Package: Ringo

Version: 1.15.1

Command: /home/biocbuild/bbs-2.8-bioc/R/bin/R CMD check --no-vignettes --timings Ringo_1.15.1.tar.gz

StartedAt: 2011-02-24 22:22:49 -0800 (Thu, 24 Feb 2011)

EndedAt: 2011-02-24 22:24:35 -0800 (Thu, 24 Feb 2011)

EllapsedTime: 106.0 seconds

RetCode: 0

Status:  OK

CheckDir: Ringo.Rcheck

Warnings: 0

* using log directory ‘/loc/home/biocbuild/bbs-2.8-bioc/meat/Ringo.Rcheck’
* using R version 2.13.0 Under development (unstable) (2011-01-10 r53950)
* 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 ‘1.15.1’
* 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 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 ... OK
* checking examples ... OK
* checking package vignettes in ‘inst/doc’ ... SKIPPED
* checking PDF version of manual ... OK

* installing *source* package ‘Ringo’ ...
** libs
g++ -I/home/biocbuild/bbs-2.8-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c mmeansd.cpp -o mmeansd.o
g++ -I/home/biocbuild/bbs-2.8-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c mmedian.cpp -o mmedian.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.8-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c region_overlap.c -o region_overlap.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.8-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -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-2.8-bioc/R/lib -lR
installing to /loc/home/biocbuild/bbs-2.8-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 ...
** testing if installed package can be loaded

* DONE (Ringo)

name	user	system	elapsed
arrayImage	0.264	0.008	0.271
asExprSet	0.408	0.004	0.412
autocorr	0.096	0.004	0.105
cherByThreshold	0.008	0.000	0.005
cherClass	0.412	0.008	0.420
chipAlongChrom	0.208	0.000	0.207
chipAlongChromOld	0.052	0.000	0.052
computeRunningMedians	0.308	0.004	0.316
compute_gc	0.004	0.000	0.000
compute_sliding_t	0.088	0.000	0.091
corrPlot	0.036	0.000	0.037
exportCherList	0	0	0
features2Probes	1.084	0.044	1.132
findChersOnSmoothed	0.316	0.004	0.320
ftr2xys	0	0	0
newCER	0.000	0.000	0.002
nonzero	0.016	0.000	0.015
plotAutocorr	0	0	0
plotBM	0.012	0.000	0.012
posToProbeAnnoEnvironment	0.04	0.00	0.04
preprocess	0.592	0.028	0.639
probeAnnoClass	0.024	0.000	0.025
qopS4	0	0	0
quantilesOverPositions	0.656	0.036	0.691
readNimblegen	0.304	0.008	0.310
regionoverlap	0.008	0.000	0.010
relateCERs	0	0	0
sigGOTable	0.000	0.000	0.001
sliding_meansd	0.000	0.000	0.002
sliding_quantile	0.012	0.000	0.014
twoGaussiansNull	0.184	0.004	0.186
upperBoundNull	0.092	0.000	0.092
validProbeAnno	0.016	0.004	0.021