Back to Multiple platform build/check report for BioC 3.19:   simplified   long
ABCDEFGHIJKLMNOPQ[R]STUVWXYZ

This page was generated on 2024-07-19 17:40 -0400 (Fri, 19 Jul 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.1 (2024-06-14) -- "Race for Your Life" 4742
palomino7Windows Server 2022 Datacenterx644.4.1 (2024-06-14 ucrt) -- "Race for Your Life" 4484
merida1macOS 12.7.5 Montereyx86_644.4.1 (2024-06-14) -- "Race for Your Life" 4513
kjohnson1macOS 13.6.6 Venturaarm644.4.1 (2024-06-14) -- "Race for Your Life" 4462
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 1698/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
RcisTarget 1.24.0  (landing page)
Gert Hulselmans
Snapshot Date: 2024-07-17 14:00 -0400 (Wed, 17 Jul 2024)
git_url: https://git.bioconductor.org/packages/RcisTarget
git_branch: RELEASE_3_19
git_last_commit: 6c20802
git_last_commit_date: 2024-04-30 11:03:32 -0400 (Tue, 30 Apr 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino7Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  
merida1macOS 12.7.5 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    OK    NA  


CHECK results for RcisTarget on merida1

To the developers/maintainers of the RcisTarget package:
- 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 Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: RcisTarget
Version: 1.24.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:RcisTarget.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings RcisTarget_1.24.0.tar.gz
StartedAt: 2024-07-18 11:17:12 -0400 (Thu, 18 Jul 2024)
EndedAt: 2024-07-18 11:30:59 -0400 (Thu, 18 Jul 2024)
EllapsedTime: 827.2 seconds
RetCode: 0
Status:   OK  
CheckDir: RcisTarget.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:RcisTarget.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings RcisTarget_1.24.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/RcisTarget.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.5
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘RcisTarget/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘RcisTarget’ version ‘1.24.0’
* 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 12.0Mb
  sub-directories of 1Mb or more:
    data  11.4Mb
* 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 code 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 ... OK
* checking Rd files ... NOTE
checkRd: (-1) dbRegionsLoc.Rd:11-14: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dbRegionsLoc.Rd:16-19: Lost braces in \itemize; meant \describe ?
checkRd: (-1) importAnnotations.Rd:44: Lost braces in \itemize; meant \describe ?
checkRd: (-1) importAnnotations.Rd:45: Lost braces in \itemize; meant \describe ?
checkRd: (-1) importAnnotations.Rd:46: Lost braces in \itemize; meant \describe ?
checkRd: (-1) importAnnotations.Rd:48-51: Lost braces in \itemize; meant \describe ?
checkRd: (-1) importAnnotations.Rd:24: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) importAnnotations.Rd:25: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) importAnnotations.Rd:27-31: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) importAnnotations.Rd:32: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) importAnnotations.Rd:33-36: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) motifAnnotations.Rd:18-20: Lost braces in \itemize; meant \describe ?
checkRd: (-1) motifAnnotations.Rd:22-24: Lost braces in \itemize; meant \describe ?
checkRd: (-1) motifAnnotations.Rd:26-28: Lost braces in \itemize; meant \describe ?
checkRd: (-1) motifAnnotations.Rd:54: Lost braces in \itemize; meant \describe ?
checkRd: (-1) motifAnnotations.Rd:55: Lost braces in \itemize; meant \describe ?
checkRd: (-1) motifAnnotations.Rd:58-61: Lost braces in \itemize; meant \describe ?
checkRd: (-1) motifAnnotations.Rd:62: Lost braces in \itemize; meant \describe ?
checkRd: (-1) motifAnnotations.Rd:63-66: Lost braces in \itemize; meant \describe ?
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                          user system elapsed
addSignificantGenes     27.551  2.831  35.107
addMotifAnnotation      26.154  1.339  30.954
getMotifAnnotation      15.373  1.776  20.885
aucScores-class         13.098  0.748  16.461
rankingRcisTarget-class 12.084  1.078  16.577
reRank                  12.395  0.304  15.169
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... 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
  ‘/Users/biocbuild/bbs-3.19-bioc/meat/RcisTarget.Rcheck/00check.log’
for details.


Installation output

RcisTarget.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL RcisTarget
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/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 4.4.1 (2024-06-14) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

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 
 77.170   6.593  96.958 

Example timings

RcisTarget.Rcheck/RcisTarget-Ex.timings

nameusersystemelapsed
RcisTarget0.3690.0980.565
addLogo0.2850.0350.383
addMotifAnnotation26.154 1.33930.954
addSignificantGenes27.551 2.83135.107
aucScores-class13.098 0.74816.461
calcAUC0.0010.0010.001
convertToTargetRegions0.0000.0000.001
getDbRegionsLoc0.0000.0000.001
getMotifAnnotation15.373 1.77620.885
importAnnotations1.3360.0441.720
importRankings1.1660.0191.464
rankingRcisTarget-class12.084 1.07816.577
reRank12.395 0.30415.169
showLogo0.1000.0360.197