Hongyu Fu
| Snapshot Date: 2024-12-23 13:40 -0500 (Mon, 23 Dec 2024) |
| git_url: https://git.bioconductor.org/packages/EnrichDO |
| git_branch: devel |
| git_last_commit: ef3d0ef |
| git_last_commit_date: 2024-11-27 22:59:18 -0500 (Wed, 27 Nov 2024) |
| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2024-12-24 11:46 -0500 (Tue, 24 Dec 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" | 4754 |
| palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" | 4472 |
| lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4426 |
| kjohnson3 | macOS 13.7.1 Ventura | arm64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4381 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" | 4373 |
| 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 639/2274 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| EnrichDO 1.1.1 (landing page) Hongyu Fu
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | OK | ||||||||||
|
To the developers/maintainers of the EnrichDO package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/EnrichDO.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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
| Package: EnrichDO |
| Version: 1.1.1 |
| Command: /home/biocbuild/R/R/bin/R CMD check --install=check:EnrichDO.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings EnrichDO_1.1.1.tar.gz |
| StartedAt: 2024-12-24 06:25:38 -0000 (Tue, 24 Dec 2024) |
| EndedAt: 2024-12-24 06:34:25 -0000 (Tue, 24 Dec 2024) |
| EllapsedTime: 526.3 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: EnrichDO.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/R/R/bin/R CMD check --install=check:EnrichDO.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings EnrichDO_1.1.1.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/EnrichDO.Rcheck’
* using R Under development (unstable) (2024-11-24 r87369)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘EnrichDO/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘EnrichDO’ version ‘1.1.1’
* 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 ‘EnrichDO’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
License stub is invalid DCF.
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code 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 loading without being on the library search path ... OK
* checking whether startup messages can be suppressed ... 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 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
drawGraphViz 6.843 0.155 7.020
drawBarGraph 6.270 0.132 6.418
drawHeatmap 6.263 0.104 6.391
doEnrich 6.149 0.079 6.246
drawPointGraph 6.104 0.023 6.145
writeResult 5.948 0.024 5.991
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... 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
‘/home/biocbuild/bbs-3.21-bioc/meat/EnrichDO.Rcheck/00check.log’
for details.
EnrichDO.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL EnrichDO ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library’ * installing *source* package ‘EnrichDO’ ... ** 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 (EnrichDO)
EnrichDO.Rcheck/tests/testthat.Rout
R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu
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.
> # This file is part of the standard setup for testthat. It is recommended that you do not modify it. Where should you do additional
> # test configuration? Learn more about the roles of various files in: *
> # https://r-pkgs.org/testing-design.html#sec-tests-files-overview * https://testthat.r-lib.org/articles/special-files.html
>
> library(testthat)
> library(EnrichDO)
>
> test_check("EnrichDO")
-- Descending rights test--
LEVEL: 13 1 nodes 72 genes to be scored
LEVEL: 12 2 nodes 457 genes to be scored
LEVEL: 11 3 nodes 907 genes to be scored
LEVEL: 10 13 nodes 2279 genes to be scored
LEVEL: 9 54 nodes 6504 genes to be scored
LEVEL: 8 130 nodes 9483 genes to be scored
LEVEL: 7 198 nodes 11209 genes to be scored
LEVEL: 6 220 nodes 12574 genes to be scored
LEVEL: 5 198 nodes 12936 genes to be scored
LEVEL: 4 103 nodes 12824 genes to be scored
LEVEL: 3 30 nodes 11683 genes to be scored
LEVEL: 2 5 nodes 8032 genes to be scored
LEVEL: 1 0 nodes 0 genes to be scored
-- Descending rights test--
LEVEL: 13 1 nodes 72 genes to be scored
LEVEL: 12 2 nodes 457 genes to be scored
LEVEL: 11 3 nodes 907 genes to be scored
LEVEL: 10 13 nodes 2279 genes to be scored
LEVEL: 9 54 nodes 6504 genes to be scored
LEVEL: 8 130 nodes 9483 genes to be scored
LEVEL: 7 198 nodes 11209 genes to be scored
LEVEL: 6 220 nodes 12574 genes to be scored
LEVEL: 5 198 nodes 12936 genes to be scored
LEVEL: 4 103 nodes 12824 genes to be scored
LEVEL: 3 30 nodes 11683 genes to be scored
LEVEL: 2 5 nodes 8032 genes to be scored
-- Descending rights test--
LEVEL: 13 1 nodes 72 genes to be scored
LEVEL: 12 2 nodes 457 genes to be scored
LEVEL: 11 3 nodes 907 genes to be scored
LEVEL: 10 13 nodes 2279 genes to be scored
LEVEL: 9 54 nodes 6504 genes to be scored
LEVEL: 8 130 nodes 9483 genes to be scored
LEVEL: 7 198 nodes 11209 genes to be scored
LEVEL: 6 220 nodes 12574 genes to be scored
LEVEL: 5 198 nodes 12936 genes to be scored
LEVEL: 4 103 nodes 12824 genes to be scored
LEVEL: 3 30 nodes 11683 genes to be scored
-- Descending rights test--
LEVEL: 13 1 nodes 72 genes to be scored
LEVEL: 12 2 nodes 457 genes to be scored
LEVEL: 11 3 nodes 907 genes to be scored
LEVEL: 10 13 nodes 2279 genes to be scored
LEVEL: 9 54 nodes 6504 genes to be scored
LEVEL: 8 130 nodes 9483 genes to be scored
LEVEL: 7 198 nodes 11209 genes to be scored
LEVEL: 6 220 nodes 12574 genes to be scored
LEVEL: 5 198 nodes 12936 genes to be scored
LEVEL: 4 103 nodes 12824 genes to be scored
-- Descending rights test--
LEVEL: 13 1 nodes 72 genes to be scored
LEVEL: 12 2 nodes 457 genes to be scored
LEVEL: 11 3 nodes 907 genes to be scored
LEVEL: 10 13 nodes 2279 genes to be scored
LEVEL: 9 54 nodes 6504 genes to be scored
LEVEL: 8 130 nodes 9483 genes to be scored
LEVEL: 7 198 nodes 11209 genes to be scored
LEVEL: 6 220 nodes 12574 genes to be scored
LEVEL: 5 198 nodes 12936 genes to be scored
-- Descending rights test--
LEVEL: 13 1 nodes 72 genes to be scored
LEVEL: 12 2 nodes 457 genes to be scored
LEVEL: 11 3 nodes 907 genes to be scored
LEVEL: 10 13 nodes 2279 genes to be scored
LEVEL: 9 54 nodes 6504 genes to be scored
LEVEL: 8 130 nodes 9483 genes to be scored
LEVEL: 7 198 nodes 11209 genes to be scored
LEVEL: 6 220 nodes 12574 genes to be scored
LEVEL: 5 198 nodes 12936 genes to be scored
LEVEL: 4 103 nodes 12824 genes to be scored
LEVEL: 3 30 nodes 11683 genes to be scored
LEVEL: 2 5 nodes 8032 genes to be scored
LEVEL: 1 0 nodes 0 genes to be scored
-- Descending rights test--
LEVEL: 13 1 nodes 72 genes to be scored
LEVEL: 12 2 nodes 457 genes to be scored
LEVEL: 11 3 nodes 907 genes to be scored
LEVEL: 10 13 nodes 2279 genes to be scored
LEVEL: 9 54 nodes 6504 genes to be scored
LEVEL: 8 130 nodes 9483 genes to be scored
LEVEL: 7 198 nodes 11209 genes to be scored
LEVEL: 6 220 nodes 12574 genes to be scored
LEVEL: 5 198 nodes 12936 genes to be scored
LEVEL: 4 103 nodes 12824 genes to be scored
LEVEL: 3 30 nodes 11683 genes to be scored
LEVEL: 2 5 nodes 8032 genes to be scored
LEVEL: 1 0 nodes 0 genes to be scored
-- Descending rights test--
LEVEL: 13 1 nodes 72 genes to be scored
LEVEL: 12 2 nodes 457 genes to be scored
LEVEL: 11 3 nodes 907 genes to be scored
LEVEL: 10 13 nodes 2279 genes to be scored
LEVEL: 9 54 nodes 6504 genes to be scored
LEVEL: 8 130 nodes 9483 genes to be scored
LEVEL: 7 198 nodes 11209 genes to be scored
LEVEL: 6 220 nodes 12574 genes to be scored
LEVEL: 5 198 nodes 12936 genes to be scored
LEVEL: 4 103 nodes 12824 genes to be scored
LEVEL: 3 30 nodes 11683 genes to be scored
LEVEL: 2 5 nodes 8032 genes to be scored
LEVEL: 1 0 nodes 0 genes to be scored
-- Descending rights test--
LEVEL: 13 1 nodes 72 genes to be scored
LEVEL: 12 2 nodes 457 genes to be scored
LEVEL: 11 3 nodes 907 genes to be scored
LEVEL: 10 13 nodes 2279 genes to be scored
LEVEL: 9 54 nodes 6504 genes to be scored
LEVEL: 8 130 nodes 9483 genes to be scored
LEVEL: 7 198 nodes 11209 genes to be scored
LEVEL: 6 220 nodes 12574 genes to be scored
LEVEL: 5 198 nodes 12936 genes to be scored
LEVEL: 4 103 nodes 12824 genes to be scored
LEVEL: 3 30 nodes 11683 genes to be scored
LEVEL: 2 5 nodes 8032 genes to be scored
LEVEL: 1 0 nodes 0 genes to be scored
[ FAIL 0 | WARN 1 | SKIP 0 | PASS 2 ]
[ FAIL 0 | WARN 1 | SKIP 0 | PASS 2 ]
>
> proc.time()
user system elapsed
257.336 2.678 268.321
EnrichDO.Rcheck/EnrichDO-Ex.timings
| name | user | system | elapsed | |
| convDraw | 2.522 | 0.280 | 2.812 | |
| doEnrich | 6.149 | 0.079 | 6.246 | |
| drawBarGraph | 6.270 | 0.132 | 6.418 | |
| drawGraphViz | 6.843 | 0.155 | 7.020 | |
| drawHeatmap | 6.263 | 0.104 | 6.391 | |
| drawPointGraph | 6.104 | 0.023 | 6.145 | |
| showDoTerms | 0.002 | 0.000 | 0.002 | |
| writeResult | 5.948 | 0.024 | 5.991 | |