Package: Ringo

Version: 1.17.1

Command: D:\biocbld\bbs-2.9-bioc\R\bin\R.exe CMD check --no-vignettes --timings --no-multiarch Ringo_1.17.1.tar.gz

StartedAt: 2011-07-07 06:04:40 -0700 (Thu, 07 Jul 2011)

EndedAt: 2011-07-07 06:07:01 -0700 (Thu, 07 Jul 2011)

EllapsedTime: 141.5 seconds

RetCode: 0

Status:  OK

CheckDir: Ringo.Rcheck

Warnings: 0

* using log directory 'D:/biocbld/bbs-2.9-bioc/meat/Ringo.Rcheck'
* using R version 2.14.0 Under development (unstable) (2011-06-03 r56036)
* using platform: x86_64-pc-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'Ringo/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'Ringo' version '1.17.1'
* 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 installed package size ... OK
* checking package directory ... OK
* checking for portable file names ... 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
x86_64-w64-mingw32-g++  -I"D:/biocbld/BBS-2˜1.9-B/R/include"          -O2 -Wall  -c mmeansd.cpp -o mmeansd.o
x86_64-w64-mingw32-g++  -I"D:/biocbld/BBS-2˜1.9-B/R/include"          -O2 -Wall  -c mmedian.cpp -o mmedian.o
x86_64-w64-mingw32-gcc  -I"D:/biocbld/BBS-2˜1.9-B/R/include"          -O2 -Wall  -std=gnu99 -c region_overlap.c -o region_overlap.o
x86_64-w64-mingw32-gcc  -I"D:/biocbld/BBS-2˜1.9-B/R/include"          -O2 -Wall  -std=gnu99 -c ringo_init.c -o ringo_init.o
x86_64-w64-mingw32-g++ -shared -s -static-libgcc -o Ringo.dll tmp.def mmeansd.o mmedian.o region_overlap.o ringo_init.o -LD:/biocbld/BBS-2˜1.9-B/R/bin/x64 -lR
installing to D:/biocbld/bbs-2.9-bioc/meat/Ringo.Rcheck/Ringo/libs/x64
** 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 generic function for "plot" from package "graphics" in package "Ringo"
Creating a generic function for "get" from package "base" in package "Ringo"
Creating a generic function for "ls" from package "base" in package "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	0.16	0.00	0.15
asExprSet	0.40	0.00	0.41
autocorr	0.30	0.00	0.29
cherByThreshold	0	0	0
cherClass	0.23	0.00	0.24
chipAlongChrom	0.22	0.00	0.22
chipAlongChromOld	0.06	0.00	0.06
computeRunningMedians	0.32	0.00	0.31
compute_gc	0	0	0
compute_sliding_t	0.09	0.00	0.10
corrPlot	0.05	0.00	0.04
exportCherList	0	0	0
features2Probes	1.16	0.01	1.17
findChersOnSmoothed	0.12	0.00	0.12
ftr2xys	0	0	0
newCER	0	0	0
nonzero	0.02	0.00	0.02
plotAutocorr	0	0	0
plotBM	0.01	0.00	0.01
posToProbeAnnoEnvironment	0.24	0.02	0.25
preprocess	0.57	0.04	0.63
probeAnnoClass	0.04	0.00	0.03
qopS4	0	0	0
quantilesOverPositions	0.76	0.02	0.78
readNimblegen	0.11	0.00	0.11
regionoverlap	0	0	0
relateCERs	0	0	0
sigGOTable	0	0	0
sliding_meansd	0	0	0
sliding_quantile	0.01	0.00	0.01
twoGaussiansNull	0.22	0.00	0.24
upperBoundNull	0.09	0.00	0.09
validProbeAnno	0.02	0.02	0.03