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This page was generated on 2021-10-15 15:06:34 -0400 (Fri, 15 Oct 2021).
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To the developers/maintainers of the DominoEffect package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/DominoEffect.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 525/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| DominoEffect 1.12.0 (landing page) Marija Buljan
| nebbiolo1 | Linux (Ubuntu 20.04.2 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: 1.12.0 |
| 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_1.12.0.tar.gz |
| StartedAt: 2021-10-14 18:32:17 -0400 (Thu, 14 Oct 2021) |
| EndedAt: 2021-10-14 18:39:56 -0400 (Thu, 14 Oct 2021) |
| EllapsedTime: 459.3 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_1.12.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.13-bioc/meat/DominoEffect.Rcheck’
* using R version 4.1.1 (2021-08-10)
* 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 ‘1.12.0’
* 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 ... NOTE
Found the following hidden files and directories:
.git_fetch_output.txt
.git_merge_output.txt
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* 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 LazyData ... 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 4.290 0.187 17.393
GPo_of_hotspots 2.880 0.084 16.305
map_to_func_elem 2.802 0.056 15.663
* 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: 2 NOTEs
See
‘/Users/biocbuild/bbs-3.13-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/4.1/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 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 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
================================================================================
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 15 ]
>
> proc.time()
user system elapsed
27.179 0.994 71.785
DominoEffect.Rcheck/DominoEffect-Ex.timings
| name | user | system | elapsed | |
| DominoEffect | 4.290 | 0.187 | 17.393 | |
| GPo_of_hotspots | 2.880 | 0.084 | 16.305 | |
| align_to_unip | 0.304 | 0.009 | 0.314 | |
| calculate_boundary | 0.000 | 0.000 | 0.001 | |
| identify_hotspots | 0.299 | 0.022 | 0.322 | |
| import_txdb | 0 | 0 | 0 | |
| map_to_func_elem | 2.802 | 0.056 | 15.663 | |