Package: genoset

Version: 1.1.0

Command: /Library/Frameworks/R.framework/Versions/2.14/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch genoset_1.1.0.tar.gz

StartedAt: 2011-07-07 03:22:05 -0700 (Thu, 07 Jul 2011)

EndedAt: 2011-07-07 03:24:54 -0700 (Thu, 07 Jul 2011)

EllapsedTime: 168.6 seconds

RetCode: 0

Status:  OK

CheckDir: genoset.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.9-bioc/meat/genoset.Rcheck'
* using R version 2.14.0 Under development (unstable) (2011-06-22 r56208)
* 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 '1.1.0'
* checking package name space information ... OK
* checking package dependencies ... NOTE
Package which this enhances but not available for checking: multicore
* 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 name space can be loaded with stated dependencies ... OK
* checking whether the name space 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 tools::resaveRdaFiles() or R CMD build --resave-data
                old_size new_size compress
  genoset.RData    146Kb     33Kb       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 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/Resources/include -I/Library/Frameworks/R.framework/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-2.9-bioc/meat/genoset.Rcheck/genoset/libs/i386
** R
** data
** inst
** preparing package for lazy loading

Welcome to Bioconductor

  Vignettes contain introductory material. To view, type
  'browseVignettes()'. To cite Bioconductor, see
  'citation("Biobase")' and for packages 'citation("pkgname")'.


Attaching package: 'IRanges'

The following object(s) are masked from 'package:Biobase':

    updateObject

The following object(s) are masked from 'package:base':

    Map, cbind, eval, intersect, mapply, order, paste, pmax, pmax.int,
    pmin, pmin.int, rbind, rep.int, setdiff, table, union


**************************************************************************
   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 ...
*** tangling vignette sources ...
   'genoset.Rnw' 
** testing if installed package can be loaded

* DONE (genoset)

name	user	system	elapsed
BAFSet	0.665	0.006	0.672
BAFSet.to.ExpressionSets	0.264	0.007	0.272
CNSet	0.302	0.002	0.315
GenoSet	0.290	0.001	0.294
baf	0.045	0.019	0.064
baf2mbaf	0.041	0.002	0.044
bafset-class	0.344	0.002	0.352
boundingIndices	0.001	0.001	0.002
boundingIndices2	0.001	0.000	0.001
chr-methods	0.285	0.002	0.291
chrIndices-methods	0.032	0.002	0.034
chrInfo	0.051	0.002	0.061
chrOrder	0.001	0.000	0.002
cn	0.045	0.018	0.068
cnset-class	0.291	0.001	0.299
colMeans	0.017	0.000	0.018
gcCorrect	0.008	0.001	0.009
genoPlot	0.103	0.003	0.106
genoPos-methods	0.164	0.021	0.187
genomeAxis	0.063	0.002	0.066
genomeOrder	0.045	0.011	0.057
genoset-class	0.285	0.005	0.324
genoset-methods	1.094	0.023	1.141
initGenoSet	0.287	0.001	0.291
isGenomeOrder	0.153	0.002	0.156
locData	0.029	0.001	0.030
lrr	0.043	0.018	0.062
modeCenter	0.009	0.002	0.012
orderedChrs	0.327	0.002	0.342
pos	0.292	0.002	0.297
rangeSampleMeans	0.302	0.003	0.307
runCBS	4.141	0.023	4.204
segTable	3.559	0.024	3.635
segs2Rle	3.066	0.024	3.154
segs2RleDataFrame	3.463	0.024	3.624
subsetAssayData	0.028	0.002	0.031
uniqueChrs	0.285	0.002	0.294
universe	0.029	0.002	0.034