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This page was generated on 2024-12-23 12:05 -0500 (Mon, 23 Dec 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4744
palomino8Windows Server 2022 Datacenterx644.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" 4487
merida1macOS 12.7.5 Montereyx86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4515
kjohnson1macOS 13.6.6 Venturaarm644.4.2 (2024-10-31) -- "Pile of Leaves" 4467
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: 2024-12-19 13:00 -0500 (Thu, 19 Dec 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)
nebbiolo2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino8Windows Server 2022 Datacenter / x64  OK    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  NO, package depends on 'TFBSTools' which is only available as a source package that needs compilation


CHECK results for motifStack on palomino8

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: 1.50.0
Command: F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:motifStack.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings motifStack_1.50.0.tar.gz
StartedAt: 2024-12-20 03:42:07 -0500 (Fri, 20 Dec 2024)
EndedAt: 2024-12-20 03:48:35 -0500 (Fri, 20 Dec 2024)
EllapsedTime: 387.3 seconds
RetCode: 0
Status:   OK  
CheckDir: motifStack.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:motifStack.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings motifStack_1.50.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/motifStack.Rcheck'
* using R version 4.4.2 (2024-10-31 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.3.0
    GNU Fortran (GCC) 13.3.0
* running under: Windows Server 2022 x64 (build 20348)
* 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 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 ... 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 8.41   0.30     8.7
pfm2pwm          5.68   0.07     6.8
* 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:
###
###   F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL motifStack
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.20-bioc/R/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 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

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 Dec 20 03:48:22 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 
  24.76    1.00   26.75 

Example timings

motifStack.Rcheck/motifStack-Ex.timings

nameusersystemelapsed
AAmotifAlignment8.410.308.70
DNAmotifAlignment0.040.020.06
DNAmotifToRNAmotif0.010.000.01
GeomMotif0.680.041.74
browseMotifs000
clusterMotifs000
colorset000
geom_motif0.250.050.39
getRankedUniqueMotifs000
highlightCol000
importMatrix0.010.000.14
marker-class000
matalign000
mergeMotifs0.090.000.09
motifCircos000
motifCloud000
motifGrob0.100.000.09
motifHclust000
motifPiles000
motifSignature000
motifStack000
ouNode-class0.010.000.02
pcm-class0.080.000.08
pfm-class0.080.000.08
pfm2pwm5.680.076.80
plotAffinityLogo0.680.020.98
plotMotifLogo0.170.020.19
plotMotifLogoA0.140.010.16
plotMotifLogoStack0.250.000.42
plotMotifLogoStackWithTree1.860.092.17
plotMotifOverMotif0.370.000.47
plotMotifStackWithPhylog000
plotMotifStackWithRadialPhylog000
psam-class0.710.070.80
pssm-class0.360.010.37
readPCM000
reorderUPGMAtree000