BioC 2.13: CHECK report for CGHcall on perceval

Package: CGHcall

Version: 2.22.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch CGHcall_2.22.0.tar.gz

StartedAt: 2014-04-05 00:08:09 -0700 (Sat, 05 Apr 2014)

EndedAt: 2014-04-05 00:09:27 -0700 (Sat, 05 Apr 2014)

EllapsedTime: 77.4 seconds

RetCode: 0

Status:  OK

CheckDir: CGHcall.Rcheck

Warnings: 0

* using log directory ‘/Users/biocbuild/bbs-2.13-bioc/meat/CGHcall.Rcheck’
* using R version 3.0.3 (2014-03-06)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘CGHcall/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘CGHcall’ version ‘2.22.0’
* 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] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ 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 dependencies in R code ... NOTE
‘library’ or ‘require’ call to ‘snowfall’ which was already attached by Depends.
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘DNAcopy’ ‘methods’ ‘snowfall’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
‘:::’ call which should be ‘::’: ‘DNAcopy:::getbdry’
  See the note in ?`:::` about the use of this operator.
Unexported objects imported by ‘:::’ calls:
  ‘Biobase:::assayDataDims’ ‘DNAcopy:::trimmed.variance’
  See the note in ?`:::` about the use of this operator.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘.alpha0all’ ‘.assignNames’ ‘.callFromSeg’ ‘.countcl’ ‘.MakeData’
  ‘.posteriorp’ ‘.reallik4’ ‘.segFromRaw’ ‘.sumreg’ ‘.sumsqreg’
  ‘.totallik’ ‘.varproffun’ ‘.varregtimescount’
See the information on DESCRIPTION files in the chapter ‘Creating R
packages’ of the ‘Writing R Extensions’ manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... NOTE
Foreign function call to 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’ ... NOTE
  ‘qpdf’ made some significant size reductions:
     compacted ‘CGHcall.pdf’ from 617Kb to 183Kb
  consider running tools::compactPDF() on these files
* checking installed files from ‘inst/doc’ ... OK
* checking for old-style vignette sources ... NOTE
Vignette sources only in ‘inst/doc’:
  ‘CGHcall.Rnw’
A ‘vignettes’ directory will be required as from R 3.1.0
* checking examples ... [5s/6s] 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 vignette outputs ... SKIPPED
* checking PDF version of manual ... OK

NOTE: There were 6 notes.
See
  ‘/Users/biocbuild/bbs-2.13-bioc/meat/CGHcall.Rcheck/00check.log’
for details.

* installing *source* package ‘CGHcall’ ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (CGHcall)

name	user	system	elapsed
CGHcall	0.782	0.028	0.812
ExpandCGHcall	0.654	0.014	0.672
normalize	0.382	0.008	0.390
postsegnormalize	0.504	0.011	0.514
preprocess	0.090	0.011	0.100
segmentData	0.038	0.012	0.049