Annekathrin Nedwed
| Snapshot Date: 2025-01-21 13:40 -0500 (Tue, 21 Jan 2025) |
| git_url: https://git.bioconductor.org/packages/GeDi |
| git_branch: devel |
| git_last_commit: 8157757 |
| git_last_commit_date: 2024-10-29 11:30:20 -0500 (Tue, 29 Oct 2024) |
| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2025-01-22 11:45 -0500 (Wed, 22 Jan 2025).
| 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" | 4779 |
| palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" | 4503 |
| lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4468 |
| kjohnson3 | macOS 13.7.1 Ventura | arm64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4423 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" | 4407 |
| 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 780/2286 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| GeDi 1.3.0 (landing page) Annekathrin Nedwed
| 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 | WARNINGS | ||||||||||
|
To the developers/maintainers of the GeDi package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/GeDi.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: GeDi |
| Version: 1.3.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:GeDi.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings GeDi_1.3.0.tar.gz |
| StartedAt: 2025-01-21 19:29:14 -0500 (Tue, 21 Jan 2025) |
| EndedAt: 2025-01-21 19:37:59 -0500 (Tue, 21 Jan 2025) |
| EllapsedTime: 525.2 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: GeDi.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:GeDi.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings GeDi_1.3.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/GeDi.Rcheck’
* using R Under development (unstable) (2024-11-20 r87352)
* using platform: aarch64-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 Ventura 13.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GeDi/DESCRIPTION’ ... OK
* this is package ‘GeDi’ version ‘1.3.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 29 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable. Move as many as possible to Suggests and
use conditionally.
* 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 ‘GeDi’ 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 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 ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
buildClusterGraph.Rd: igraph
dot-graphMetricsGenesetsDT.Rd: igraph
getAnnotation.Rd: STRINGdb
getId.Rd: STRINGdb
getPPI.Rd: STRINGdb
getStringDB.Rd: STRINGdb
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* 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 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
getAnnotation 46.137 1.617 186.464
getPPI 28.353 1.031 29.914
getId 0.068 0.013 6.879
* 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-3.21-bioc/meat/GeDi.Rcheck/00check.log’
for details.
GeDi.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL GeDi ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library’ * installing *source* package ‘GeDi’ ... ** using staged installation ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** 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 (GeDi)
GeDi.Rcheck/tests/testthat.Rout
R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-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.
> library(testthat)
> library(GeDi)
>
> test_check("GeDi")
trying URL 'https://stringdb-downloads.org/download/protein.aliases.v12.0/9606.protein.aliases.v12.0.txt.gz'
Content type 'application/octet-stream' length 19777800 bytes (18.9 MB)
==================================================
downloaded 18.9 MB
trying URL 'https://stringdb-downloads.org/download/protein.info.v12.0/9606.protein.info.v12.0.txt.gz'
Content type 'application/octet-stream' length 1970090 bytes (1.9 MB)
==================================================
downloaded 1.9 MB
trying URL 'https://stringdb-downloads.org/download/protein.links.v12.0/9606.protein.links.v12.0.txt.gz'
Content type 'application/octet-stream' length 83164437 bytes (79.3 MB)
==================================================
downloaded 79.3 MB
preparing gene to GO mapping data...
preparing gene to GO mapping data...
[ FAIL 0 | WARN 9 | SKIP 0 | PASS 185 ]
[ FAIL 0 | WARN 9 | SKIP 0 | PASS 185 ]
>
> proc.time()
user system elapsed
52.119 2.126 156.874
GeDi.Rcheck/GeDi-Ex.timings
| name | user | system | elapsed | |
| GeDi | 0.003 | 0.000 | 0.003 | |
| buildClusterGraph | 0.090 | 0.004 | 0.094 | |
| buildGraph | 0.003 | 0.000 | 0.003 | |
| buildHistogramData | 0.003 | 0.001 | 0.004 | |
| calculateJaccard | 0.003 | 0.000 | 0.003 | |
| calculateKappa | 0.008 | 0.000 | 0.008 | |
| calculateSorensenDice | 0.002 | 0.000 | 0.004 | |
| checkInclusion | 0.002 | 0.000 | 0.003 | |
| clustering | 0.055 | 0.001 | 0.056 | |
| deprecated | 0 | 0 | 0 | |
| distanceDendro | 0.046 | 0.001 | 0.048 | |
| distanceHeatmap | 0.059 | 0.004 | 0.064 | |
| enrichmentWordcloud | 0.108 | 0.003 | 0.112 | |
| fuzzyClustering | 0.002 | 0.000 | 0.002 | |
| getAdjacencyMatrix | 0.016 | 0.000 | 0.016 | |
| getAnnotation | 46.137 | 1.617 | 186.464 | |
| getBipartiteGraph | 0.002 | 0.000 | 0.003 | |
| getClusterAdjacencyMatrix | 0.026 | 0.000 | 0.026 | |
| getGraphTitle | 0.001 | 0.000 | 0.002 | |
| getId | 0.068 | 0.013 | 6.879 | |
| getInteractionScore | 0.011 | 0.001 | 0.013 | |
| getJaccardMatrix | 0.156 | 0.005 | 0.162 | |
| getKappaMatrix | 0.242 | 0.026 | 0.267 | |
| getMeetMinMatrix | 0.216 | 0.020 | 0.236 | |
| getPPI | 28.353 | 1.031 | 29.914 | |
| getSorensenDiceMatrix | 0.125 | 0.004 | 0.129 | |
| getStringDB | 0.047 | 0.007 | 4.792 | |
| getpMMMatrix | 0.249 | 0.027 | 0.278 | |
| goDistance | 2.108 | 0.196 | 2.324 | |
| gsHistogram | 0.007 | 0.002 | 0.009 | |
| kMeansClustering | 0.006 | 0.002 | 0.008 | |
| kNN_clustering | 0.003 | 0.002 | 0.005 | |
| louvainClustering | 0.015 | 0.002 | 0.017 | |
| markovClustering | 0.019 | 0.004 | 0.022 | |
| pMMlocal | 0.012 | 0.006 | 0.018 | |
| pamClustering | 0.003 | 0.002 | 0.005 | |
| prepareGenesetData | 0.003 | 0.002 | 0.004 | |
| scaleGO | 1.832 | 0.140 | 1.983 | |
| seedFinding | 0.002 | 0.001 | 0.003 | |