Package: Ringo

Version: 1.17.0

Command: /Library/Frameworks/R.framework/Versions/2.14/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch Ringo_1.17.0.tar.gz

StartedAt: 2011-05-09 16:39:05 -0700 (Mon, 09 May 2011)

EndedAt: 2011-05-09 16:42:32 -0700 (Mon, 09 May 2011)

EllapsedTime: 206.9 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 2.14.0 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 ‘Ringo/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘Ringo’ version ‘1.17.0’
* 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 sizes of PDF files under ‘inst/doc’ ... NOTE
  ‘qpdf’ made some significant size reductions:
     compacted ‘Ringo.pdf’ from 1140Kb to 422Kb
  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/2.14/Resources/include -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include/i386  -I/usr/local/include    -fPIC  -g -O2 -c mmeansd.cpp -o mmeansd.o
g++-4.2 -arch i386 -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 mmedian.cpp -o mmedian.o
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 region_overlap.c -o region_overlap.o
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 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-2.9-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 ...
*** tangling vignette sources ...
   ‘Ringo.Rnw’ 
** testing if installed package can be loaded

* DONE (Ringo)

name	user	system	elapsed
arrayImage	0.155	0.007	0.162
asExprSet	0.470	0.010	0.481
autocorr	0.280	0.007	0.288
cherByThreshold	0.007	0.001	0.007
cherClass	0.335	0.011	0.346
chipAlongChrom	0.300	0.005	0.305
chipAlongChromOld	0.072	0.003	0.076
computeRunningMedians	0.456	0.004	0.461
compute_gc	0.001	0.000	0.001
compute_sliding_t	0.134	0.002	0.137
corrPlot	0.064	0.010	0.125
exportCherList	0.000	0.001	0.001
features2Probes	0.969	0.086	1.056
findChersOnSmoothed	0.175	0.006	0.182
ftr2xys	0.001	0.001	0.000
newCER	0.002	0.001	0.002
nonzero	0.021	0.001	0.023
plotAutocorr	0	0	0
plotBM	0.016	0.001	0.017
posToProbeAnnoEnvironment	0.058	0.004	0.062
preprocess	1.032	0.052	1.113
probeAnnoClass	0.035	0.002	0.039
qopS4	0.000	0.000	0.003
quantilesOverPositions	0.889	0.098	1.000
readNimblegen	0.132	0.005	0.137
regionoverlap	0.015	0.001	0.015
relateCERs	0.001	0.000	0.000
sigGOTable	0.000	0.000	0.001
sliding_meansd	0.003	0.001	0.003
sliding_quantile	0.016	0.001	0.017
twoGaussiansNull	0.274	0.009	0.284
upperBoundNull	0.135	0.004	0.139
validProbeAnno	0.043	0.002	0.044