Jianhong Ou
| Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019) |
| URL: https://git.bioconductor.org/packages/motifStack |
| Branch: RELEASE_3_9 |
| Last Commit: 29bfa7b |
| Last Changed Date: 2019-05-02 11:53:38 -0400 (Thu, 02 May 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-10-16 12:50:35 -0400 (Wed, 16 Oct 2019).
| Package 1044/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| motifStack 1.28.0 Jianhong Ou
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK | |
| Package: motifStack |
| Version: 1.28.0 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:motifStack.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings motifStack_1.28.0.tar.gz |
| StartedAt: 2019-10-16 04:49:47 -0400 (Wed, 16 Oct 2019) |
| EndedAt: 2019-10-16 04:55:53 -0400 (Wed, 16 Oct 2019) |
| EllapsedTime: 366.0 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: motifStack.Rcheck |
| Warnings: 0 |
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:motifStack.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings motifStack_1.28.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/motifStack.Rcheck’
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘1.28.0’
* 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 or elapsed time > 5s
user system elapsed
browseMotifs 10.318 0.383 10.72
* 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
motifStack.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL motifStack ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/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)
motifStack.Rcheck/tests/runTests.Rout
R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (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
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:BiocGenerics':
score
Loading required package: Biostrings
Loading required package: S4Vectors
Loading required package: stats4
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
Loading required package: IRanges
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 -- Wed Oct 16 04:55:44 2019
***********************************************
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
15.846 1.342 17.176
motifStack.Rcheck/motifStack-Ex.timings
| name | user | system | elapsed | |
| DNAmotifAlignment | 0.337 | 0.006 | 0.346 | |
| browseMotifs | 10.318 | 0.383 | 10.720 | |
| colorset | 0.001 | 0.000 | 0.000 | |
| getRankedUniqueMotifs | 0.003 | 0.000 | 0.004 | |
| highlightCol | 0.001 | 0.000 | 0.002 | |
| importMatrix | 0.029 | 0.008 | 0.037 | |
| mergeMotifs | 0.147 | 0.002 | 0.149 | |
| motifCircos | 0.010 | 0.001 | 0.011 | |
| motifCloud | 0.007 | 0.001 | 0.007 | |
| motifPiles | 0.011 | 0.001 | 0.012 | |
| motifSignature | 0.005 | 0.001 | 0.005 | |
| motifStack | 0.003 | 0.001 | 0.003 | |
| ouNode-class | 0.006 | 0.001 | 0.006 | |
| pcm-class | 0.860 | 0.083 | 0.955 | |
| pcm-methods | 0.009 | 0.002 | 0.012 | |
| pfm-class | 0.231 | 0.003 | 0.234 | |
| pfm-methods | 0.012 | 0.004 | 0.016 | |
| pfm2pwm | 0.204 | 0.003 | 0.208 | |
| plotAffinityLogo | 1.607 | 0.018 | 1.629 | |
| plotMotifLogo | 0.605 | 0.003 | 0.610 | |
| plotMotifLogoA | 0.495 | 0.003 | 0.498 | |
| plotMotifLogoStack | 0.558 | 0.007 | 0.565 | |
| plotMotifLogoStackWithTree | 4.807 | 0.038 | 4.865 | |
| plotMotifOverMotif | 0.752 | 0.009 | 0.765 | |
| plotMotifStackWithPhylog | 0.007 | 0.001 | 0.008 | |
| plotMotifStackWithRadialPhylog | 0.008 | 0.001 | 0.010 | |
| psam-class | 1.739 | 0.033 | 1.789 | |
| psam-methods | 0.026 | 0.007 | 0.034 | |
| readPCM | 0.019 | 0.002 | 0.020 | |
| reorderUPGMAtree | 0.004 | 0.001 | 0.005 | |