Package: tilingArray

Version: 1.32.0

Command: /home/biocbuild/bbs-2.9-bioc/R/bin/R CMD check --no-vignettes --timings tilingArray_1.32.0.tar.gz

StartedAt: 2012-03-24 03:01:29 -0700 (Sat, 24 Mar 2012)

EndedAt: 2012-03-24 03:03:38 -0700 (Sat, 24 Mar 2012)

EllapsedTime: 129.1 seconds

RetCode: 0

Status:  OK

CheckDir: tilingArray.Rcheck

Warnings: 0

* using log directory ‘/loc/home/biocbuild/bbs-2.9-bioc/meat/tilingArray.Rcheck’
* using R version 2.14.2 (2012-02-29)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘tilingArray/DESCRIPTION’ ... OK
* this is package ‘tilingArray’ version ‘1.32.0’
* 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 ‘tilingArray’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is  7.5Mb
  sub-directories of 1Mb or more:
    doc       3.9Mb
    scripts   3.1Mb
* 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 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 ‘tilingArray/R/zzz.R’:
  .onLoad calls:
    require("methods")

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

* 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 ... NOTE
S3 methods shown with full name in documentation object 'breakpointsPretend':
  ‘residuals.breakpointsPretend’

The \usage entries for S3 methods should use the \method markup and not
their full name.
See the chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... 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 ‘tilingArray’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c findsegments.c -o findsegments.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c sampleStep.c -o sampleStep.o
gcc -std=gnu99 -shared -L/usr/local/lib64 -o tilingArray.so findsegments.o sampleStep.o -L/home/biocbuild/bbs-2.9-bioc/R/lib -lR
installing to /loc/home/biocbuild/bbs-2.9-bioc/meat/tilingArray.Rcheck/tilingArray/libs
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices ...
*** tangling vignette sources ...
   ‘assessNorm.Rnw’ 
   ‘costMatrix.Rnw’ 
   ‘findsegments.Rnw’ 
   ‘plotAlongChrom.Rnw’ 
   ‘segmentation.Rnw’ 
** testing if installed package can be loaded

* DONE (tilingArray)

name	user	system	elapsed
PMindex	0	0	0
class-segmentation	0.292	0.004	0.301
comparisonPlot	0	0	0
costMatrix	0.060	0.004	0.064
findsegments	0.000	0.000	0.001
gffSub	0.372	0.008	0.383
normalizeByReference	0.000	0.000	0.001
otherStrand	0.000	0.000	0.001
plotAlongChrom	0.260	0.000	0.264
plotAlongChromLegend	0	0	0
plotSegmentationHeatmap	0.368	0.000	0.369
plotpenLL	0.036	0.000	0.035
posMin	0	0	0
qcPlots	0.000	0.000	0.001
readCel2eSet	0	0	0
sampleStep	0.000	0.004	0.000
segChrom	0	0	0
segment	0.000	0.000	0.002
segnf	0.112	0.000	0.113