Package: chipseq

Version: 1.6.0

Command: /home/hpages/test-puck5/bbs-2.10-bioc/R/bin/R CMD check --no-vignettes --timings chipseq_1.6.0.tar.gz

StartedAt: 2012-04-01 00:14:00 -0700 (Sun, 01 Apr 2012)

EndedAt: 2012-04-01 00:16:47 -0700 (Sun, 01 Apr 2012)

EllapsedTime: 167.1 seconds

RetCode: 0

Status:  OK

CheckDir: chipseq.Rcheck

Warnings: 0

* using log directory '/loc/home/hpages/test-puck5/bbs-2.10-bioc/meat/chipseq.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 'chipseq/DESCRIPTION' ... OK
* this is package 'chipseq' version '1.6.0'
* 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 'chipseq' can be installed ... OK
* checking installed package size ... OK
* 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
correlation.estimate: no visible binding for global variable 'mu'
correlation.estimate: no visible binding for global variable 'corr'
coverage.estimate: no visible binding for global variable 'mu'
coverage.estimate: no visible binding for global variable 'covered'
islandDepthPlot: no visible binding for global variable 'depth'
* 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' ... 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

NOTE: There was 1 note.
See
  '/loc/home/hpages/test-puck5/bbs-2.10-bioc/meat/chipseq.Rcheck/00check.log'
for details.

* installing *source* package 'chipseq' ...
** libs
gcc -std=gnu99 -I/home/hpages/test-puck5/bbs-2.10-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c rlesumprod.c -o rlesumprod.o
gcc -std=gnu99 -shared -L/usr/local/lib -o chipseq.so rlesumprod.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/chipseq.Rcheck/chipseq/libs
** R
** data
** inst
** preparing package for lazy loading
Warning: replacing previous import 'density' when loading 'stats'
** help
*** installing help indices
** building package indices
** installing vignettes
   'Workflow.Rnw' 
** testing if installed package can be loaded
Warning: replacing previous import 'density' when loading 'stats'

* DONE (chipseq)

name	user	system	elapsed
chipseqFilter	0.392	0.004	0.407
coverageplot	0.112	0.000	0.112
cstest	1.388	0.012	1.408
diffPeakSummary	11.229	0.096	11.358
estimate.mean.fraglen	1.416	0.016	1.442
islandDepthPlot	2.556	0.000	2.564
laneSubsample	2.336	0.004	2.354
peakCutoff	2.828	0.000	2.836
subsetSummary	1.864	0.012	1.903