Package: Ringo

Version: 1.23.1

Command: /home/biocbuild/bbs-2.12-bioc/R/bin/R CMD check --no-vignettes --timings Ringo_1.23.1.tar.gz

StartedAt: 2013-01-16 05:54:48 -0800 (Wed, 16 Jan 2013)

EndedAt: 2013-01-16 05:58:58 -0800 (Wed, 16 Jan 2013)

EllapsedTime: 250.8 seconds

RetCode: 0

Status:  OK

CheckDir: Ringo.Rcheck

Warnings: 0

* using log directory ‘/loc/home/biocbuild/bbs-2.12-bioc/meat/Ringo.Rcheck’
* using R Under development (unstable) (2012-12-17 r61365)
* 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 ‘1.23.1’
* 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 for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘Ringo’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over 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
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 installed files from ‘inst/doc’ ... NOTE
The following files should probably not be installed:
  ‘Makefile’, ‘Ringo.tex’

Consider the use of a .Rinstignore file: see ‘Writing R Extensions’,
or move the vignette sources from ‘inst/doc’ to ‘vignettes’.
* 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

NOTE: There were 2 notes.
See
  ‘/loc/home/biocbuild/bbs-2.12-bioc/meat/Ringo.Rcheck/00check.log’
for details.

* installing *source* package ‘Ringo’ ...
** libs
g++ -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c mmeansd.cpp -o mmeansd.o
g++ -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c mmedian.cpp -o mmedian.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c region_overlap.c -o region_overlap.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -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-2.12-bioc/R/lib -lR
installing to /loc/home/biocbuild/bbs-2.12-bioc/meat/Ringo.Rcheck/Ringo/libs
** R
** inst
** preparing package for lazy loading
Creating a generic function for ‘ls’ from package ‘base’ in package ‘Ringo’
** help
*** installing help indices
** building package indices
** installing vignettes
   ‘Ringo.Rnw’ 
** testing if installed package can be loaded

* DONE (Ringo)

name	user	system	elapsed
arrayImage	0.536	0.004	0.541
asExprSet	0.624	0.016	0.639
autocorr	0.116	0.012	0.129
cherByThreshold	0.020	0.004	0.025
cherClass	0.244	0.004	0.250
chipAlongChrom	0.628	0.016	0.645
chipAlongChromOld	0.064	0.004	0.068
computeRunningMedians	0.320	0.008	0.328
compute_gc	0.008	0.004	0.012
compute_sliding_t	0.100	0.000	0.105
corrPlot	0.028	0.012	0.060
exportCherList	0.008	0.000	0.010
features2Probes	2.637	0.052	2.691
findChersOnSmoothed	0.108	0.016	0.125
ftr2xys	0.000	0.004	0.004
newCER	0.008	0.000	0.006
nonzero	0.020	0.000	0.022
plotAutocorr	0.004	0.000	0.004
plotBM	0.020	0.000	0.018
posToProbeAnnoEnvironment	0.048	0.008	0.056
preprocess	0.308	0.004	0.312
probeAnnoClass	0.04	0.00	0.04
qopS4	0.004	0.000	0.004
quantilesOverPositions	1.852	0.036	1.890
readNimblegen	0.076	0.008	0.086
regionoverlap	0.008	0.004	0.013
relateCERs	0.004	0.000	0.003
sigGOTable	0.008	0.000	0.005
sliding_meansd	0.012	0.000	0.014
sliding_quantile	0.02	0.00	0.02
twoGaussiansNull	0.188	0.004	0.197
upperBoundNull	0.088	0.000	0.086
validProbeAnno	0.032	0.000	0.035