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This page was generated on 2021-10-15 15:05:50 -0400 (Fri, 15 Oct 2021).

CHECK results for RcisTarget on nebbiolo1

To the developers/maintainers of the RcisTarget package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/RcisTarget.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1520/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
RcisTarget 1.12.0  (landing page)
Sara Aibar
Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021)
git_url: https://git.bioconductor.org/packages/RcisTarget
git_branch: RELEASE_3_13
git_last_commit: da8bb0d
git_last_commit_date: 2021-05-19 12:32:51 -0400 (Wed, 19 May 2021)
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

Package: RcisTarget
Version: 1.12.0
Command: /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:RcisTarget.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings RcisTarget_1.12.0.tar.gz
StartedAt: 2021-10-14 11:15:00 -0400 (Thu, 14 Oct 2021)
EndedAt: 2021-10-14 11:20:13 -0400 (Thu, 14 Oct 2021)
EllapsedTime: 313.1 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: RcisTarget.Rcheck
Warnings: 1

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:RcisTarget.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings RcisTarget_1.12.0.tar.gz
###
##############################################################################
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* using log directory ‘/home/biocbuild/bbs-3.13-bioc/meat/RcisTarget.Rcheck’
* using R version 4.1.1 (2021-08-10)
* 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 ‘1.12.0’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Package which this enhances but not available for checking: ‘doMC’
* 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  8.9Mb
  sub-directories of 1Mb or more:
    data   8.3Mb
* 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
Namespace in Imports field not imported from: ‘feather’
  All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
convertToTargetRegions: no visible global function definition for
  ‘isClass’
convertToTargetRegions: no visible global function definition for
  ‘findOverlaps’
convertToTargetRegions: no visible global function definition for
  ‘pintersect’
convertToTargetRegions: no visible global function definition for
  ‘subjectHits’
convertToTargetRegions: no visible global function definition for
  ‘width’
convertToTargetRegions: no visible global function definition for
  ‘elementMetadata’
Undefined global functions or variables:
  elementMetadata findOverlaps isClass pintersect subjectHits width
Consider adding
  importFrom("methods", "isClass")
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 ... WARNING
Undocumented arguments in documentation object 'getDbRegionsLoc'
  ‘indexCol’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                          user system elapsed
addMotifAnnotation      18.338  0.836  19.128
addSignificantGenes     16.538  1.024  17.550
getMotifAnnotation       8.444  0.283   8.686
aucScores-class          8.141  0.384   8.533
reRank                   8.344  0.176   8.520
rankingRcisTarget-class  8.060  0.168   8.229
* 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: 1 WARNING, 4 NOTEs
See
  ‘/home/biocbuild/bbs-3.13-bioc/meat/RcisTarget.Rcheck/00check.log’
for details.



Installation output

RcisTarget.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD INSTALL RcisTarget
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.13-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
** 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 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 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")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 58 ]
> 
> proc.time()
   user  system elapsed 
 38.409   6.010  42.523 

Example timings

RcisTarget.Rcheck/RcisTarget-Ex.timings

nameusersystemelapsed
RcisTarget0.1260.0360.164
addLogo0.0940.0320.127
addMotifAnnotation18.338 0.83619.128
addSignificantGenes16.538 1.02417.550
aucScores-class8.1410.3848.533
calcAUC0.0010.0000.000
convertToTargetRegions0.0010.0000.000
getDbRegionsLoc000
getMotifAnnotation8.4440.2838.686
importAnnotations0.460.000.46
importRankings0.4660.0000.466
rankingRcisTarget-class8.0600.1688.229
reRank8.3440.1768.520