Package: Ringo

Version: 1.17.0

Command: /home/biocbuild/bbs-2.9-bioc/R/bin/R CMD check --no-vignettes --timings Ringo_1.17.0.tar.gz

StartedAt: 2011-05-09 13:57:40 -0700 (Mon, 09 May 2011)

EndedAt: 2011-05-09 14:00:07 -0700 (Mon, 09 May 2011)

EllapsedTime: 146.5 seconds

RetCode: 0

Status:  OK

CheckDir: Ringo.Rcheck

Warnings: 0

* using log directory ‘/loc/home/biocbuild/bbs-2.9-bioc/meat/Ringo.Rcheck’
* using R version 2.14.0 Under development (unstable) (2011-04-18 r55504)
* using platform: x86_64-unknown-linux-gnu (64-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 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
g++ -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c mmeansd.cpp -o mmeansd.o
g++ -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c mmedian.cpp -o mmedian.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c region_overlap.c -o region_overlap.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c ringo_init.c -o ringo_init.o
g++ -shared -L/usr/local/lib64 -o Ringo.so mmeansd.o mmedian.o region_overlap.o ringo_init.o -L/home/biocbuild/bbs-2.9-bioc/R/lib -lR
installing to /loc/home/biocbuild/bbs-2.9-bioc/meat/Ringo.Rcheck/Ringo/libs
** 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	0.088	0.008	0.097
asExprSet	0.432	0.004	0.437
autocorr	0.288	0.012	0.298
cherByThreshold	0.004	0.000	0.005
cherClass	0.228	0.004	0.508
chipAlongChrom	0.196	0.000	0.195
chipAlongChromOld	0.048	0.000	0.048
computeRunningMedians	0.276	0.000	0.277
compute_gc	0	0	0
compute_sliding_t	0.080	0.004	0.085
corrPlot	0.024	0.004	0.044
exportCherList	0	0	0
features2Probes	1.148	0.052	1.199
findChersOnSmoothed	0.100	0.004	0.106
ftr2xys	0	0	0
newCER	0.000	0.000	0.001
nonzero	0.012	0.000	0.012
plotAutocorr	0	0	0
plotBM	0.012	0.000	0.011
posToProbeAnnoEnvironment	0.240	0.008	0.248
preprocess	0.536	0.024	0.561
probeAnnoClass	0.028	0.000	0.028
qopS4	0	0	0
quantilesOverPositions	0.612	0.044	0.656
readNimblegen	0.072	0.004	0.076
regionoverlap	0.008	0.000	0.008
relateCERs	0	0	0
sigGOTable	0	0	0
sliding_meansd	0.004	0.000	0.001
sliding_quantile	0.012	0.000	0.012
twoGaussiansNull	0.176	0.004	0.178
upperBoundNull	0.072	0.008	0.079
validProbeAnno	0.024	0.000	0.022