Annekathrin Nedwed
| Snapshot Date: 2024-05-29 14:00:10 -0400 (Wed, 29 May 2024) |
| git_url: https://git.bioconductor.org/packages/GeDi |
| git_branch: RELEASE_3_19 |
| git_last_commit: 1ad6866 |
| git_last_commit_date: 2024-04-30 11:56:08 -0400 (Tue, 30 Apr 2024) |
| Back to Multiple platform build/check report for BioC 3.19: simplified long |
|
This page was generated on 2024-05-30 11:35:35 -0400 (Thu, 30 May 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4753 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4518 |
| 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 794/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| GeDi 1.0.0 (landing page) Annekathrin Nedwed
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.6.5 Ventura / arm64 | see weekly results here | ||||||||||||
|
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: 1.0.0 |
| 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_1.0.0.tar.gz |
| StartedAt: 2024-05-29 20:57:34 -0400 (Wed, 29 May 2024) |
| EndedAt: 2024-05-29 21:19:59 -0400 (Wed, 29 May 2024) |
| EllapsedTime: 1345.0 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: GeDi.Rcheck |
| Warnings: 0 |
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### 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_1.0.0.tar.gz
###
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##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/GeDi.Rcheck’
* using R version 4.4.0 (2024-04-24)
* 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 12.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GeDi/DESCRIPTION’ ... OK
* this is package ‘GeDi’ version ‘1.0.0’
* 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 ‘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 ... 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 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 113.411 6.052 400.533
getPPI 75.576 2.216 79.924
goSimilarity 6.766 0.809 7.682
scaleGO 5.330 0.455 5.882
getId 0.184 0.016 5.478
* 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: OK
GeDi.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL GeDi ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/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 version 4.4.0 (2024-04-24) -- "Puppy Cup"
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.
> library(testthat)
> library(GeDi)
>
> test_check("GeDi")
trying URL 'https://stringdb-downloads.org/download/protein.aliases.v11.5/9606.protein.aliases.v11.5.txt.gz'
Content type 'application/octet-stream' length 21726816 bytes (20.7 MB)
==================================================
downloaded 20.7 MB
trying URL 'https://stringdb-downloads.org/download/protein.info.v11.5/9606.protein.info.v11.5.txt.gz'
Content type 'application/octet-stream' length 1901833 bytes (1.8 MB)
==================================================
downloaded 1.8 MB
trying URL 'https://stringdb-downloads.org/download/protein.links.v11.5/9606.protein.links.v11.5.txt.gz'
Content type 'application/octet-stream' length 72718210 bytes (69.3 MB)
==================================================
downloaded 69.3 MB
preparing gene to GO mapping data...
preparing gene to GO mapping data...
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 182 ]
>
> proc.time()
user system elapsed
161.852 10.532 527.267
GeDi.Rcheck/GeDi-Ex.timings
| name | user | system | elapsed | |
| GeDi | 0.007 | 0.002 | 0.008 | |
| buildClusterGraph | 0.143 | 0.011 | 0.155 | |
| buildGraph | 0.007 | 0.001 | 0.008 | |
| buildHistogramData | 0.013 | 0.003 | 0.017 | |
| calculateJaccard | 0.011 | 0.002 | 0.013 | |
| calculateKappa | 0.032 | 0.002 | 0.036 | |
| calculateSorensenDice | 0.011 | 0.002 | 0.013 | |
| checkInclusion | 0.009 | 0.001 | 0.010 | |
| clustering | 0.160 | 0.009 | 0.171 | |
| distanceDendro | 0.163 | 0.005 | 0.170 | |
| distanceHeatmap | 0.177 | 0.013 | 0.195 | |
| enrichmentWordcloud | 0.335 | 0.018 | 0.356 | |
| fuzzyClustering | 0.005 | 0.001 | 0.006 | |
| getAdjacencyMatrix | 0.085 | 0.002 | 0.087 | |
| getAnnotation | 113.411 | 6.052 | 400.533 | |
| getBipartiteGraph | 0.007 | 0.001 | 0.007 | |
| getClusterAdjacencyMatrix | 0.036 | 0.001 | 0.037 | |
| getGenes | 0.011 | 0.009 | 0.022 | |
| getGraphTitle | 0.003 | 0.000 | 0.003 | |
| getId | 0.184 | 0.016 | 5.478 | |
| getInteractionScore | 0.032 | 0.016 | 0.049 | |
| getJaccardMatrix | 0.556 | 0.022 | 0.583 | |
| getKappaMatrix | 1.601 | 0.117 | 1.737 | |
| getMeetMinMatrix | 0.910 | 0.117 | 1.037 | |
| getPPI | 75.576 | 2.216 | 79.924 | |
| getSorensenDiceMatrix | 0.572 | 0.008 | 0.588 | |
| getStringDB | 0.128 | 0.011 | 2.338 | |
| getpMMMatrix | 0.817 | 0.028 | 0.851 | |
| goSimilarity | 6.766 | 0.809 | 7.682 | |
| gsHistogram | 0.023 | 0.005 | 0.028 | |
| kNN_clustering | 0.041 | 0.005 | 0.047 | |
| pMMlocal | 0.039 | 0.009 | 0.050 | |
| scaleGO | 5.330 | 0.455 | 5.882 | |
| seedFinding | 0.006 | 0.004 | 0.010 | |