Jianhong Ou
| Snapshot Date: 2020-01-15 16:46:30 -0500 (Wed, 15 Jan 2020) |
| URL: https://git.bioconductor.org/packages/dagLogo |
| Branch: master |
| Last Commit: 155dd9c |
| Last Changed Date: 2019-10-29 13:37:06 -0500 (Tue, 29 Oct 2019) |
| Back to Multiple platform build/check report for BioC 3.11 |
|
This page was generated on 2020-01-16 13:37:51 -0500 (Thu, 16 Jan 2020).
| Package 402/1818 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| dagLogo 1.25.0 Jianhong Ou
| malbec2 | Linux (Ubuntu 18.04.3 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: dagLogo |
| Version: 1.25.0 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:dagLogo.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings dagLogo_1.25.0.tar.gz |
| StartedAt: 2020-01-16 03:28:40 -0500 (Thu, 16 Jan 2020) |
| EndedAt: 2020-01-16 03:37:48 -0500 (Thu, 16 Jan 2020) |
| EllapsedTime: 548.2 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: dagLogo.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:dagLogo.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings dagLogo_1.25.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/dagLogo.Rcheck’
* using R Under development (unstable) (2019-12-14 r77572)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘dagLogo/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘dagLogo’ version ‘1.25.0’
* 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 ‘dagLogo’ 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
testDAU 49.993 6.150 56.157
buildBackgroundModel 15.085 0.203 15.294
formatSequence 11.496 0.017 11.518
dagLogo 10.966 0.345 11.373
dagLogo-package 5.575 0.562 6.200
* 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
dagLogo.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL dagLogo ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’ * installing *source* package ‘dagLogo’ ... ** using staged installation ** R ** data ** 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 (dagLogo)
dagLogo.Rcheck/tests/runTests.Rout
R Under development (unstable) (2019-12-14 r77572) -- "Unsuffered Consequences"
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("dagLogo") || stop("unable to load Package:dagLogo")
Loading required package: dagLogo
Loading required package: biomaRt
Loading required package: grImport2
Loading required package: grid
Loading required package: motifStack
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("Biostrings") || stop("unable to load Package:Biostrings")
[1] TRUE
> require("biomaRt") || stop("unable to load Package:biomaRt")
[1] TRUE
> data(seq.example)
> data(proteome.example)
> library(testthat)
>
> test_check("dagLogo")
══ testthat results ═══════════════════════════════════════════════════════════
[ OK: 3 | SKIPPED: 4 | WARNINGS: 0 | FAILED: 0 ]
>
> proc.time()
user system elapsed
24.977 2.013 26.941
dagLogo.Rcheck/dagLogo-Ex.timings
| name | user | system | elapsed | |
| addScheme | 0.002 | 0.001 | 0.002 | |
| buildBackgroundModel | 15.085 | 0.203 | 15.294 | |
| cleanPeptides | 0.008 | 0.001 | 0.010 | |
| colorsets | 0.001 | 0.000 | 0.001 | |
| dagHeatmap | 1.200 | 0.078 | 1.278 | |
| dagLogo-package | 5.575 | 0.562 | 6.200 | |
| dagLogo | 10.966 | 0.345 | 11.373 | |
| ecoli.proteome | 0.185 | 0.017 | 0.202 | |
| fetchSequence | 0.005 | 0.001 | 0.006 | |
| formatSequence | 11.496 | 0.017 | 11.518 | |
| getGroupingSymbol | 0.000 | 0.000 | 0.001 | |
| prepareProteome | 0.000 | 0.000 | 0.001 | |
| prepareProteomeByFTP | 0.014 | 0.001 | 0.015 | |
| prepareProteomeByUniProtWS | 0.001 | 0.000 | 0.001 | |
| proteome.example | 0.048 | 0.010 | 0.059 | |
| seq.example | 0.018 | 0.009 | 0.026 | |
| testDAU | 49.993 | 6.150 | 56.157 | |