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CHECK report for oppti on malbec1

This page was generated on 2021-05-06 12:28:28 -0400 (Thu, 06 May 2021).

To the developers/maintainers of the oppti package:
Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1274/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
oppti 1.4.0  (landing page)
Abdulkadir Elmas
Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021)
URL: https://git.bioconductor.org/packages/oppti
Branch: RELEASE_3_12
Last Commit: 0014713
Last Changed Date: 2020-10-27 11:51:09 -0400 (Tue, 27 Oct 2020)
malbec1Linux (Ubuntu 18.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version exists in internal repository
tokay1Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository

Summary

Package: oppti
Version: 1.4.0
Command: /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:oppti.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings oppti_1.4.0.tar.gz
StartedAt: 2021-05-06 04:13:11 -0400 (Thu, 06 May 2021)
EndedAt: 2021-05-06 04:14:08 -0400 (Thu, 06 May 2021)
EllapsedTime: 57.3 seconds
RetCode: 0
Status:   OK  
CheckDir: oppti.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:oppti.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings oppti_1.4.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.12-bioc/meat/oppti.Rcheck’
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘oppti/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘oppti’ version ‘1.4.0’
* package encoding: UTF-8
* 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 ‘oppti’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
License components which are templates and need '+ file LICENSE':
  MIT
* 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
gqplot: no visible binding for global variable ‘variable2’
gqplot: no visible binding for global variable ‘variable1’
gqplot: no visible binding for global variable ‘cupper’
gqplot: no visible binding for global variable ‘clower’
markOut: no visible binding for global variable ‘data’
Undefined global functions or variables:
  clower cupper data variable1 variable2
Consider adding
  importFrom("utils", "data")
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 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: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.12-bioc/meat/oppti.Rcheck/00check.log’
for details.



Installation output

oppti.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD INSTALL oppti
###
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* installing to library ‘/home/biocbuild/bbs-3.12-bioc/R/library’
* installing *source* package ‘oppti’ ...
** using staged installation
** 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 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 (oppti)

Tests output


Example timings

oppti.Rcheck/oppti-Ex.timings

nameusersystemelapsed
artImpute0.0280.0000.026
clusterData0.0400.0040.045
dropMarkers0.0040.0000.005
dysReg0.1800.0000.182
markOut4.2440.0244.269
oppti0.2720.0000.271
outScores0.0200.0000.019
plotDen0.0520.0000.051
rankPerOut0.2680.0000.271
statTest0.0280.0000.032