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This page was generated on 2023-09-21 11:41:00 -0400 (Thu, 21 Sep 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.2 LTS)x86_644.3.1 (2023-06-16) -- "Beagle Scouts" 4654
palomino4Windows Server 2022 Datacenterx644.3.1 (2023-06-16 ucrt) -- "Beagle Scouts" 4388
lconwaymacOS 12.6.5 Montereyx86_644.3.1 Patched (2023-06-17 r84564) -- "Beagle Scouts" 4402
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch644.3.1 (2023-06-16) -- "Beagle Scouts" 4391
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 1293/2229HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
motifStack 1.45.1  (landing page)
Jianhong Ou
Snapshot Date: 2023-09-20 14:05:05 -0400 (Wed, 20 Sep 2023)
git_url: https://git.bioconductor.org/packages/motifStack
git_branch: devel
git_last_commit: 4a7f8eb
git_last_commit_date: 2023-04-26 18:01:26 -0400 (Wed, 26 Apr 2023)
nebbiolo2Linux (Ubuntu 22.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.6.5 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    OK  

CHECK results for motifStack on kunpeng2


To the developers/maintainers of the motifStack package:
- 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 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.
- See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host.

raw results


Summary

Package: motifStack
Version: 1.45.1
Command: /home/biocbuild/R/R-4.3.1/bin/R CMD check --install=check:motifStack.install-out.txt --library=/home/biocbuild/R/R-4.3.1/site-library --timings motifStack_1.45.1.tar.gz
StartedAt: 2023-09-21 07:30:56 -0000 (Thu, 21 Sep 2023)
EndedAt: 2023-09-21 07:40:06 -0000 (Thu, 21 Sep 2023)
EllapsedTime: 550.1 seconds
RetCode: 0
Status:   OK  
CheckDir: motifStack.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/R/R-4.3.1/bin/R CMD check --install=check:motifStack.install-out.txt --library=/home/biocbuild/R/R-4.3.1/site-library --timings motifStack_1.45.1.tar.gz
###
##############################################################################
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* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/motifStack.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
    gcc (GCC) 10.3.1
    GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* checking for file ‘motifStack/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘motifStack’ version ‘1.45.1’
* 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 loading without being on the library search path ... 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 14.250  0.204  14.484
pfm2pwm           6.176  0.084   6.271
* 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 ...
  ‘motifStack_HTML.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: OK


Installation output

motifStack.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R-4.3.1/bin/R CMD INSTALL motifStack
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-4.3.1/site-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 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-unknown-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 -- Thu Sep 21 07:38:08 2023 
*********************************************** 
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 
 17.136   0.548  17.719 

Example timings

motifStack.Rcheck/motifStack-Ex.timings

nameusersystemelapsed
AAmotifAlignment14.250 0.20414.484
DNAmotifAlignment0.1510.0000.155
DNAmotifToRNAmotif0.0050.0080.014
GeomMotif0.8960.0560.954
browseMotifs0.0000.0000.001
clusterMotifs0.0000.0000.001
colorset000
geom_motif0.4090.0240.434
getRankedUniqueMotifs0.0010.0000.001
highlightCol0.0010.0000.001
importMatrix0.0190.0000.019
marker-class0.0020.0000.002
matalign000
mergeMotifs0.1470.0040.152
motifCircos0.0010.0000.002
motifCloud0.0010.0000.001
motifGrob0.1580.0080.167
motifHclust000
motifPiles0.0020.0000.002
motifSignature0.0010.0000.001
motifStack0.0020.0000.002
ouNode-class0.0030.0000.003
pcm-class0.1770.0160.193
pfm-class0.1340.0000.134
pfm2pwm6.1760.0846.271
plotAffinityLogo2.1750.0912.272
plotMotifLogo0.2890.0150.305
plotMotifLogoA0.2660.0120.279
plotMotifLogoStack0.3560.0160.373
plotMotifLogoStackWithTree2.8840.0162.909
plotMotifOverMotif0.4200.0080.429
plotMotifStackWithPhylog0.0010.0000.001
plotMotifStackWithRadialPhylog0.0020.0000.001
psam-class0.8830.0080.892
pssm-class0.5980.0080.607
readPCM0.0090.0040.013
reorderUPGMAtree0.0010.0000.001