Package: genoset

Version: 1.0.0

Command: /Library/Frameworks/R.framework/Versions/2.13/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch genoset_1.0.0.tar.gz

StartedAt: 2011-10-20 15:10:12 -0700 (Thu, 20 Oct 2011)

EndedAt: 2011-10-20 15:12:52 -0700 (Thu, 20 Oct 2011)

EllapsedTime: 160.0 seconds

RetCode: 0

Status:  OK

CheckDir: genoset.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.8-bioc/meat/genoset.Rcheck'
* using R version 2.13.2 (2011-09-30)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'genoset/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'genoset' version '1.0.0'
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... 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 ... 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 sizes of PDF files under inst/doc ... 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' ... OK
 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
*** arch - i386
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/i386  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic -c genoset.c -o genoset.o
gcc-4.2 -arch i386 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o genoset.so genoset.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.8-bioc/meat/genoset.Rcheck/genoset/libs/i386
** R
** data
** inst
** preparing package for lazy loading

**************************************************************************
   The plan to change the data format for CNA object has been postponed   
 in order to ensure backward compatibility with older versions of DNAcopy 
**************************************************************************

** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded

* DONE (genoset)

name	user	system	elapsed
BAFSet	0.624	0.005	0.686
BAFSet.to.ExpressionSets	0.251	0.007	0.275
CNSet	0.303	0.002	0.328
GenoSet	0.284	0.001	0.305
baf	0.042	0.018	0.061
baf2mbaf	0.039	0.003	0.044
bafset-class	0.322	0.001	0.338
boundingIndices	0.001	0.001	0.002
boundingIndices2	0.000	0.000	0.001
chr-methods	0.274	0.001	0.283
chrIndices-methods	0.034	0.002	0.037
chrInfo	0.048	0.002	0.050
chrOrder	0.002	0.000	0.002
cn	0.043	0.018	0.062
cnset-class	0.279	0.001	0.280
colMeans	0.016	0.001	0.016
gcCorrect	0.008	0.001	0.008
genoPlot	0.097	0.002	0.100
genoPos-methods	0.067	0.020	0.086
genomeAxis	0.064	0.002	0.066
genomeOrder	0.045	0.010	0.055
genoset-class	0.359	0.001	0.364
genoset-methods	1.021	0.024	1.088
initGenoSet	0.274	0.001	0.304
isGenomeOrder	0.141	0.001	0.142
locData	0.027	0.001	0.028
lrr	0.042	0.018	0.060
modeCenter	0.009	0.003	0.012
orderedChrs	0.301	0.002	0.308
pos	0.273	0.002	0.281
rangeSampleMeans	0.274	0.003	0.278
runCBS	4.051	0.021	4.101
segTable	3.448	0.022	3.504
segs2Rle	3.030	0.016	3.065
segs2RleDataFrame	3.399	0.020	3.443
subsetAssayData	0.027	0.002	0.031
uniqueChrs	0.279	0.001	0.281
universe	0.028	0.001	0.030