Package: Ringo

Version: 1.12.0

Command: /home/biocbuild/bbs-2.6-bioc/R/bin/R CMD check --no-vignettes --timings Ringo_1.12.0.tar.gz

StartedAt: 2010-10-04 19:31:47 -0700 (Mon, 04 Oct 2010)

EndedAt: 2010-10-04 19:33:38 -0700 (Mon, 04 Oct 2010)

EllapsedTime: 111.6 seconds

RetCode: 0

Status:  OK

CheckDir: Ringo.Rcheck

Warnings: 0

* checking for working pdflatex ... OK
* using log directory '/loc/home/biocbuild/bbs-2.6-bioc/meat/Ringo.Rcheck'
* using R version 2.11.1 (2010-05-31)
* using session charset: ISO8859-1
* 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
g++ -I/home/biocbuild/bbs-2.6-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c mmeansd.cpp -o mmeansd.o
g++ -I/home/biocbuild/bbs-2.6-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c mmedian.cpp -o mmedian.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.6-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-2.6-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-2.6-bioc/R/lib -lR
installing to /loc/home/biocbuild/bbs-2.6-bioc/meat/Ringo.Rcheck/Ringo/libs
** 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	0.260	0.000	0.268
asExprSet	0.408	0.008	0.421
autocorr	0.104	0.008	0.110
cherByThreshold	0.004	0.000	0.004
cherClass	0.452	0.004	0.459
chipAlongChrom	0.212	0.000	0.215
chipAlongChromOld	0.040	0.004	0.075
computeRunningMedians	0.396	0.000	0.396
compute_gc	0.000	0.000	0.001
compute_sliding_t	0.088	0.008	0.116
corrPlot	0.036	0.004	0.068
exportCherList	0	0	0
features2Probes	1.244	0.056	1.302
findChersOnSmoothed	0.124	0.004	0.129
ftr2xys	0.000	0.000	0.001
newCER	0.000	0.000	0.002
nonzero	0.016	0.000	0.016
plotAutocorr	0	0	0
plotBM	0.012	0.000	0.012
posToProbeAnnoEnvironment	0.256	0.008	0.263
preprocess	0.612	0.016	0.694
probeAnnoClass	0.036	0.000	0.036
qopS4	0	0	0
quantilesOverPositions	0.620	0.032	0.656
readNimblegen	0.292	0.012	0.307
regionoverlap	0.012	0.000	0.012
relateCERs	0	0	0
sigGOTable	0	0	0
sliding_meansd	0.004	0.000	0.002
sliding_quantile	0.012	0.000	0.010
twoGaussiansNull	0.212	0.008	0.222
upperBoundNull	0.100	0.000	0.099
validProbeAnno	0.020	0.000	0.021