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CHECK report for CGHcall on malbec2

This page was generated on 2020-10-17 11:54:32 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE CGHcall PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 265/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CGHcall 2.50.0
Mark van de Wiel
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/CGHcall
Branch: RELEASE_3_11
Last Commit: 0055950
Last Changed Date: 2020-04-27 14:15:39 -0400 (Mon, 27 Apr 2020)
malbec2 Linux (Ubuntu 18.04.4 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
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: CGHcall
Version: 2.50.0
Command: /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:CGHcall.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings CGHcall_2.50.0.tar.gz
StartedAt: 2020-10-16 23:43:04 -0400 (Fri, 16 Oct 2020)
EndedAt: 2020-10-16 23:43:51 -0400 (Fri, 16 Oct 2020)
EllapsedTime: 47.0 seconds
RetCode: 0
Status:  OK 
CheckDir: CGHcall.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:CGHcall.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings CGHcall_2.50.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.11-bioc/meat/CGHcall.Rcheck’
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-pc-linux-gnu (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 ‘2.50.0’
* 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 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
  ‘/home/biocbuild/bbs-3.11-bioc/meat/CGHcall.Rcheck/00check.log’
for details.



Installation output

CGHcall.Rcheck/00install.out

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### Running command:
###
###   /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD INSTALL CGHcall
###
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* installing to library ‘/home/biocbuild/bbs-3.11-bioc/R/library’
* installing *source* package ‘CGHcall’ ...
** using staged installation
** 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 from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (CGHcall)

Tests output


Example timings

CGHcall.Rcheck/CGHcall-Ex.timings

nameusersystemelapsed
CGHcall0.2100.0040.214
ExpandCGHcall0.1840.0060.190
normalize0.1620.0000.161
postsegnormalize0.1370.0000.137
preprocess0.050.000.05
segmentData0.0210.0000.020