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: 2011-05-09 14:51:18 -0700 (Mon, 09 May 2011)

EndedAt: 2011-05-09 14:53:58 -0700 (Mon, 09 May 2011)

EllapsedTime: 160.1 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) (2011-04-24 r55634)
* using platform: i386-apple-darwin9.8.0 (32-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 ‘1.1.0’
* checking package name space 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 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 ... 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/2.14/Resources/include -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include/i386  -I/usr/local/include    -fPIC  -g -O2 -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	0.660	0.009	0.674
BAFSet.to.ExpressionSets	0.240	0.008	0.249
CNSet	0.299	0.001	0.301
GenoSet	0.275	0.001	0.276
baf	0.053	0.018	0.072
baf2mbaf	0.040	0.002	0.043
bafset-class	0.326	0.002	0.332
boundingIndices	0.001	0.000	0.002
boundingIndices2	0.001	0.000	0.001
chr-methods	0.275	0.001	0.276
chrIndices-methods	0.031	0.001	0.032
chrInfo	0.046	0.001	0.048
chrOrder	0.002	0.000	0.002
cn	0.054	0.018	0.071
cnset-class	0.270	0.001	0.271
colMeans	0.02	0.00	0.02
gcCorrect	0.008	0.001	0.010
genoPlot	0.097	0.002	0.100
genoPos-methods	0.083	0.019	0.103
genomeAxis	0.068	0.002	0.071
genomeOrder	0.044	0.010	0.054
genoset-class	0.272	0.002	0.274
genoset-methods	1.116	0.022	1.152
initGenoSet	0.304	0.001	0.308
isGenomeOrder	0.151	0.001	0.153
locData	0.028	0.001	0.030
lrr	0.054	0.018	0.075
modeCenter	0.009	0.002	0.011
orderedChrs	0.342	0.002	0.348
pos	0.313	0.002	0.318
rangeSampleMeans	0.289	0.003	0.295
runCBS	4.154	0.024	4.266
segTable	3.479	0.025	3.585
segs2Rle	3.032	0.026	3.123
segs2RleDataFrame	3.397	0.022	3.646
subsetAssayData	0.029	0.002	0.033
uniqueChrs	0.264	0.000	0.265
universe	0.029	0.001	0.030