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This page was generated on 2024-11-20 12:07 -0500 (Wed, 20 Nov 2024).

HostnameOSArch (*)R versionInstalled pkgs
teran2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4481
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4479
palomino8Windows Server 2022 Datacenterx644.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" 4359
lconwaymacOS 12.7.1 Montereyx86_644.4.1 (2024-06-14) -- "Race for Your Life" 4539
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch644.4.1 (2024-06-14) -- "Race for Your Life" 4493
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 1319/2289HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
motifStack 1.50.0  (landing page)
Jianhong Ou
Snapshot Date: 2024-11-19 13:40 -0500 (Tue, 19 Nov 2024)
git_url: https://git.bioconductor.org/packages/motifStack
git_branch: RELEASE_3_20
git_last_commit: c1ec2e8
git_last_commit_date: 2024-10-29 09:42:41 -0500 (Tue, 29 Oct 2024)
teran2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
nebbiolo2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  
palomino8Windows 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  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: 1.50.0
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_1.50.0.tar.gz
StartedAt: 2024-11-20 10:07:17 -0000 (Wed, 20 Nov 2024)
EndedAt: 2024-11-20 10:14:47 -0000 (Wed, 20 Nov 2024)
EllapsedTime: 450.8 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_1.50.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/motifStack.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    gcc (GCC) 12.2.1 20220819 (openEuler 12.2.1-14)
    GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘motifStack/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘motifStack’ version ‘1.50.0’
* 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 12.571  0.259  12.858
pfm2pwm           7.321  0.264   7.601
* 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

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


* installing to library ‘/home/biocbuild/R/R-4.4.1/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 4.4.1 (2024-06-14) -- "Race for Your Life"
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

[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 -- Wed Nov 20 10:14:42 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 
 28.613   2.482  31.095 

Example timings

motifStack.Rcheck/motifStack-Ex.timings

nameusersystemelapsed
AAmotifAlignment12.571 0.25912.858
DNAmotifAlignment0.1350.0000.140
DNAmotifToRNAmotif0.0120.0000.011
GeomMotif0.8460.0120.861
browseMotifs0.0010.0000.001
clusterMotifs0.0000.0000.001
colorset000
geom_motif0.3710.0000.372
getRankedUniqueMotifs0.0000.0000.001
highlightCol0.0000.0000.001
importMatrix0.0110.0040.015
marker-class0.0020.0000.002
matalign0.0000.0000.001
mergeMotifs0.1350.0000.135
motifCircos0.0020.0000.002
motifCloud0.0010.0000.001
motifGrob0.1420.0000.142
motifHclust000
motifPiles0.0020.0000.002
motifSignature0.0010.0000.001
motifStack0.0010.0000.001
ouNode-class0.0020.0000.003
pcm-class0.1290.0120.142
pfm-class0.1290.0080.137
pfm2pwm7.3210.2647.601
plotAffinityLogo0.8210.0000.823
plotMotifLogo0.2820.0000.282
plotMotifLogoA0.2870.0030.291
plotMotifLogoStack0.3390.0040.344
plotMotifLogoStackWithTree2.8470.0282.881
plotMotifOverMotif0.4040.0000.406
plotMotifStackWithPhylog0.0010.0000.001
plotMotifStackWithRadialPhylog0.0010.0000.002
psam-class0.9370.0000.940
pssm-class0.5370.0080.547
readPCM0.0090.0040.013
reorderUPGMAtree0.0010.0000.000