| Back to Multiple platform build/check report for BioC 3.18: simplified long |
|
This page was generated on 2024-03-04 11:37:18 -0500 (Mon, 04 Mar 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.3.2 Patched (2023-11-13 r85521) -- "Eye Holes" | 4692 |
| palomino4 | Windows Server 2022 Datacenter | x64 | 4.3.2 (2023-10-31 ucrt) -- "Eye Holes" | 4445 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.3.2 Patched (2023-11-01 r85457) -- "Eye Holes" | 4466 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
| Package 590/2266 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| DominoEffect 1.22.0 (landing page) Marija Buljan
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK |  | ||||||||
| palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson1 | macOS 13.6.1 Ventura / arm64 | see weekly results here | ||||||||||||
|
To the developers/maintainers of the DominoEffect package: - 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 Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: DominoEffect |
| Version: 1.22.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:DominoEffect.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings DominoEffect_1.22.0.tar.gz |
| StartedAt: 2024-03-03 20:16:49 -0500 (Sun, 03 Mar 2024) |
| EndedAt: 2024-03-03 20:23:50 -0500 (Sun, 03 Mar 2024) |
| EllapsedTime: 421.0 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: DominoEffect.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:DominoEffect.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings DominoEffect_1.22.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.18-bioc/meat/DominoEffect.Rcheck’
* using R version 4.3.2 Patched (2023-11-01 r85457)
* using platform: x86_64-apple-darwin20 (64-bit)
* R was compiled by
Apple clang version 14.0.3 (clang-1403.0.22.14.1)
GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘DominoEffect/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘DominoEffect’ version ‘1.22.0’
* 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 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
GPo_of_hotspots 2.049 0.115 16.538
DominoEffect 1.531 0.173 17.576
map_to_func_elem 0.979 0.114 14.840
* 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-3.18-bioc/meat/DominoEffect.Rcheck/00check.log’
for details.
DominoEffect.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL DominoEffect ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-x86_64/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 4.3.2 Patched (2023-11-01 r85457) -- "Eye Holes"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20 (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;format=fasta' length 483 bytes
==================================================
downloaded 483 bytes
trying URL 'http://www.uniprot.org/uniprot/P29992.fasta'
Content type 'text/plain;format=fasta' length 483 bytes
==================================================
downloaded 483 bytes
trying URL 'http://www.uniprot.org/uniprot/O75533.fasta'
Content type 'text/plain;format=fasta' length 1421 bytes
==================================================
downloaded 1421 bytes
trying URL 'http://www.uniprot.org/uniprot/Q9NR22.fasta'
Content type 'text/plain;format=fasta' length 505 bytes
==================================================
downloaded 505 bytes
trying URL 'http://www.uniprot.org/uniprot/O96017.fasta'
Content type 'text/plain;format=fasta' length 655 bytes
==================================================
downloaded 655 bytes
================================================================================
trying URL 'http://www.uniprot.org/uniprot/P50148.fasta'
Content type 'text/plain;format=fasta' length 483 bytes
==================================================
downloaded 483 bytes
trying URL 'http://www.uniprot.org/uniprot/P29992.fasta'
Content type 'text/plain;format=fasta' length 483 bytes
==================================================
downloaded 483 bytes
trying URL 'http://www.uniprot.org/uniprot/Q9NR22.fasta'
Content type 'text/plain;format=fasta' length 505 bytes
==================================================
downloaded 505 bytes
================================================================================
trying URL 'http://www.uniprot.org/uniprot/P50148.fasta'
Content type 'text/plain;format=fasta' length 483 bytes
==================================================
downloaded 483 bytes
trying URL 'http://www.uniprot.org/uniprot/P29992.fasta'
Content type 'text/plain;format=fasta' length 483 bytes
==================================================
downloaded 483 bytes
================================================================================
trying URL 'http://www.uniprot.org/uniprot/P50148.fasta'
Content type 'text/plain;format=fasta' length 483 bytes
==================================================
downloaded 483 bytes
trying URL 'http://www.uniprot.org/uniprot/P29992.fasta'
Content type 'text/plain;format=fasta' length 483 bytes
==================================================
downloaded 483 bytes
trying URL 'http://www.uniprot.org/uniprot/O75533.fasta'
Content type 'text/plain;format=fasta' length 1421 bytes
==================================================
downloaded 1421 bytes
trying URL 'http://www.uniprot.org/uniprot/Q9NR22.fasta'
Content type 'text/plain;format=fasta' length 505 bytes
==================================================
downloaded 505 bytes
trying URL 'http://www.uniprot.org/uniprot/O96017.fasta'
Content type 'text/plain;format=fasta' length 655 bytes
==================================================
downloaded 655 bytes
================================================================================
[ FAIL 0 | WARN 4 | SKIP 0 | PASS 15 ]
[ FAIL 0 | WARN 4 | SKIP 0 | PASS 15 ]
>
> proc.time()
user system elapsed
20.777 1.344 64.567
DominoEffect.Rcheck/DominoEffect-Ex.timings
| name | user | system | elapsed | |
| DominoEffect | 1.531 | 0.173 | 17.576 | |
| GPo_of_hotspots | 2.049 | 0.115 | 16.538 | |
| align_to_unip | 0.247 | 0.027 | 0.277 | |
| calculate_boundary | 0 | 0 | 0 | |
| identify_hotspots | 0.184 | 0.028 | 0.214 | |
| import_txdb | 0 | 0 | 0 | |
| map_to_func_elem | 0.979 | 0.114 | 14.840 | |