Package: Ringo

Version: 1.16.0

Command: /Library/Frameworks/R.framework/Versions/2.13/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch Ringo_1.16.0.tar.gz

StartedAt: 2011-10-20 16:58:57 -0700 (Thu, 20 Oct 2011)

EndedAt: 2011-10-20 17:02:08 -0700 (Thu, 20 Oct 2011)

EllapsedTime: 190.2 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 2.13.2 (2011-09-30)
* 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 '1.16.0'
* checking package namespace 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 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
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 sizes of PDF files under inst/doc ... NOTE
  'qpdf' made some significant size reductions:
     compacted 'Ringo.pdf' from 1202Kb to 521Kb
  consider running tools::compactPDF() on these files
* 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++-4.2 -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++-4.2 -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-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 region_overlap.c -o region_overlap.o
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 ringo_init.c -o ringo_init.o
g++-4.2 -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
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	0.273	0.009	0.290
asExprSet	0.427	0.010	0.442
autocorr	0.156	0.008	0.164
cherByThreshold	0.006	0.000	0.006
cherClass	0.445	0.006	0.452
chipAlongChrom	0.301	0.009	0.311
chipAlongChromOld	0.073	0.004	0.078
computeRunningMedians	0.451	0.004	0.461
compute_gc	0.001	0.000	0.001
compute_sliding_t	0.132	0.003	0.135
corrPlot	0.067	0.005	0.072
exportCherList	0	0	0
features2Probes	0.943	0.089	1.050
findChersOnSmoothed	0.173	0.006	0.178
ftr2xys	0	0	0
newCER	0.001	0.000	0.002
nonzero	0.020	0.000	0.021
plotAutocorr	0.001	0.000	0.001
plotBM	0.015	0.001	0.016
posToProbeAnnoEnvironment	0.054	0.003	0.057
preprocess	0.936	0.056	1.088
probeAnnoClass	0.035	0.002	0.037
qopS4	0	0	0
quantilesOverPositions	0.865	0.094	0.959
readNimblegen	0.121	0.004	0.125
regionoverlap	0.013	0.001	0.014
relateCERs	0.000	0.001	0.000
sigGOTable	0.000	0.000	0.001
sliding_meansd	0.002	0.001	0.003
sliding_quantile	0.016	0.001	0.017
twoGaussiansNull	0.269	0.008	0.277
upperBoundNull	0.138	0.006	0.147
validProbeAnno	0.040	0.003	0.044