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CHECK report for cqn on machv2

This page was generated on 2020-10-17 11:58:19 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE cqn PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 389/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
cqn 1.34.0
Kasper Daniel Hansen
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/cqn
Branch: RELEASE_3_11
Last Commit: f35ba91
Last Changed Date: 2020-04-27 14:25:59 -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: cqn
Version: 1.34.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:cqn.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings cqn_1.34.0.tar.gz
StartedAt: 2020-10-17 00:06:28 -0400 (Sat, 17 Oct 2020)
EndedAt: 2020-10-17 00:07:44 -0400 (Sat, 17 Oct 2020)
EllapsedTime: 75.9 seconds
RetCode: 0
Status:  OK 
CheckDir: cqn.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:cqn.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings cqn_1.34.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/cqn.Rcheck’
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘cqn/DESCRIPTION’ ... OK
* this is package ‘cqn’ version ‘1.34.0’
* 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 ‘cqn’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘splines’
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 ... NOTE
Packages in Depends field not imported from:
  ‘mclust’ ‘preprocessCore’ ‘quantreg’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
SQN2: no visible binding for global variable ‘median’
SQN2: no visible global function definition for ‘Mclust’
cqn : fixPredictor: no visible global function definition for
  ‘quantile’
cqn: no visible global function definition for ‘median’
cqn : <anonymous>: no visible global function definition for ‘rq’
cqn : <anonymous>: no visible global function definition for ‘predict’
cqn : <anonymous>: no visible global function definition for ‘coef’
cqnplot: no visible global function definition for ‘matplot’
cqnplot: no visible global function definition for ‘rug’
mix.qn: no visible global function definition for ‘ecdf’
mix.qn: no visible global function definition for ‘quantile’
norm.pickrell: no visible global function definition for ‘quantile’
norm.pickrell : <anonymous>: no visible global function definition for
  ‘smooth.spline’
norm.pickrell : <anonymous>: no visible global function definition for
  ‘predict’
Undefined global functions or variables:
  Mclust coef ecdf matplot median predict quantile rq rug smooth.spline
Consider adding
  importFrom("graphics", "matplot", "rug")
  importFrom("stats", "coef", "ecdf", "median", "predict", "quantile",
             "smooth.spline")
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
* 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: 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.11-bioc/meat/cqn.Rcheck/00check.log’
for details.



Installation output

cqn.Rcheck/00install.out

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL cqn
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’
* installing *source* package ‘cqn’ ...
** using staged installation
** R
** data
** inst
** 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 (cqn)

Tests output


Example timings

cqn.Rcheck/cqn-Ex.timings

nameusersystemelapsed
cqn3.6160.1853.802
cqnplot3.9110.1754.096