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BioC 3.0: CHECK report for CGHcall on oaxaca

This page was generated on 2015-04-10 10:02:38 -0700 (Fri, 10 Apr 2015).

Package 137/933HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CGHcall 2.28.0
Mark van de Wiel
Snapshot Date: 2015-04-09 16:20:12 -0700 (Thu, 09 Apr 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_0/madman/Rpacks/CGHcall
Last Changed Rev: 95439 / Revision: 102249
Last Changed Date: 2014-10-13 14:38:33 -0700 (Mon, 13 Oct 2014)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  OK  OK  OK 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK  OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  OK  OK 
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  OK  OK [ OK ] OK 

Summary

Package: CGHcall
Version: 2.28.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch CGHcall_2.28.0.tar.gz
StartedAt: 2015-04-09 22:04:29 -0700 (Thu, 09 Apr 2015)
EndedAt: 2015-04-09 22:05:34 -0700 (Thu, 09 Apr 2015)
EllapsedTime: 64.8 seconds
RetCode: 0
Status:  OK 
CheckDir: CGHcall.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch CGHcall_2.28.0.tar.gz
###
##############################################################################
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* using log directory ‘/Users/biocbuild/bbs-3.0-bioc/meat/CGHcall.Rcheck’
* using R version 3.1.3 (2015-03-09)
* using platform: x86_64-apple-darwin13.4.0 (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 ‘2.28.0’
* 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 ... [5s/5s] 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:
  ‘.MakeData’ ‘.alpha0all’ ‘.assignNames’ ‘.callFromSeg’ ‘.countcl’
  ‘.posteriorp’ ‘.reallik4’ ‘.segFromRaw’ ‘.sumreg’ ‘.sumsqreg’
  ‘.totallik’ ‘.varproffun’ ‘.varregtimescount’
* 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 chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
* checking R code for possible problems ... NOTE
.changepoints2: no visible global function definition for
  ‘changepoints.prune’
.segment2: no visible binding for global variable
  ‘default.DNAcopy.bdry’
.totallik: no visible global function definition for ‘sfExport’
.totallik: no visible global function definition for ‘sfSapply’
CGHcall: no visible global function definition for ‘sfInit’
CGHcall: no visible global function definition for ‘sfLibrary’
CGHcall: no visible global function definition for ‘sfExport’
CGHcall: no visible global function definition for ‘sfRemoveAll’
CGHcall: no visible global function definition for ‘sfStop’
* 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 files in ‘vignettes’ ... OK
* checking examples ... [4s/4s] 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
* DONE

NOTE: There were 4 notes.
See
  ‘/Users/biocbuild/bbs-3.0-bioc/meat/CGHcall.Rcheck/00check.log’
for details.

CGHcall.Rcheck/00install.out:

* 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)

CGHcall.Rcheck/CGHcall-Ex.timings:

nameusersystemelapsed
CGHcall0.4990.0150.516
ExpandCGHcall0.4280.0080.446
normalize0.4280.0040.467
postsegnormalize0.4280.0050.455
preprocess0.0680.0050.095
segmentData0.0260.0040.050