Package: genoset

Version: 1.2.0

Command: /home/biocbuild/bbs-2.9-bioc/R/bin/R CMD check --no-vignettes --timings genoset_1.2.0.tar.gz

StartedAt: 2012-03-24 00:38:16 -0700 (Sat, 24 Mar 2012)

EndedAt: 2012-03-24 00:41:09 -0700 (Sat, 24 Mar 2012)

EllapsedTime: 172.9 seconds

RetCode: 0

Status:  OK

CheckDir: genoset.Rcheck

Warnings: 0

* using log directory ‘/loc/home/biocbuild/bbs-2.9-bioc/meat/genoset.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 ‘genoset/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘genoset’ version ‘1.2.0’
* 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 ‘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 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 ... NOTE
  
  Note: significantly better compression could be obtained
        by using R CMD build --resave-data
                old_size new_size compress
  genoset.RData    142Kb     32Kb       xz
* 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 ... OK
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘prove.pmh.utils.R’
  Comparing ‘prove.pmh.utils.Rout’ to ‘prove.pmh.utils.Rout.save’ ...23,26d22
< Error in !all.equal(rownames(calls), rownames(baf)) : 
<   invalid argument type
< Error in checkEquals(gcCorrect(input.vector, gc), output.vector) : 
<   Mean relative difference: 1
 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-2.9-bioc/R/include  -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-2.9-bioc/R/lib -lR
installing to /loc/home/biocbuild/bbs-2.9-bioc/meat/genoset.Rcheck/genoset/libs
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices ...
*** tangling vignette sources ...
   ‘genoset.Rnw’ 
** testing if installed package can be loaded

* DONE (genoset)

name	user	system	elapsed
BAFSet	0.896	0.016	0.909
BAFSet.to.ExpressionSets	0.144	0.004	0.148
CNSet	0.116	0.000	0.114
GenoSet	0.104	0.000	0.103
baf	0.024	0.008	0.030
baf2mbaf	0.024	0.000	0.027
bafset-class	0.188	0.000	0.216
boundingIndices	0.000	0.000	0.001
boundingIndices2	0	0	0
chr-methods	0.104	0.000	0.114
chrIndices-methods	0.012	0.004	0.014
chrInfo	0.028	0.004	0.029
chrOrder	0.000	0.000	0.001
cn	0.024	0.008	0.030
cnset-class	0.108	0.000	0.110
colMeans	0.008	0.000	0.013
convertToBigMatrix	0	0	0
gcCorrect	0.004	0.008	0.010
genoPlot	0.068	0.004	0.074
genoPos-methods	0.040	0.008	0.048
genomeAxis	0.040	0.000	0.041
genomeorder	0.636	0.000	0.638
genoset-class	0.100	0.000	0.099
genoset-methods	0.484	0.008	0.494
initGenoSet	0.108	0.000	0.106
isGenomeOrder	0.024	0.000	0.023
locData	0.032	0.000	0.033
lrr	0.028	0.008	0.034
modeCenter	0.008	0.000	0.007
orderedChrs	0.120	0.000	0.118
pos	0.116	0.000	0.114
rangeSampleMeans	0.076	0.000	0.077
readGenoSet	0	0	0
runCBS	2.388	0.000	2.396
segTable-methods	2.184	0.000	2.194
segs2Rle	2.105	0.008	2.124
segs2RleDataFrame	2.048	0.004	2.075
subsetAssayData	0.012	0.000	0.013
uniqueChrs	0.108	0.000	0.107
universe	0.016	0.000	0.014