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This page was generated on 2024-12-24 11:47 -0500 (Tue, 24 Dec 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.1 LTS)x86_64R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" 4754
palomino7Windows Server 2022 Datacenterx64R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" 4472
lconwaymacOS 12.7.1 Montereyx86_64R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" 4426
kjohnson3macOS 13.7.1 Venturaarm64R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" 4381
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch64R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" 4373
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 1313/2274HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
motifStack 1.51.0  (landing page)
Jianhong Ou
Snapshot Date: 2024-12-23 13:40 -0500 (Mon, 23 Dec 2024)
git_url: https://git.bioconductor.org/packages/motifStack
git_branch: devel
git_last_commit: 2974913
git_last_commit_date: 2024-10-29 09:42:41 -0500 (Tue, 29 Oct 2024)
nebbiolo1Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino7Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  NO, package depends on 'TFBSTools' which is only available as a source package that needs compilation
kjohnson3macOS 13.7.1 Ventura / arm64  OK    OK    OK    OK  NO, package depends on 'TFBSTools' which is only available as a source package that needs compilation
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: 1.51.0
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:motifStack.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings motifStack_1.51.0.tar.gz
StartedAt: 2024-12-24 08:53:19 -0000 (Tue, 24 Dec 2024)
EndedAt: 2024-12-24 09:00:45 -0000 (Tue, 24 Dec 2024)
EllapsedTime: 446.5 seconds
RetCode: 0
Status:   OK  
CheckDir: motifStack.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:motifStack.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings motifStack_1.51.0.tar.gz
###
##############################################################################
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* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/motifStack.Rcheck’
* using R Under development (unstable) (2024-11-24 r87369)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘motifStack/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘motifStack’ version ‘1.51.0’
* 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 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 12.559  0.339  12.936
pfm2pwm           6.155  0.100   6.269
* 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: OK


Installation output

motifStack.Rcheck/00install.out

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


* installing to library ‘/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library’
* installing *source* package ‘motifStack’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
No methods found in package ‘Biostrings’ for request: ‘pattern’ when loading ‘TFBSTools’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
No methods found in package ‘Biostrings’ for request: ‘pattern’ when loading ‘TFBSTools’
** testing if installed package can be loaded from final location
No methods found in package ‘Biostrings’ for request: ‘pattern’ when loading ‘TFBSTools’
** testing if installed package keeps a record of temporary installation path
* DONE (motifStack)

Tests output

motifStack.Rcheck/tests/runTests.Rout


R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu

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

No methods found in package 'Biostrings' for request: 'pattern' when loading 'TFBSTools'
[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 -- Tue Dec 24 09:00:40 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 
There were 32 warnings (use warnings() to see them)
> 
> proc.time()
   user  system elapsed 
 28.704   0.753  29.525 

Example timings

motifStack.Rcheck/motifStack-Ex.timings

nameusersystemelapsed
AAmotifAlignment12.559 0.33912.936
DNAmotifAlignment0.1370.0090.149
DNAmotifToRNAmotif0.0120.0000.012
GeomMotif0.8540.0670.927
browseMotifs0.0000.0000.001
clusterMotifs0.0000.0000.001
colorset000
geom_motif0.3890.0100.399
getRankedUniqueMotifs0.0010.0000.000
highlightCol0.0000.0010.000
importMatrix0.0130.0020.016
marker-class0.0010.0000.002
matalign0.0000.0000.001
mergeMotifs0.1410.0000.142
motifCircos0.0020.0000.001
motifCloud0.0010.0000.001
motifGrob0.1550.0000.155
motifHclust0.0000.0000.001
motifPiles0.0020.0000.002
motifSignature0.0010.0000.001
motifStack0.0010.0000.001
ouNode-class0.0030.0000.003
pcm-class0.1270.0160.143
pfm-class0.1120.0230.135
pfm2pwm6.1550.1006.269
plotAffinityLogo2.1150.0722.196
plotMotifLogo0.2820.0000.283
plotMotifLogoA0.2590.0080.267
plotMotifLogoStack0.3020.0040.307
plotMotifLogoStackWithTree2.6920.0122.710
plotMotifOverMotif0.3700.0080.379
plotMotifStackWithPhylog0.0010.0000.002
plotMotifStackWithRadialPhylog0.0010.0000.001
psam-class0.8610.0280.891
pssm-class0.5040.0350.541
readPCM0.0080.0040.012
reorderUPGMAtree0.0010.0000.001