.008	0.000	0.005
runCBS	2.292	0.004	2.298
sampleNames	0.020	0.004	0.024
segPairTable-methods	0.044	0.000	0.044
segTable-methods	1.744	0.000	1.744
segs2Rle	1.712	0.000	1.709
segs2RleDataFrame	1.721	0.000	1.717
subsetAssayData	0.020	0.004	0.026
toGenomeOrder-methods	0.140	0.004	0.142