Jianhong Ou
| Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019) |
| URL: https://git.bioconductor.org/packages/motifStack |
| Branch: RELEASE_3_8 |
| Last Commit: 04a10c3 |
| Last Changed Date: 2018-10-30 11:41:49 -0400 (Tue, 30 Oct 2018) |
| Back to Multiple platform build/check report for BioC 3.8 |
|
This page was generated on 2019-04-16 11:56:33 -0400 (Tue, 16 Apr 2019).
| Package 998/1649 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| motifStack 1.26.0 Jianhong Ou
| malbec1 | Linux (Ubuntu 16.04.6 LTS) / x86_64 | OK | OK | OK | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK | |
| Package: motifStack |
| Version: 1.26.0 |
| 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_1.26.0.tar.gz |
| StartedAt: 2019-04-16 01:25:14 -0400 (Tue, 16 Apr 2019) |
| EndedAt: 2019-04-16 01:29:55 -0400 (Tue, 16 Apr 2019) |
| EllapsedTime: 280.7 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_1.26.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/motifStack.Rcheck’
* using R version 3.5.3 (2019-03-11)
* 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 ‘1.26.0’
* 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 7.288 0.277 7.649
* 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/3.5/Resources/library’ * installing *source* package ‘motifStack’ ... ** 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 * DONE (motifStack)
motifStack.Rcheck/tests/runTests.Rout
R version 3.5.3 (2019-03-11) -- "Great Truth"
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: grImport
Loading required package: grid
Loading required package: XML
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, colMeans, colSums, colnames,
dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
intersect, is.unsorted, lapply, lengths, mapply, match, mget,
order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
rowMeans, rowSums, 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 -- Tue Apr 16 01:29:48 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
12.243 0.620 12.932
motifStack.Rcheck/motifStack-Ex.timings
| name | user | system | elapsed | |
| DNAmotifAlignment | 0.266 | 0.008 | 0.284 | |
| browseMotifs | 7.288 | 0.277 | 7.649 | |
| colorset | 0.000 | 0.000 | 0.001 | |
| getRankedUniqueMotifs | 0.003 | 0.001 | 0.003 | |
| highlightCol | 0.001 | 0.000 | 0.002 | |
| importMatrix | 0.018 | 0.003 | 0.021 | |
| mergeMotifs | 0.193 | 0.003 | 0.201 | |
| motifCircos | 0.011 | 0.000 | 0.012 | |
| motifCloud | 0.006 | 0.000 | 0.006 | |
| motifPiles | 0.012 | 0.001 | 0.012 | |
| motifSignature | 0.006 | 0.000 | 0.007 | |
| motifStack | 0.003 | 0.000 | 0.003 | |
| ouNode-class | 0.002 | 0.001 | 0.003 | |
| pcm-class | 0.715 | 0.181 | 0.953 | |
| pcm-methods | 0.008 | 0.001 | 0.009 | |
| pfm-class | 0.062 | 0.002 | 0.065 | |
| pfm-methods | 0.008 | 0.001 | 0.008 | |
| pfm2pwm | 0.187 | 0.002 | 0.190 | |
| plotAffinityLogo | 0.477 | 0.005 | 0.484 | |
| plotMotifLogo | 0.077 | 0.002 | 0.081 | |
| plotMotifLogoA | 0.295 | 0.003 | 0.301 | |
| plotMotifLogoStack | 0.799 | 0.175 | 1.033 | |
| plotMotifLogoStackWithTree | 2.125 | 0.382 | 2.644 | |
| plotMotifOverMotif | 0.995 | 0.167 | 1.216 | |
| plotMotifStackWithPhylog | 0.007 | 0.000 | 0.007 | |
| plotMotifStackWithRadialPhylog | 0.008 | 0.000 | 0.008 | |
| psam-class | 0.621 | 0.007 | 0.635 | |
| psam-methods | 0.018 | 0.003 | 0.021 | |
| readPCM | 0.012 | 0.001 | 0.013 | |
| reorderUPGMAtree | 0.003 | 0.000 | 0.004 | |