Hongyu Fu
| Snapshot Date: 2024-11-28 13:00 -0500 (Thu, 28 Nov 2024) |
| git_url: https://git.bioconductor.org/packages/EnrichDO |
| git_branch: RELEASE_3_20 |
| git_last_commit: 49283aa |
| git_last_commit_date: 2024-10-29 11:33:46 -0500 (Tue, 29 Oct 2024) |
| Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2024-12-02 12:03 -0500 (Mon, 02 Dec 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4739 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4482 |
| merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4510 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4462 |
| 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 646/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| EnrichDO 1.0.0 (landing page) Hongyu Fu
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 12.7.5 Monterey / x86_64 | OK | ERROR | skipped | skipped | |||||||||
| kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | ERROR | skipped | skipped | |||||||||
|
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. |
| Package: EnrichDO |
| Version: 1.0.0 |
| Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:EnrichDO.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings EnrichDO_1.0.0.tar.gz |
| StartedAt: 2024-11-28 23:22:15 -0500 (Thu, 28 Nov 2024) |
| EndedAt: 2024-11-28 23:31:59 -0500 (Thu, 28 Nov 2024) |
| EllapsedTime: 584.4 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: EnrichDO.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:EnrichDO.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings EnrichDO_1.0.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/EnrichDO.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* checking for file ‘EnrichDO/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘EnrichDO’ version ‘1.0.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
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
* 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 1 NOTE
See
‘/home/biocbuild/bbs-3.20-bioc/meat/EnrichDO.Rcheck/00check.log’
for details.
EnrichDO.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL EnrichDO ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/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 version 4.4.2 (2024-10-31) -- "Pile of Leaves"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-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
chr [1:3] "DOID:1561" "DOID:150" "DOID:4"
chr [1:3] "DOID:1561" "DOID:150" "DOID:4"
chr [1:6] "DOID:680" "DOID:1289" "DOID:331" "DOID:863" "DOID:7" "DOID:4"
chr [1:6] "DOID:0050890" "DOID:1289" "DOID:331" "DOID:863" "DOID:7" ...
chr [1:5] "DOID:1289" "DOID:331" "DOID:863" "DOID:7" "DOID:4"
-- 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
chr [1:3] "DOID:1561" "DOID:150" "DOID:4"
chr [1:3] "DOID:1561" "DOID:150" "DOID:4"
chr [1:6] "DOID:680" "DOID:1289" "DOID:331" "DOID:863" "DOID:7" "DOID:4"
chr [1:6] "DOID:0050890" "DOID:1289" "DOID:331" "DOID:863" "DOID:7" ...
chr [1:5] "DOID:1289" "DOID:331" "DOID:863" "DOID:7" "DOID:4"
-- 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
chr [1:3] "DOID:1561" "DOID:150" "DOID:4"
chr [1:3] "DOID:1561" "DOID:150" "DOID:4"
chr [1:6] "DOID:680" "DOID:1289" "DOID:331" "DOID:863" "DOID:7" "DOID:4"
chr [1:6] "DOID:0050890" "DOID:1289" "DOID:331" "DOID:863" "DOID:7" ...
chr [1:5] "DOID:1289" "DOID:331" "DOID:863" "DOID:7" "DOID:4"
-- 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
chr [1:3] "DOID:1561" "DOID:150" "DOID:4"
chr [1:3] "DOID:1561" "DOID:150" "DOID:4"
chr [1:6] "DOID:680" "DOID:1289" "DOID:331" "DOID:863" "DOID:7" "DOID:4"
chr [1:6] "DOID:0050890" "DOID:1289" "DOID:331" "DOID:863" "DOID:7" ...
chr [1:5] "DOID:1289" "DOID:331" "DOID:863" "DOID:7" "DOID:4"
[ FAIL 0 | WARN 1 | SKIP 0 | PASS 2 ]
[ FAIL 0 | WARN 1 | SKIP 0 | PASS 2 ]
>
> proc.time()
user system elapsed
128.494 1.673 130.158
EnrichDO.Rcheck/EnrichDO-Ex.timings
| name | user | system | elapsed | |
| convDraw | 1.615 | 0.164 | 1.779 | |
| doEnrich | 2.953 | 0.036 | 2.989 | |
| drawBarGraph | 3.163 | 0.048 | 3.211 | |
| drawGraphViz | 3.589 | 0.148 | 3.736 | |
| drawHeatmap | 3.121 | 0.054 | 3.175 | |
| drawPointGraph | 2.997 | 0.021 | 3.017 | |
| showDoTerms | 0.001 | 0.000 | 0.001 | |
| writeDoTerms | 0.528 | 0.243 | 0.750 | |
| writeResult | 2.940 | 0.022 | 2.962 | |