Package: Ringo

Version: 1.20.0

Command: /Library/Frameworks/R.framework/Versions/2.15/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch Ringo_1.20.0.tar.gz

StartedAt: 2012-09-24 01:33:44 -0700 (Mon, 24 Sep 2012)

EndedAt: 2012-09-24 01:37:37 -0700 (Mon, 24 Sep 2012)

EllapsedTime: 232.7 seconds

RetCode: 0

Status:  OK

CheckDir: Ringo.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.10-bioc/meat/Ringo.Rcheck'
* using R version 2.15.1 (2012-06-22)
* 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 '1.20.0'
* 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
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 installed files from 'inst/doc' ... NOTE
The following files should probably not be installed:
  'Makefile', 'Ringo.tex'

Consider the use of a .Rinstignore file: see 'Writing R Extensions',
or move the vignette sources from 'inst/doc' to 'vignettes'.
* 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

NOTE: There were 2 notes.
See
  '/Users/biocbuild/bbs-2.10-bioc/meat/Ringo.Rcheck/00check.log'
for details.

* installing *source* package 'Ringo' ...
** libs
*** arch - i386
g++ -arch i386 -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include/i386 -DNDEBUG  -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/2.15/Resources/include -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include/i386 -DNDEBUG  -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/2.15/Resources/include -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include/i386 -DNDEBUG  -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/2.15/Resources/include -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include/i386 -DNDEBUG  -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-2.10-bioc/meat/Ringo.Rcheck/Ringo/libs/i386
** R
** inst
** preparing package for lazy loading
Creating a generic function for 'ls' from package 'base' in package 'Ringo'
** help
*** installing help indices
** building package indices
** installing vignettes
   'Ringo.Rnw' 
** testing if installed package can be loaded

* DONE (Ringo)

name	user	system	elapsed
arrayImage	0.296	0.009	0.307
asExprSet	0.214	0.008	0.223
autocorr	0.342	0.007	0.349
cherByThreshold	0.006	0.001	0.007
cherClass	0.296	0.010	0.306
chipAlongChrom	0.412	0.005	0.417
chipAlongChromOld	0.055	0.006	0.066
computeRunningMedians	0.358	0.006	0.365
compute_gc	0.001	0.000	0.002
compute_sliding_t	0.099	0.004	0.103
corrPlot	0.055	0.007	0.061
exportCherList	0.000	0.000	0.001
features2Probes	1.149	0.070	1.219
findChersOnSmoothed	0.119	0.005	0.123
ftr2xys	0.000	0.001	0.000
newCER	0.001	0.000	0.002
nonzero	0.018	0.001	0.018
plotAutocorr	0.000	0.000	0.001
plotBM	0.018	0.002	0.020
posToProbeAnnoEnvironment	0.039	0.004	0.043
preprocess	0.880	0.073	0.956
probeAnnoClass	0.027	0.003	0.029
qopS4	0	0	0
quantilesOverPositions	0.784	0.088	0.882
readNimblegen	0.130	0.007	0.138
regionoverlap	0.013	0.001	0.015
relateCERs	0.000	0.000	0.001
sigGOTable	0.000	0.001	0.000
sliding_meansd	0.003	0.000	0.003
sliding_quantile	0.017	0.002	0.019
twoGaussiansNull	0.300	0.019	0.319
upperBoundNull	0.136	0.004	0.140
validProbeAnno	0.040	0.004	0.043