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CHECK report for CGHcall on merida2

This page was generated on 2019-04-09 13:23:56 -0400 (Tue, 09 Apr 2019).

Package 237/1703HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CGHcall 2.45.0
Mark van de Wiel
Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019)
URL: https://git.bioconductor.org/packages/CGHcall
Branch: master
Last Commit: 6d1aadb
Last Changed Date: 2018-10-30 11:54:27 -0400 (Tue, 30 Oct 2018)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK 

Summary

Package: CGHcall
Version: 2.45.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:CGHcall.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings CGHcall_2.45.0.tar.gz
StartedAt: 2019-04-08 23:46:46 -0400 (Mon, 08 Apr 2019)
EndedAt: 2019-04-08 23:47:31 -0400 (Mon, 08 Apr 2019)
EllapsedTime: 44.3 seconds
RetCode: 0
Status:  OK 
CheckDir: CGHcall.Rcheck
Warnings: 0

Command output

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:CGHcall.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings CGHcall_2.45.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/CGHcall.Rcheck’
* using R Under development (unstable) (2018-11-27 r75683)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘2.45.0’
* 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 ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Title field: should not end in a period.
Non-standard license specification:
  GPL (http://www.gnu.org/copyleft/gpl.html)
Standardizable: FALSE
* 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
.callFromSeg: no visible global function definition for ‘new’
.changepoints.sdundo2 : <anonymous>: no visible global function
  definition for ‘median’
.changepoints2: no visible global function definition for ‘mad’
.changepoints2: no visible global function definition for
  ‘changepoints.prune’
.makeEmptyFeatureData: no visible global function definition for ‘is’
.makeEmptyFeatureData: no visible global function definition for ‘new’
.profreg: no visible binding for global variable ‘profile’
.segFromRaw: no visible global function definition for ‘new’
.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’
.varregtimescount: no visible global function definition for ‘var’
CGHcall: no visible global function definition for ‘mad’
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 ‘optim’
CGHcall: no visible global function definition for ‘sfRemoveAll’
CGHcall: no visible global function definition for ‘sfStop’
ExpandCGHcall: no visible global function definition for ‘new’
normalize: no visible global function definition for ‘median’
postsegnormalize: no visible global function definition for ‘median’
Undefined global functions or variables:
  changepoints.prune default.DNAcopy.bdry is mad median new optim
  profile sfExport sfInit sfLibrary sfRemoveAll sfSapply sfStop var
Consider adding
  importFrom("methods", "is", "new")
  importFrom("stats", "mad", "median", "optim", "profile", "var")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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 files in ‘vignettes’ ... 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 vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 4 NOTEs
See
  ‘/Users/biocbuild/bbs-3.9-bioc/meat/CGHcall.Rcheck/00check.log’
for details.



Installation output

CGHcall.Rcheck/00install.out

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL CGHcall
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘CGHcall’ ...
** R
** data
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (CGHcall)

Tests output


Example timings

CGHcall.Rcheck/CGHcall-Ex.timings

nameusersystemelapsed
CGHcall0.2830.0200.307
ExpandCGHcall0.2110.0150.227
normalize0.1580.0150.176
postsegnormalize0.1970.0120.212
preprocess0.0440.0030.047
segmentData0.0230.0020.025