Marija Buljan
| Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020) |
| URL: https://git.bioconductor.org/packages/DominoEffect |
| Branch: RELEASE_3_11 |
| Last Commit: c907bc2 |
| Last Changed Date: 2020-04-27 15:14:06 -0400 (Mon, 27 Apr 2020) |
| Back to Multiple platform build/check report for BioC 3.11 |
|
This page was generated on 2020-10-17 11:58:24 -0400 (Sat, 17 Oct 2020).
| TO THE DEVELOPERS/MAINTAINERS OF THE DominoEffect PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 497/1905 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| DominoEffect 1.8.0 Marija Buljan
| malbec2 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | [ OK ] | OK | |
| Package: DominoEffect |
| Version: 1.8.0 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:DominoEffect.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings DominoEffect_1.8.0.tar.gz |
| StartedAt: 2020-10-17 00:40:28 -0400 (Sat, 17 Oct 2020) |
| EndedAt: 2020-10-17 00:48:46 -0400 (Sat, 17 Oct 2020) |
| EllapsedTime: 497.8 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: DominoEffect.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:DominoEffect.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings DominoEffect_1.8.0.tar.gz
###
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##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/DominoEffect.Rcheck’
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘DominoEffect/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘DominoEffect’ version ‘1.8.0’
* 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 ‘DominoEffect’ 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 ... NOTE
import_txdb: no visible binding for global variable ‘TXTYPE’
Undefined global functions or variables:
TXTYPE
* 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
DominoEffect 4.167 0.150 11.785
GPo_of_hotspots 2.904 0.096 10.491
map_to_func_elem 2.644 0.060 10.574
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘test-all.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: 1 NOTE
See
‘/Users/biocbuild/bbs-3.11-bioc/meat/DominoEffect.Rcheck/00check.log’
for details.
DominoEffect.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL DominoEffect ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’ * installing *source* package ‘DominoEffect’ ... ** using staged installation ** R ** data *** moving datasets to lazyload DB ** 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 (DominoEffect)
DominoEffect.Rcheck/tests/test-all.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-apple-darwin17.0 (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.
> library(testthat)
> test_check("DominoEffect")
Loading required package: DominoEffect
trying URL 'http://www.uniprot.org/uniprot/P50148.fasta'
Content type 'text/plain' length 483 bytes
==================================================
downloaded 483 bytes
trying URL 'http://www.uniprot.org/uniprot/P29992.fasta'
Content type 'text/plain' length 483 bytes
==================================================
downloaded 483 bytes
trying URL 'http://www.uniprot.org/uniprot/O75533.fasta'
Content type 'text/plain' length 1421 bytes
==================================================
downloaded 1421 bytes
trying URL 'http://www.uniprot.org/uniprot/Q9NR22.fasta'
Content type 'text/plain' length 505 bytes
==================================================
downloaded 505 bytes
trying URL 'http://www.uniprot.org/uniprot/O96017.fasta'
Content type 'text/plain' length 655 bytes
==================================================
downloaded 655 bytes
================================================================================
trying URL 'http://www.uniprot.org/uniprot/P50148.fasta'
Content type 'text/plain' length 483 bytes
==================================================
downloaded 483 bytes
trying URL 'http://www.uniprot.org/uniprot/P29992.fasta'
Content type 'text/plain' length 483 bytes
==================================================
downloaded 483 bytes
trying URL 'http://www.uniprot.org/uniprot/Q9NR22.fasta'
Content type 'text/plain' length 505 bytes
==================================================
downloaded 505 bytes
================================================================================
trying URL 'http://www.uniprot.org/uniprot/P50148.fasta'
Content type 'text/plain' length 483 bytes
==================================================
downloaded 483 bytes
trying URL 'http://www.uniprot.org/uniprot/P29992.fasta'
Content type 'text/plain' length 483 bytes
==================================================
downloaded 483 bytes
================================================================================
trying URL 'http://www.uniprot.org/uniprot/P50148.fasta'
Content type 'text/plain' length 483 bytes
==================================================
downloaded 483 bytes
trying URL 'http://www.uniprot.org/uniprot/P29992.fasta'
Content type 'text/plain' length 483 bytes
==================================================
downloaded 483 bytes
trying URL 'http://www.uniprot.org/uniprot/O75533.fasta'
Content type 'text/plain' length 1421 bytes
==================================================
downloaded 1421 bytes
trying URL 'http://www.uniprot.org/uniprot/Q9NR22.fasta'
Content type 'text/plain' length 505 bytes
==================================================
downloaded 505 bytes
trying URL 'http://www.uniprot.org/uniprot/O96017.fasta'
Content type 'text/plain' length 655 bytes
==================================================
downloaded 655 bytes
================================================================================
══ testthat results ═══════════════════════════════════════════════════════════
[ OK: 15 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
>
> proc.time()
user system elapsed
31.584 1.032 61.121
DominoEffect.Rcheck/DominoEffect-Ex.timings
| name | user | system | elapsed | |
| DominoEffect | 4.167 | 0.150 | 11.785 | |
| GPo_of_hotspots | 2.904 | 0.096 | 10.491 | |
| align_to_unip | 0.267 | 0.009 | 0.278 | |
| calculate_boundary | 0.000 | 0.001 | 0.002 | |
| identify_hotspots | 0.219 | 0.012 | 0.233 | |
| import_txdb | 0.000 | 0.000 | 0.001 | |
| map_to_func_elem | 2.644 | 0.060 | 10.574 | |