Package: REDseq

Version: 1.2.0

Command: /Library/Frameworks/R.framework/Versions/2.15/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch REDseq_1.2.0.tar.gz

StartedAt: 2012-09-24 01:30:33 -0700 (Mon, 24 Sep 2012)

EndedAt: 2012-09-24 01:34:51 -0700 (Mon, 24 Sep 2012)

EllapsedTime: 258.0 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: REDseq.Rcheck

Warnings: 1

* using log directory '/Users/biocbuild/bbs-2.10-bioc/meat/REDseq.Rcheck'
* using R version 2.15.1 (2012-06-22)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'REDseq/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'REDseq' version '1.2.0'
* 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 'REDseq' 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 ... 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 sizes of PDF files under 'inst/doc' ... OK
* checking installed files from 'inst/doc' ... OK
* checking examples ... WARNING
Found the following significant warnings:

  Warning: 'matchMatrix' is deprecated.
  Warning: 'matchMatrix' is deprecated.
  Warning: 'matchMatrix' is deprecated.
  Warning: 'matchMatrix' is deprecated.
  Warning: 'matchMatrix' is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
* 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

WARNING: There was 1 warning.
See
  '/Users/biocbuild/bbs-2.10-bioc/meat/REDseq.Rcheck/00check.log'
for details.

* installing *source* package 'REDseq' ...
** R
** data
** inst
** preparing package for lazy loading
Warning: replacing previous import 'space' when loading 'IRanges'
** help
*** installing help indices
** building package indices
** installing vignettes
   'REDseq.Rnw' 
** testing if installed package can be loaded
Warning: replacing previous import 'space' when loading 'IRanges'

* DONE (REDseq)

name	user	system	elapsed
REDseq-package	0.005	0.001	0.004
assignSeq2REsite	1.199	0.013	1.313
binom.test.REDseq	0.016	0.000	0.016
buildREmap	7.832	0.495	9.743
compareREDseq	0.024	0.001	0.026
distanceHistSeq2RE	0.019	0.002	0.022
example.REDseq	0.003	0.001	0.004
example.assignedREDseq	0.004	0.001	0.005
example.map	0.003	0.001	0.004
plotCutDistribution	0.034	0.002	0.038
searchPattern	3.783	0.288	4.116
summarizeByRE	0.007	0.001	0.008
summarizeBySeq	0.007	0.001	0.008
writeHits	0.009	0.001	0.009