Package: Ringo

Version: 1.12.0

Command: /Library/Frameworks/R.framework/Versions/2.11/Resources/bin/R CMD check --no-vignettes --timings Ringo_1.12.0.tar.gz

StartedAt: 2010-10-04 18:28:38 -0700 (Mon, 04 Oct 2010)

EndedAt: 2010-10-04 18:30:55 -0700 (Mon, 04 Oct 2010)

EllapsedTime: 137.1 seconds

RetCode: 0

Status:  OK

CheckDir: Ringo.Rcheck

Warnings: 0

* checking for working pdflatex ... OK
* using log directory '/Users/biocbuild/bbs-2.6-bioc/meat/Ringo.Rcheck'
* using R version 2.11.1 Patched (2010-05-31 r52167)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'Ringo/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'Ringo' version '1.12.0'
* 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 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 line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking for portable use of $BLAS_LIBS ... OK
* checking examples ... OK
* checking package vignettes in 'inst/doc' ... SKIPPED
* checking PDF version of manual ... OK

* install options are ' --no-html'

* installing *source* package ‘Ringo’ ...
** libs
*** arch - i386
g++ -arch i386 -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include -I/Library/Frameworks/R.framework/Versions/2.11/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/2.11/Resources/include -I/Library/Frameworks/R.framework/Versions/2.11/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/2.11/Resources/include -I/Library/Frameworks/R.framework/Versions/2.11/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/2.11/Resources/include -I/Library/Frameworks/R.framework/Versions/2.11/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-2.6-bioc/meat/Ringo.Rcheck/Ringo/libs/i386
*** arch - ppc
g++ -arch ppc -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include/ppc  -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks -c mmeansd.cpp -o mmeansd.o
g++ -arch ppc -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include/ppc  -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks -c mmedian.cpp -o mmedian.o
gcc -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include/ppc  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic -c region_overlap.c -o region_overlap.o
gcc -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include/ppc  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic -c ringo_init.c -o ringo_init.o
g++ -arch ppc -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-2.6-bioc/meat/Ringo.Rcheck/Ringo/libs/ppc
*** arch - x86_64
g++ -arch x86_64 -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include/x86_64  -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks -c mmeansd.cpp -o mmeansd.o
g++ -arch x86_64 -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include/x86_64  -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks -c mmedian.cpp -o mmedian.o
gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include/x86_64  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic -c region_overlap.c -o region_overlap.o
gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include/x86_64  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic -c ringo_init.c -o ringo_init.o
g++ -arch x86_64 -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-2.6-bioc/meat/Ringo.Rcheck/Ringo/libs/x86_64
** R
** inst
** preparing package for lazy loading

Welcome to Bioconductor

  Vignettes contain introductory material. To view, type
  'openVignette()'. 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	0.293	0.009	0.302
asExprSet	0.516	0.010	0.528
autocorr	0.158	0.008	0.166
cherByThreshold	0.006	0.000	0.007
cherClass	0.379	0.006	0.387
chipAlongChrom	0.451	0.008	0.464
chipAlongChromOld	0.069	0.004	0.073
computeRunningMedians	0.573	0.005	0.579
compute_gc	0.001	0.000	0.001
compute_sliding_t	0.155	0.003	0.158
corrPlot	0.057	0.006	0.075
exportCherList	0.000	0.000	0.001
features2Probes	0.986	0.102	1.105
findChersOnSmoothed	0.341	0.019	0.359
ftr2xys	0.001	0.000	0.000
newCER	0.003	0.000	0.003
nonzero	0.025	0.002	0.033
plotAutocorr	0	0	0
plotBM	0.019	0.001	0.025
posToProbeAnnoEnvironment	0.065	0.004	0.069
preprocess	1.075	0.039	1.147
probeAnnoClass	0.039	0.002	0.040
qopS4	0	0	0
quantilesOverPositions	0.802	0.096	0.906
readNimblegen	0.290	0.016	0.307
regionoverlap	0.018	0.000	0.019
relateCERs	0.001	0.000	0.001
sigGOTable	0.001	0.000	0.000
sliding_meansd	0.003	0.001	0.004
sliding_quantile	0.017	0.001	0.018
twoGaussiansNull	0.322	0.008	0.364
upperBoundNull	0.153	0.003	0.155
validProbeAnno	0.042	0.002	0.045