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This page was generated on 2024-11-16 12:04 -0500 (Sat, 16 Nov 2024).

HostnameOSArch (*)R versionInstalled pkgs
teran2Linux (Ubuntu 24.04.1 LTS)x86_644.4.1 (2024-06-14) -- "Race for Your Life" 4505
palomino8Windows Server 2022 Datacenterx644.4.1 (2024-06-14 ucrt) -- "Race for Your Life" 4506
lconwaymacOS 12.7.1 Montereyx86_644.4.1 (2024-06-14) -- "Race for Your Life" 4538
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch644.4.1 (2024-06-14) -- "Race for Your Life" 4493
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 646/2289HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
EnrichDO 1.0.0  (landing page)
Hongyu Fu
Snapshot Date: 2024-11-15 13:40 -0500 (Fri, 15 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)
teran2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino8Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    OK  

CHECK results for EnrichDO on lconway

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.

raw results


Summary

Package: EnrichDO
Version: 1.0.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:EnrichDO.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings EnrichDO_1.0.0.tar.gz
StartedAt: 2024-11-15 21:40:04 -0500 (Fri, 15 Nov 2024)
EndedAt: 2024-11-15 21:48:37 -0500 (Fri, 15 Nov 2024)
EllapsedTime: 512.8 seconds
RetCode: 0
Status:   OK  
CheckDir: EnrichDO.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:EnrichDO.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings EnrichDO_1.0.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/EnrichDO.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘EnrichDO/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘EnrichDO’ version ‘1.0.0’
* 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 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 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-3.20-bioc/meat/EnrichDO.Rcheck/00check.log’
for details.

Installation output

EnrichDO.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL EnrichDO
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/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)

Tests output

EnrichDO.Rcheck/tests/testthat.Rout


R version 4.4.1 (2024-06-14) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

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 
112.772  15.951 129.514

Example timings

EnrichDO.Rcheck/EnrichDO-Ex.timings

nameusersystemelapsed
convDraw1.6030.0781.694
doEnrich2.6430.3563.012
drawBarGraph2.6680.3243.000
drawGraphViz3.0030.3683.385
drawHeatmap2.5980.3182.926
drawPointGraph2.5570.2782.843
showDoTerms0.0010.0000.001
writeDoTerms0.5640.2150.627
writeResult2.5700.3002.884