Package: Ringo

Version: 1.15.1

Command: /Library/Frameworks/R.framework/Versions/2.13/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch Ringo_1.15.1.tar.gz

StartedAt: 2011-03-17 17:19:28 -0700 (Thu, 17 Mar 2011)

EndedAt: 2011-03-17 17:21:50 -0700 (Thu, 17 Mar 2011)

EllapsedTime: 142.0 seconds

RetCode: 0

Status:  OK

CheckDir: Ringo.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.8-bioc/meat/Ringo.Rcheck'
* using R version 2.13.0 Under development (unstable) (2011-03-06 r54683)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'Ringo/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'Ringo' version '1.15.1'
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'Ringo' 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 ... NOTE
oneChannelVSN: no visible global function definition for 'vsnMatrix'
sigGOTable: no visible binding for global variable 'p.value'
* 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 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 examples ... OK
* checking package vignettes in 'inst/doc' ... SKIPPED
* checking PDF version of manual ... OK

* installing *source* package 'Ringo' ...
** libs
*** arch - i386
g++ -arch i386 -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 -fasm-blocks -c mmeansd.cpp -o mmeansd.o
g++ -arch i386 -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 -fasm-blocks -c mmedian.cpp -o mmedian.o
gcc -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 region_overlap.c -o region_overlap.o
gcc -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 ringo_init.c -o ringo_init.o
g++ -arch i386 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o Ringo.so mmeansd.o mmedian.o region_overlap.o ringo_init.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.8-bioc/meat/Ringo.Rcheck/Ringo/libs/i386
** R
** 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")'.

Loading required package: lattice

Attaching package: 'Matrix'

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

    det

Creating a new generic function for "plot" in "Ringo"
Creating a new generic function for "get" in "Ringo"
Creating a new generic function for "ls" in "Ringo"
** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded

* DONE (Ringo)

name	user	system	elapsed
arrayImage	0.139	0.004	0.143
asExprSet	0.348	0.004	0.351
autocorr	0.208	0.003	0.212
cherByThreshold	0.005	0.000	0.005
cherClass	0.237	0.005	0.242
chipAlongChrom	0.215	0.002	0.217
chipAlongChromOld	0.051	0.001	0.052
computeRunningMedians	0.331	0.002	0.332
compute_gc	0.001	0.000	0.001
compute_sliding_t	0.098	0.001	0.099
corrPlot	0.046	0.002	0.047
exportCherList	0.000	0.001	0.000
features2Probes	0.703	0.044	0.747
findChersOnSmoothed	0.130	0.002	0.132
ftr2xys	0.000	0.000	0.001
newCER	0.001	0.000	0.001
nonzero	0.016	0.001	0.017
plotAutocorr	0	0	0
plotBM	0.013	0.001	0.013
posToProbeAnnoEnvironment	0.056	0.002	0.059
preprocess	0.763	0.026	0.804
probeAnnoClass	0.037	0.001	0.039
qopS4	0.001	0.000	0.000
quantilesOverPositions	0.560	0.042	0.602
readNimblegen	0.244	0.009	0.253
regionoverlap	0.011	0.000	0.011
relateCERs	0.000	0.001	0.000
sigGOTable	0	0	0
sliding_meansd	0.002	0.001	0.002
sliding_quantile	0.012	0.000	0.012
twoGaussiansNull	0.205	0.004	0.208
upperBoundNull	0.102	0.001	0.104
validProbeAnno	0.028	0.000	0.030