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This page was generated on 2022-10-19 13:20:33 -0400 (Wed, 19 Oct 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.5 LTS)x86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4386
palomino3Windows Server 2022 Datacenterx644.2.1 (2022-06-23 ucrt) -- "Funny-Looking Kid" 4138
merida1macOS 10.14.6 Mojavex86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4205
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

CHECK results for motifStack on nebbiolo1


To the developers/maintainers of the motifStack package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/motifStack.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? 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 1236/2140HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
motifStack 1.40.0  (landing page)
Jianhong Ou
Snapshot Date: 2022-10-18 13:55:19 -0400 (Tue, 18 Oct 2022)
git_url: https://git.bioconductor.org/packages/motifStack
git_branch: RELEASE_3_15
git_last_commit: 175f1b5
git_last_commit_date: 2022-04-26 11:12:06 -0400 (Tue, 26 Apr 2022)
nebbiolo1Linux (Ubuntu 20.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: motifStack
Version: 1.40.0
Command: /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:motifStack.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings motifStack_1.40.0.tar.gz
StartedAt: 2022-10-18 20:42:40 -0400 (Tue, 18 Oct 2022)
EndedAt: 2022-10-18 20:47:41 -0400 (Tue, 18 Oct 2022)
EllapsedTime: 300.8 seconds
RetCode: 0
Status:   OK  
CheckDir: motifStack.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:motifStack.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings motifStack_1.40.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.15-bioc/meat/motifStack.Rcheck’
* using R version 4.2.1 (2022-06-23)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘motifStack/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘motifStack’ version ‘1.40.0’
* 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 ‘motifStack’ 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 ... 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                  user system elapsed
AAmotifAlignment 8.494  0.264   8.758
pfm2pwm          5.629  0.340   5.969
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.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: OK


Installation output

motifStack.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD INSTALL motifStack
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.15-bioc/R/library’
* installing *source* package ‘motifStack’ ...
** using staged installation
** R
** 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 (motifStack)

Tests output

motifStack.Rcheck/tests/runTests.Rout


R version 4.2.1 (2022-06-23) -- "Funny-Looking Kid"
Copyright (C) 2022 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.

> require("motifStack") || stop("unable to load Package:motifStack")
Loading required package: motifStack
Loading required package: grid

[1] TRUE
> require("TFBSTools") || stop("unable to load Package:TFBSTools")
Loading required package: TFBSTools
[1] TRUE
> #require("MotifDb") || stop("unalble to load Package::motifDb")
> BiocGenerics:::testPackage("motifStack")


RUNIT TEST PROTOCOL -- Tue Oct 18 20:47:37 2022 
*********************************************** 
Number of test functions: 10 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
motifStack RUnit Tests - 10 test functions, 0 errors, 0 failures
Number of test functions: 10 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
 13.591   0.671  14.258 

Example timings

motifStack.Rcheck/motifStack-Ex.timings

nameusersystemelapsed
AAmotifAlignment8.4940.2648.758
DNAmotifAlignment0.0900.0000.091
DNAmotifToRNAmotif0.010.000.01
GeomMotif0.5760.0280.606
browseMotifs0.0000.0010.001
clusterMotifs000
colorset0.0010.0000.000
geom_motif0.2780.0120.290
getRankedUniqueMotifs0.0000.0000.001
highlightCol0.0000.0010.000
importMatrix0.0120.0050.016
marker-class0.0000.0020.002
matalign0.0000.0010.000
mergeMotifs0.0870.0010.088
motifCircos0.0010.0000.002
motifCloud0.0010.0000.001
motifGrob0.0910.0040.095
motifHclust000
motifPiles0.0000.0020.002
motifSignature0.0010.0010.001
motifStack0.0020.0000.002
ouNode-class0.0030.0000.003
pcm-class0.1030.0000.103
pfm-class0.0860.0040.091
pfm2pwm5.6290.3405.969
plotAffinityLogo0.5660.0000.566
plotMotifLogo0.1790.0000.179
plotMotifLogoA0.1630.0040.168
plotMotifLogoStack0.2260.0040.230
plotMotifLogoStackWithTree1.8050.0161.821
plotMotifOverMotif0.2710.0080.278
plotMotifStackWithPhylog0.0000.0010.002
plotMotifStackWithRadialPhylog0.0000.0020.002
psam-class0.5850.0070.592
pssm-class0.3510.0080.359
readPCM0.0050.0040.009
reorderUPGMAtree0.0010.0000.001