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This page was generated on 2024-04-18 11:32:14 -0400 (Thu, 18 Apr 2024).

HostnameOSArch (*)R versionInstalled pkgs
kjohnson1macOS 13.6.1 Venturaarm644.3.3 (2024-02-29) -- "Angel Food Cake" 4388
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Package 1314/2266HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
motifStack 1.46.0  (landing page)
Jianhong Ou
Snapshot Date: 2024-04-16 09:00:03 -0400 (Tue, 16 Apr 2024)
git_url: https://git.bioconductor.org/packages/motifStack
git_branch: RELEASE_3_18
git_last_commit: 80200b0
git_last_commit_date: 2023-10-24 09:51:18 -0400 (Tue, 24 Oct 2023)
kjohnson1macOS 13.6.1 Ventura / arm64  OK    OK    OK    OK  NO, package depends on 'TFBSTools' which is only available as a source package that needs compilation

CHECK results for motifStack on kjohnson1


To the developers/maintainers of the motifStack package:
- 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: 1.46.0
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_1.46.0.tar.gz
StartedAt: 2024-04-17 20:17:17 -0400 (Wed, 17 Apr 2024)
EndedAt: 2024-04-17 20:26:18 -0400 (Wed, 17 Apr 2024)
EllapsedTime: 540.7 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_1.46.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.18-bioc-mac-arm64/meat/motifStack.Rcheck’
* using R version 4.3.3 (2024-02-29)
* using platform: aarch64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.6.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘motifStack/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘motifStack’ version ‘1.46.0’
* 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 8.404  0.239   8.669
* 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

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/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 4.3.3 (2024-02-29) -- "Angel Food Cake"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20 (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 -- Wed Apr 17 20:26:06 2024 
*********************************************** 
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 
 16.895   0.577  17.509 

Example timings

motifStack.Rcheck/motifStack-Ex.timings

nameusersystemelapsed
AAmotifAlignment8.4040.2398.669
DNAmotifAlignment0.0830.0030.087
DNAmotifToRNAmotif0.0080.0020.009
GeomMotif0.6560.0400.704
browseMotifs0.0010.0000.001
clusterMotifs0.0000.0000.001
colorset0.0000.0000.001
geom_motif0.3170.0170.335
getRankedUniqueMotifs0.0010.0000.001
highlightCol0.0000.0000.001
importMatrix0.0110.0050.016
marker-class0.0020.0010.002
matalign0.0000.0000.001
mergeMotifs0.0850.0020.087
motifCircos0.0040.0000.004
motifCloud0.0020.0000.002
motifGrob0.0910.0010.091
motifHclust0.0010.0000.000
motifPiles0.0040.0000.004
motifSignature0.0020.0010.002
motifStack0.0020.0000.002
ouNode-class0.0020.0000.003
pcm-class0.1050.0050.110
pfm-class0.0950.0050.101
pfm2pwm4.3180.1044.500
plotAffinityLogo0.5520.0150.569
plotMotifLogo0.2010.0030.207
plotMotifLogoA0.1750.0030.180
plotMotifLogoStack0.2450.0130.260
plotMotifLogoStackWithTree3.1380.0383.211
plotMotifOverMotif0.2830.0090.296
plotMotifStackWithPhylog0.0020.0010.002
plotMotifStackWithRadialPhylog0.0030.0000.003
psam-class0.5480.0170.567
pssm-class0.3940.0160.411
readPCM0.0060.0020.008
reorderUPGMAtree0.0010.0000.001