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CHECK report for motifStack on malbec2

This page was generated on 2020-10-17 11:55:12 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE motifStack PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1129/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
motifStack 1.32.1
Jianhong Ou
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/motifStack
Branch: RELEASE_3_11
Last Commit: 566ff1f
Last Changed Date: 2020-08-02 19:57:55 -0400 (Sun, 02 Aug 2020)
malbec2 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: motifStack
Version: 1.32.1
Command: /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:motifStack.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings motifStack_1.32.1.tar.gz
StartedAt: 2020-10-17 03:24:16 -0400 (Sat, 17 Oct 2020)
EndedAt: 2020-10-17 03:29:02 -0400 (Sat, 17 Oct 2020)
EllapsedTime: 285.4 seconds
RetCode: 0
Status:  OK 
CheckDir: motifStack.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:motifStack.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings motifStack_1.32.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.11-bioc/meat/motifStack.Rcheck’
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘motifStack/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘motifStack’ version ‘1.32.1’
* 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
browseMotifs 6.76  0.128   6.902
* 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

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### Running command:
###
###   /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD INSTALL motifStack
###
##############################################################################
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* installing to library ‘/home/biocbuild/bbs-3.11-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 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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: grImport2
Loading required package: grid
Loading required package: MotIV
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which, which.max, which.min

Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following object is masked from 'package:base':

    expand.grid

Loading required package: IRanges
Loading required package: GenomeInfoDb

Attaching package: 'MotIV'

The following object is masked from 'package:stats':

    filter

Loading required package: ade4

Attaching package: 'ade4'

The following object is masked from 'package:GenomicRanges':

    score

The following object is masked from 'package:BiocGenerics':

    score

Loading required package: Biostrings
Loading required package: XVector

Attaching package: 'Biostrings'

The following object is masked from 'package:base':

    strsplit

[1] TRUE
> #require("MotifDb") || stop("unalble to load Package::motifDb")
> BiocGenerics:::testPackage("motifStack")


RUNIT TEST PROTOCOL -- Sat Oct 17 03:28:57 2020 
*********************************************** 
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 
 10.613   0.353  10.959 

Example timings

motifStack.Rcheck/motifStack-Ex.timings

nameusersystemelapsed
DNAmotifAlignment0.2140.0000.231
GeomMotif0.5680.0520.620
browseMotifs6.7600.1286.902
colorset000
geom_motif0.2290.0070.237
getRankedUniqueMotifs0.0010.0000.001
highlightCol0.0010.0000.001
importMatrix0.0050.0080.013
marker-class0.0010.0000.002
mergeMotifs0.0910.0040.095
motifCircos0.0020.0000.003
motifCloud0.0020.0000.002
motifGrob0.1840.0000.183
motifPiles0.0050.0010.006
motifSignature0.0000.0020.003
motifStack0.0010.0000.001
ouNode-class0.0030.0000.003
pcm-class0.1410.0000.141
pcm-methods0.0080.0040.012
pfm-class0.1250.0000.125
pfm-methods0.0060.0000.007
pfm2pwm0.1310.0000.131
plotAffinityLogo0.6770.0040.689
plotMotifLogo0.2860.0000.287
plotMotifLogoA0.1810.0000.182
plotMotifLogoStack0.2250.0000.225
plotMotifLogoStackWithTree1.6510.0121.663
plotMotifOverMotif0.330.000.33
plotMotifStackWithPhylog0.0020.0000.002
plotMotifStackWithRadialPhylog0.0020.0000.003
psam-class0.8800.0080.888
psam-methods0.0240.0000.024
readPCM0.0140.0000.015
reorderUPGMAtree0.0020.0010.002