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CHECK report for zFPKM on merida1

This page was generated on 2019-04-16 12:00:52 -0400 (Tue, 16 Apr 2019).

Package 1647/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
zFPKM 1.4.1
Ron Ammar
Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019)
URL: https://git.bioconductor.org/packages/zFPKM
Branch: RELEASE_3_8
Last Commit: e1c2a03
Last Changed Date: 2019-01-04 13:18:32 -0400 (Fri, 04 Jan 2019)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: zFPKM
Version: 1.4.1
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:zFPKM.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings zFPKM_1.4.1.tar.gz
StartedAt: 2019-04-16 03:25:35 -0400 (Tue, 16 Apr 2019)
EndedAt: 2019-04-16 03:27:41 -0400 (Tue, 16 Apr 2019)
EllapsedTime: 125.3 seconds
RetCode: 0
Status:  OK 
CheckDir: zFPKM.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:zFPKM.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings zFPKM_1.4.1.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/zFPKM.Rcheck’
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘zFPKM/DESCRIPTION’ ... OK
* this is package ‘zFPKM’ version ‘1.4.1’
* 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 ‘zFPKM’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* 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
PlotGaussianFitDF: no visible global function definition for ‘dnorm’
PlotGaussianFitDF: no visible binding for global variable ‘density’
PlotGaussianFitDF: no visible binding for global variable ‘log2fpkm’
PlotGaussianFitDF: no visible binding for global variable ‘sample_name’
zFPKMCalc: no visible global function definition for ‘density’
zFPKMTransform: no visible global function definition for ‘is’
Undefined global functions or variables:
  density dnorm is log2fpkm sample_name
Consider adding
  importFrom("methods", "is")
  importFrom("stats", "density", "dnorm")
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 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: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.8-bioc/meat/zFPKM.Rcheck/00check.log’
for details.



Installation output

zFPKM.Rcheck/00install.out

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL zFPKM
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘zFPKM’ ...
** R
** 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 (zFPKM)

Tests output


Example timings

zFPKM.Rcheck/zFPKM-Ex.timings

nameusersystemelapsed
zFPKM0.3500.0230.885
zFPKMPlot1.3630.0502.346