Package: Ringo

Version: 1.18.0

Command: E:\biocbld\bbs-2.9-bioc\R\bin\R.exe CMD check --no-vignettes --timings --no-multiarch Ringo_1.18.0.tar.gz

StartedAt: 2012-01-09 05:16:30 -0800 (Mon, 09 Jan 2012)

EndedAt: 2012-01-09 05:19:07 -0800 (Mon, 09 Jan 2012)

EllapsedTime: 156.7 seconds

RetCode: 0

Status:  OK

CheckDir: Ringo.Rcheck

Warnings: 0

* using log directory 'E:/biocbld/bbs-2.9-bioc/meat/Ringo.Rcheck'
* using R version 2.14.1 (2011-12-22)
* using platform: i386-pc-mingw32 (32-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 '1.18.0'
* 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 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 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
File 'Ringo/R/zzz.R':
  .onAttach calls:
    require(Biobase)

Package startup functions should not change the search path.
See section 'Good practice' in ?.onAttach.

exportCherList: no visible global function definition for 'IRanges'
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 compiled code ... 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"E:/biocbld/BBS-2˜1.9-B/R/include"          -O2 -Wall  -mtune=core2 -c mmeansd.cpp -o mmeansd.o
g++  -I"E:/biocbld/BBS-2˜1.9-B/R/include"          -O2 -Wall  -mtune=core2 -c mmedian.cpp -o mmedian.o
gcc  -I"E:/biocbld/BBS-2˜1.9-B/R/include"          -O3 -Wall  -std=gnu99 -mtune=core2 -c region_overlap.c -o region_overlap.o
gcc  -I"E:/biocbld/BBS-2˜1.9-B/R/include"          -O3 -Wall  -std=gnu99 -mtune=core2 -c ringo_init.c -o ringo_init.o
g++ -shared -s -static-libgcc -o Ringo.dll tmp.def mmeansd.o mmedian.o region_overlap.o ringo_init.o -LE:/biocbld/BBS-2˜1.9-B/R/bin/i386 -lR
installing to E:/biocbld/bbs-2.9-bioc/meat/Ringo.Rcheck/Ringo/libs/i386
** R
** inst
** preparing package for lazy loading
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	0.12	0.02	0.14
asExprSet	0.39	0.00	0.39
autocorr	0.11	0.00	0.11
cherByThreshold	0	0	0
cherClass	0.39	0.01	0.41
chipAlongChrom	0.41	0.00	0.41
chipAlongChromOld	0.04	0.00	0.04
computeRunningMedians	0.24	0.00	0.24
compute_gc	0	0	0
compute_sliding_t	0.06	0.00	0.06
corrPlot	0.04	0.00	0.09
exportCherList	0	0	0
features2Probes	1.19	0.00	1.19
findChersOnSmoothed	0.11	0.00	0.11
ftr2xys	0	0	0
newCER	0	0	0
nonzero	0.02	0.00	0.03
plotAutocorr	0	0	0
plotBM	0.01	0.00	0.01
posToProbeAnnoEnvironment	0.05	0.00	0.05
preprocess	0.76	0.00	0.78
probeAnnoClass	0.02	0.02	0.03
qopS4	0	0	0
quantilesOverPositions	0.61	0.03	0.64
readNimblegen	0.09	0.00	0.10
regionoverlap	0.02	0.00	0.01
relateCERs	0	0	0
sigGOTable	0	0	0
sliding_meansd	0	0	0
sliding_quantile	0.03	0.00	0.03
twoGaussiansNull	0.47	0.00	0.47
upperBoundNull	0.06	0.00	0.06
validProbeAnno	0.03	0.00	0.04