Package: tilingArray

Version: 1.34.0

Command: /home/hpages/test-puck5/bbs-2.10-bioc/R/bin/R CMD check --no-vignettes --timings tilingArray_1.34.0.tar.gz

StartedAt: 2012-04-01 03:42:54 -0700 (Sun, 01 Apr 2012)

EndedAt: 2012-04-01 03:44:41 -0700 (Sun, 01 Apr 2012)

EllapsedTime: 106.3 seconds

RetCode: 0

Status:  OK

CheckDir: tilingArray.Rcheck

Warnings: 0

* using log directory '/loc/home/hpages/test-puck5/bbs-2.10-bioc/meat/tilingArray.Rcheck'
* using R version 2.15.0 RC (2012-03-22 r58802)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'tilingArray/DESCRIPTION' ... OK
* this is package 'tilingArray' version '1.34.0'
* 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 ... OK
* 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 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 installed files from 'inst/doc' ... NOTE
The following files should probably not be installed:
  'Makefile'

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/hpages/test-puck5/bbs-2.10-bioc/meat/tilingArray.Rcheck/00check.log'
for details.

* installing *source* package 'tilingArray' ...
** libs
gcc -std=gnu99 -I/home/hpages/test-puck5/bbs-2.10-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c findsegments.c -o findsegments.o
gcc -std=gnu99 -I/home/hpages/test-puck5/bbs-2.10-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c sampleStep.c -o sampleStep.o
gcc -std=gnu99 -shared -L/usr/local/lib -o tilingArray.so findsegments.o sampleStep.o -L/home/hpages/test-puck5/bbs-2.10-bioc/R/lib -lR
installing to /loc/home/hpages/test-puck5/bbs-2.10-bioc/meat/tilingArray.Rcheck/tilingArray/libs
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
   '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	0.056	0.000	0.057
comparisonPlot	0	0	0
costMatrix	0.060	0.000	0.062
findsegments	0.004	0.000	0.000
gffSub	0.240	0.004	0.259
normalizeByReference	0	0	0
otherStrand	0	0	0
plotAlongChrom	0.200	0.004	0.221
plotAlongChromLegend	0	0	0
plotSegmentationHeatmap	0.092	0.000	0.099
plotpenLL	0.028	0.000	0.031
posMin	0	0	0
qcPlots	0	0	0
readCel2eSet	0.000	0.000	0.001
sampleStep	0.000	0.000	0.001
segChrom	0.004	0.000	0.000
segment	0.000	0.000	0.001
segnf	0.324	0.008	0.345