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CHECK report for RcisTarget on malbec2

This page was generated on 2020-10-17 11:55:32 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE RcisTarget PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1434/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
RcisTarget 1.8.0
Sara Aibar
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/RcisTarget
Branch: RELEASE_3_11
Last Commit: c80c3b2
Last Changed Date: 2020-04-27 15:13:19 -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: RcisTarget
Version: 1.8.0
Command: /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:RcisTarget.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings RcisTarget_1.8.0.tar.gz
StartedAt: 2020-10-17 04:32:45 -0400 (Sat, 17 Oct 2020)
EndedAt: 2020-10-17 04:38:06 -0400 (Sat, 17 Oct 2020)
EllapsedTime: 321.3 seconds
RetCode: 0
Status:  OK 
CheckDir: RcisTarget.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:RcisTarget.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings RcisTarget_1.8.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.11-bioc/meat/RcisTarget.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 ‘RcisTarget/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘RcisTarget’ version ‘1.8.0’
* 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 ‘RcisTarget’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is  6.6Mb
  sub-directories of 1Mb or more:
    data   4.4Mb
    doc    1.7Mb
* 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 ... NOTE
Missing or unexported object: ‘arrow::parquet_file_reader’
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                          user system elapsed
addSignificantGenes     18.774  0.659  19.268
addMotifAnnotation      17.558  0.984  17.887
getMotifAnnotation      11.212  0.088  10.573
aucScores-class         10.292  0.105  10.401
reRank                   9.980  0.028  10.008
rankingRcisTarget-class  9.417  0.072   9.489
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 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-3.11-bioc/meat/RcisTarget.Rcheck/00check.log’
for details.



Installation output

RcisTarget.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD INSTALL RcisTarget
###
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* installing to library ‘/home/biocbuild/bbs-3.11-bioc/R/library’
* installing *source* package ‘RcisTarget’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
   ‘RcisTarget.Rmd’ 
** 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 (RcisTarget)

Tests output

RcisTarget.Rcheck/tests/testthat.Rout


R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(RcisTarget)
> 
> test_check("RcisTarget")
══ testthat results  ═══════════════════════════════════════════════════════════
[ OK: 58 | SKIPPED: 0 | WARNINGS: 4 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
 43.296   3.313  45.420 

Example timings

RcisTarget.Rcheck/RcisTarget-Ex.timings

nameusersystemelapsed
RcisTarget0.1840.0040.205
addLogo0.1710.0280.200
addMotifAnnotation17.558 0.98417.887
addSignificantGenes18.774 0.65919.268
aucScores-class10.292 0.10510.401
calcAUC000
getMotifAnnotation11.212 0.08810.573
importAnnotations0.4950.0200.515
importRankings0.4800.0160.496
rankingRcisTarget-class9.4170.0729.489
reRank 9.980 0.02810.008