Package: genoset

Version: 1.10.1

Command: /home/biocbuild/bbs-2.11-bioc/R/bin/R CMD check --no-vignettes --timings genoset_1.10.1.tar.gz

StartedAt: 2013-03-25 01:31:32 -0700 (Mon, 25 Mar 2013)

EndedAt: 2013-03-25 01:34:50 -0700 (Mon, 25 Mar 2013)

EllapsedTime: 197.8 seconds

RetCode: 0

Status:  OK

CheckDir: genoset.Rcheck

Warnings: 0

* using log directory ‘/loc/home/biocbuild/bbs-2.11-bioc/meat/genoset.Rcheck’
* using R version 2.15.3 (2013-03-01)
* 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 ‘1.10.1’
* 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 ‘genoset’ 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 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 ... OK
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘prove.R’
  Comparing ‘prove.Rout’ to ‘prove.Rout.save’ ...27c27,32
< Using mclapply for segmentation ...
---
> 
> **************************************************************************
>    The plan to change the data format for CNA object has been postponed   
>  in order to ensure backward compatibility with older versions of DNAcopy 
> **************************************************************************
> 
30d34
< Using mclapply for segmentation ...
33d36
< Using mclapply for segmentation ...
36d38
< Using mclapply for segmentation ...
39d40
< Using mclapply for segmentation ...
42,43d42
< Using mclapply for segmentation ...
< Working on segmentation for sample number 2 : a2
45d43
< Using mclapply for segmentation ...
48d45
< Using mclapply for segmentation ...
51c48
< Using mclapply for segmentation ...
---
> Working on segmentation for sample number 2 : a2
54d50
< Using mclapply for segmentation ...
59c55
< RUNIT TEST PROTOCOL -- Mon Mar 25 01:34:47 2013 
---
> RUNIT TEST PROTOCOL -- Tue Oct  2 21:13:24 2012 
71c67
< There were 37 warnings (use warnings() to see them)
---
> There were 50 or more warnings (use warnings() to see the first 50)
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignettes ... SKIPPED
* checking PDF version of manual ... OK

* installing *source* package ‘genoset’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-2.11-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c genoset.c -o genoset.o
gcc -std=gnu99 -shared -L/usr/local/lib64 -o genoset.so genoset.o -L/home/biocbuild/bbs-2.11-bioc/R/lib -lR
installing to /loc/home/biocbuild/bbs-2.11-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	0.440	0.000	0.439
BAFSet	0.240	0.004	0.243
BAFSet.to.ExpressionSets	0.144	0.004	0.162
CNSet-class	0.068	0.000	0.067
CNSet	0.124	0.000	0.122
GenoSet-class	0.064	0.000	0.065
GenoSet	0.108	0.000	0.112
baf	0.020	0.016	0.036
baf2mbaf	0.020	0.004	0.027
boundingIndices	0.000	0.000	0.001
boundingIndices2	0	0	0
chr-methods	0.108	0.000	0.110
chrIndices-methods	0.016	0.000	0.015
chrInfo	0.024	0.004	0.027
chrNames	0.112	0.000	0.110
chrOrder	0.000	0.000	0.001
cn	0.020	0.012	0.034
colMeans	0.012	0.000	0.014
featureNames	0.056	0.000	0.057
gcCorrect	0.008	0.000	0.007
genoPlot-methods	0.060	0.000	0.059
genoPos-methods	0.024	0.004	0.027
genomeAxis	0.036	0.000	0.038
genoset-methods	0.620	0.012	0.634
initGenoSet	0.104	0.000	0.105
isGenomeOrder-methods	0.012	0.004	0.030
locData-methods	0.016	0.000	0.016
lrr	0.028	0.004	0.032
modeCenter	0.008	0.000	0.007
pos	0.104	0.004	0.110
rangeSampleMeans	0.056	0.000	0.059
readGenoSet	0	0	0
runCBS	2.500	0.004	2.570
sampleNames	0.016	0.000	0.035
segPairTable-methods	0.036	0.000	0.043
segTable-methods	2.096	0.008	2.236
segs2Rle	1.796	0.016	1.913
segs2RleDataFrame	2.117	0.008	2.137
subsetAssayData	0.016	0.000	0.018
toGenomeOrder-methods	0.124	0.004	0.137