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This page was generated on 2025-09-22 11:39 -0400 (Mon, 22 Sep 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4827
merida1macOS 12.7.5 Montereyx86_644.5.1 RC (2025-06-05 r88288) -- "Great Square Root" 4608
kjohnson1macOS 13.6.6 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4549
kunpeng2Linux (openEuler 24.03 LTS)aarch64R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" 4581
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 1348/2341HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
motifStack 1.52.0  (landing page)
Jianhong Ou
Snapshot Date: 2025-09-18 13:40 -0400 (Thu, 18 Sep 2025)
git_url: https://git.bioconductor.org/packages/motifStack
git_branch: RELEASE_3_21
git_last_commit: 6cf9408
git_last_commit_date: 2025-04-15 10:15:33 -0400 (Tue, 15 Apr 2025)
nebbiolo1Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
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    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  


CHECK results for motifStack on merida1

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.

raw results


Summary

Package: motifStack
Version: 1.52.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:motifStack.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings motifStack_1.52.0.tar.gz
StartedAt: 2025-09-19 06:58:57 -0400 (Fri, 19 Sep 2025)
EndedAt: 2025-09-19 07:09:55 -0400 (Fri, 19 Sep 2025)
EllapsedTime: 657.7 seconds
RetCode: 0
Status:   OK  
CheckDir: motifStack.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:motifStack.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings motifStack_1.52.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/motifStack.Rcheck’
* using R version 4.5.1 RC (2025-06-05 r88288)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘motifStack/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘motifStack’ version ‘1.52.0’
* 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 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 ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Non-topic package-anchored link(s) in Rd file 'importMatrix.Rd':
  ‘[TFBSTools:XMatrixList-class]{XMatrixList}’

See section 'Cross-references' in the 'Writing R Extensions' manual.
* 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           25.586  0.619  26.952
pfm2pwm                    14.781  0.190  16.230
plotMotifLogoStackWithTree  4.852  0.046   5.062
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.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: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.21-bioc/meat/motifStack.Rcheck/00check.log’
for details.


Installation output

motifStack.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’
* installing *source* package ‘motifStack’ ...
** this is package ‘motifStack’ version ‘1.52.0’
** 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 4.5.1 RC (2025-06-05 r88288) -- "Great Square Root"
Copyright (C) 2025 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.

> 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")
Loading required namespace: Cairo
only the first revcomp will be used.
only the first revcomp will be used.
only the first revcomp will be used.
only the first revcomp will be used.


RUNIT TEST PROTOCOL -- Fri Sep 19 07:09:38 2025 
*********************************************** 
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 
There were 32 warnings (use warnings() to see them)
> 
> proc.time()
   user  system elapsed 
 43.401   2.072  50.398 

Example timings

motifStack.Rcheck/motifStack-Ex.timings

nameusersystemelapsed
AAmotifAlignment25.586 0.61926.952
DNAmotifAlignment0.2610.0050.267
DNAmotifToRNAmotif0.0170.0020.020
GeomMotif1.6850.0661.878
browseMotifs0.0010.0010.003
clusterMotifs0.0010.0010.001
colorset0.0000.0010.001
geom_motif0.9230.0521.083
getRankedUniqueMotifs0.0010.0010.002
highlightCol0.0020.0010.002
importMatrix0.0280.0160.048
marker-class0.0030.0010.004
matalign0.0010.0010.001
mergeMotifs0.2980.0490.390
motifCircos0.0050.0010.007
motifCloud0.0030.0010.005
motifGrob0.2990.0140.345
motifHclust0.0000.0010.001
motifPiles0.0050.0020.010
motifSignature0.0030.0010.003
motifStack0.0030.0020.006
ouNode-class0.0040.0020.006
pcm-class0.2400.0110.274
pfm-class0.2260.0110.260
pfm2pwm14.781 0.19016.230
plotAffinityLogo1.4040.0191.493
plotMotifLogo0.4920.0060.544
plotMotifLogoA0.4540.0110.490
plotMotifLogoStack0.5730.0360.690
plotMotifLogoStackWithTree4.8520.0465.062
plotMotifOverMotif0.6450.0130.675
plotMotifStackWithPhylog0.0030.0010.004
plotMotifStackWithRadialPhylog0.0020.0010.003
psam-class1.4760.0301.510
pssm-class0.9110.0210.938
readPCM0.0190.0020.022
reorderUPGMAtree0.0030.0010.003