Package: CGHcall

Version: 2.19.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch CGHcall_2.19.0.tar.gz

StartedAt: 2013-03-25 01:40:05 -0700 (Mon, 25 Mar 2013)

EndedAt: 2013-03-25 01:41:26 -0700 (Mon, 25 Mar 2013)

EllapsedTime: 80.5 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: CGHcall.Rcheck

Warnings: 2

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/CGHcall.Rcheck'
* using R Under development (unstable) (2013-02-26 r62077)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'CGHcall/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'CGHcall' version '2.19.0'
* 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 for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package 'CGHcall' can be installed ... [7s/7s] WARNING
Found the following significant warnings:
  Warning: '.find.package' is deprecated.
  Warning: '.find.package' is deprecated.
  Warning: '.find.package' is deprecated.
  Warning: '.find.package' is deprecated.
  Warning: '.find.package' is deprecated.
  Warning: '.find.package' is deprecated.
See '/Users/biocbuild/bbs-2.12-bioc/meat/CGHcall.Rcheck/00install.out' for details.
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Non-standard license specification:
  GPL (http://www.gnu.org/copyleft/gpl.html)
Standardizable: TRUE
Standardized license specification:
  GPL
* 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 ... NOTE
Foreign function call with 'PACKAGE' argument in a different package:
  .Fortran("fndcpt", ..., PACKAGE = "DNAcopy")
See the chapter 'System and foreign language interfaces' of the
'Writing R Extensions' manual.
* checking R code for possible problems ... NOTE
.changepoints2: no visible global function definition for
  'changepoints.prune'
* 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 ... [6s/6s] WARNING
Found the following significant warnings:

  Warning: '.find.package' is deprecated.
  Warning: '.find.package' is deprecated.
  Warning: '.find.package' 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 were 2 warnings.
NOTE: There were 3 notes.
See
  '/Users/biocbuild/bbs-2.12-bioc/meat/CGHcall.Rcheck/00check.log'
for details.

* installing *source* package 'CGHcall' ...
** R
** data
** inst
** preparing package for lazy loading
Warning: '.find.package' is deprecated.
Use 'find.package' instead.
See help("Deprecated")
Warning: '.find.package' is deprecated.
Use 'find.package' instead.
See help("Deprecated")
Warning: '.find.package' is deprecated.
Use 'find.package' instead.
See help("Deprecated")
** help
*** installing help indices
** building package indices
** installing vignettes
   'CGHcall.Rnw' 
** testing if installed package can be loaded
Warning: '.find.package' is deprecated.
Use 'find.package' instead.
See help("Deprecated")
Warning: '.find.package' is deprecated.
Use 'find.package' instead.
See help("Deprecated")
Warning: '.find.package' is deprecated.
Use 'find.package' instead.
See help("Deprecated")
* DONE (CGHcall)

name	user	system	elapsed
CGHcall	0.759	0.079	0.861
ExpandCGHcall	0.424	0.056	0.480
normalize	0.462	0.062	0.526
postsegnormalize	0.524	0.069	0.594
preprocess	0.201	0.013	0.227
segmentData	0.051	0.009	0.061