Package: Ringo

Version: 1.18.0

Command: /Library/Frameworks/R.framework/Versions/2.14/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch Ringo_1.18.0.tar.gz

StartedAt: 2012-03-24 03:47:14 -0700 (Sat, 24 Mar 2012)

EndedAt: 2012-03-24 03:51:03 -0700 (Sat, 24 Mar 2012)

EllapsedTime: 228.8 seconds

RetCode: 0

Status:  OK

CheckDir: Ringo.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.9-bioc/meat/Ringo.Rcheck'
* using R version 2.14.2 (2012-02-29)
* 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 '1.18.0'
* 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 '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 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 ... NOTE
File 'Ringo/R/zzz.R':
  .onAttach calls:
    require(Biobase)

Package startup functions should not change the search path.
See section 'Good practice' in ?.onAttach.

exportCherList: no visible global function definition for 'IRanges'
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 compiled code ... OK
* checking sizes of PDF files under 'inst/doc' ... OK
* checking examples ... 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 'Ringo' ...
** libs
*** arch - i386
g++ -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/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/Resources/include -I/Library/Frameworks/R.framework/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/Resources/include -I/Library/Frameworks/R.framework/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/Resources/include -I/Library/Frameworks/R.framework/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-2.9-bioc/meat/Ringo.Rcheck/Ringo/libs/i386
** R
** inst
** preparing package for lazy loading
Creating a generic function for 'plot' from package 'graphics' in package 'Ringo'
Creating a generic function for 'get' from package 'base' in package 'Ringo'
Creating a generic function for 'ls' from package 'base' in package 'Ringo'
** help
*** installing help indices
** building package indices ...
*** tangling vignette sources ...
   'Ringo.Rnw' 
** testing if installed package can be loaded

* DONE (Ringo)

name	user	system	elapsed
arrayImage	0.150	0.009	0.160
asExprSet	0.481	0.013	0.497
autocorr	0.148	0.008	0.157
cherByThreshold	0.005	0.001	0.006
cherClass	0.495	0.008	0.501
chipAlongChrom	0.274	0.010	0.285
chipAlongChromOld	0.078	0.004	0.082
computeRunningMedians	0.563	0.005	0.570
compute_gc	0.000	0.000	0.001
compute_sliding_t	0.115	0.004	0.119
corrPlot	0.083	0.009	0.118
exportCherList	0.000	0.001	0.001
features2Probes	1.370	0.092	1.466
findChersOnSmoothed	0.156	0.006	0.162
ftr2xys	0.001	0.000	0.001
newCER	0.001	0.000	0.002
nonzero	0.027	0.002	0.029
plotAutocorr	0.000	0.000	0.001
plotBM	0.016	0.003	0.019
posToProbeAnnoEnvironment	0.052	0.003	0.056
preprocess	1.003	0.059	1.064
probeAnnoClass	0.036	0.004	0.041
qopS4	0.000	0.001	0.000
quantilesOverPositions	1.130	0.107	1.239
readNimblegen	0.116	0.005	0.120
regionoverlap	0.012	0.000	0.012
relateCERs	0.000	0.001	0.000
sigGOTable	0.001	0.000	0.000
sliding_meansd	0.002	0.001	0.002
sliding_quantile	0.016	0.002	0.017
twoGaussiansNull	0.280	0.011	0.292
upperBoundNull	0.127	0.010	0.137
validProbeAnno	0.039	0.002	0.041