Package: Ringo

Version: 1.24.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch Ringo_1.24.0.tar.gz

StartedAt: 2013-05-01 10:17:43 -0700 (Wed, 01 May 2013)

EndedAt: 2013-05-01 10:23:00 -0700 (Wed, 01 May 2013)

EllapsedTime: 316.6 seconds

RetCode: 0

Status:  OK

CheckDir: Ringo.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/Ringo.Rcheck'
* using R version 3.0.0 Patched (2013-04-08 r62531)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'Ringo/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'Ringo' version '1.24.0'
* 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 for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package 'Ringo' can be installed ... [29s/31s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over 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
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 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 ... [24s/25s] 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-2.12-bioc/meat/Ringo.Rcheck/00check.log'
for details.

* installing *source* package 'Ringo' ...
** libs
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c mmeansd.cpp -o mmeansd.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c mmedian.cpp -o mmedian.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c region_overlap.c -o region_overlap.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c ringo_init.c -o ringo_init.o
clang++ -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -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-2.12-bioc/meat/Ringo.Rcheck/Ringo/libs
** 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
** testing if installed package can be loaded
* DONE (Ringo)

name	user	system	elapsed
arrayImage	0.594	0.015	0.614
asExprSet	0.806	0.035	0.842
autocorr	0.314	0.009	0.326
cherByThreshold	0.023	0.007	0.031
cherClass	0.339	0.018	0.361
chipAlongChrom	0.711	0.020	0.737
chipAlongChromOld	0.078	0.009	0.090
computeRunningMedians	0.435	0.027	0.462
compute_gc	0.012	0.005	0.016
compute_sliding_t	0.111	0.009	0.120
corrPlot	0.054	0.015	0.087
exportCherList	0.012	0.004	0.016
features2Probes	1.756	0.088	1.860
findChersOnSmoothed	0.165	0.021	0.185
ftr2xys	0.013	0.009	0.022
newCER	0.006	0.007	0.012
nonzero	0.030	0.012	0.042
plotAutocorr	0.002	0.004	0.006
plotBM	0.025	0.011	0.042
posToProbeAnnoEnvironment	0.513	0.017	0.532
preprocess	0.458	0.034	0.493
probeAnnoClass	0.055	0.017	0.072
qopS4	0.002	0.004	0.006
quantilesOverPositions	1.764	0.101	1.878
readNimblegen	0.184	0.009	0.194
regionoverlap	0.013	0.007	0.020
relateCERs	0.002	0.004	0.006
sigGOTable	0.004	0.007	0.011
sliding_meansd	0.013	0.012	0.024
sliding_quantile	0.025	0.012	0.037
twoGaussiansNull	0.237	0.020	0.284
upperBoundNull	0.120	0.010	0.131
validProbeAnno	0.041	0.015	0.056