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CHECK report for CGHnormaliter on merida1

This page was generated on 2020-08-13 11:49:21 -0400 (Thu, 13 Aug 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE CGHnormaliter PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 259/1885HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CGHnormaliter 1.43.0
Bart P.P. van Houte
Snapshot Date: 2020-08-12 14:52:00 -0400 (Wed, 12 Aug 2020)
URL: https://git.bioconductor.org/packages/CGHnormaliter
Branch: master
Last Commit: 56b60be
Last Changed Date: 2020-04-27 14:20:11 -0400 (Mon, 27 Apr 2020)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
nebbiolo1 Linux (Ubuntu 20.04.1 LTS) / x86_64  OK  OK  OK 
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
merida1 macOS 10.14.6 Mojave / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: CGHnormaliter
Version: 1.43.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:CGHnormaliter.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings CGHnormaliter_1.43.0.tar.gz
StartedAt: 2020-08-12 23:18:52 -0400 (Wed, 12 Aug 2020)
EndedAt: 2020-08-12 23:20:53 -0400 (Wed, 12 Aug 2020)
EllapsedTime: 120.4 seconds
RetCode: 0
Status:  OK 
CheckDir: CGHnormaliter.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:CGHnormaliter.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings CGHnormaliter_1.43.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.12-bioc/meat/CGHnormaliter.Rcheck’
* using R version 4.0.2 (2020-06-22)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘CGHnormaliter/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘CGHnormaliter’ version ‘1.43.0’
* 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 ‘CGHnormaliter’ 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.
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘CGHbase’ ‘CGHcall’
A package should be listed in only one of these fields.
* 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.plotMA: no visible global function definition for ‘pdf’
.plotMA: no visible global function definition for ‘palette’
.plotMA: no visible global function definition for ‘par’
.plotMA: no visible global function definition for ‘title’
.plotMA: no visible global function definition for ‘abline’
.plotMA: no visible global function definition for ‘dev.off’
.readCghRaw: no visible global function definition for ‘read.table’
.readCghRaw: no visible global function definition for ‘make_cghRaw’
.runCGHcall: no visible global function definition for ‘capture.output’
.runCGHcall: no visible global function definition for ‘ExpandCGHcall’
CGHnormaliter: no visible binding for global variable ‘segment’
CGHnormaliter: no visible global function definition for
  ‘capture.output’
CGHnormaliter: no visible global function definition for ‘normalize’
CGHnormaliter: no visible global function definition for
  ‘postsegnormalize’
CGHnormaliter.write.table: no visible global function definition for
  ‘segmented’
CGHnormaliter.write.table: no visible global function definition for
  ‘calls’
Undefined global functions or variables:
  ExpandCGHcall abline calls capture.output dev.off make_cghRaw
  normalize palette par pdf postsegnormalize read.table segment
  segmented title
Consider adding
  importFrom("grDevices", "dev.off", "palette", "pdf")
  importFrom("graphics", "abline", "par", "title")
  importFrom("utils", "capture.output", "read.table")
to your NAMESPACE file.
* 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
Examples with CPU (user + system) or elapsed time > 5s
                user system elapsed
CGHnormaliter 63.569  0.438  64.083
* 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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.12-bioc/meat/CGHnormaliter.Rcheck/00check.log’
for details.



Installation output

CGHnormaliter.Rcheck/00install.out

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL CGHnormaliter
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’
* installing *source* package ‘CGHnormaliter’ ...
** 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 (CGHnormaliter)

Tests output


Example timings

CGHnormaliter.Rcheck/CGHnormaliter-Ex.timings

nameusersystemelapsed
CGHnormaliter63.569 0.43864.083
CGHnormaliter.write.table0.2950.0060.301