Annekathrin Nedwed
| Snapshot Date: 2024-05-18 09:00:01 -0400 (Sat, 18 May 2024) |
| git_url: https://git.bioconductor.org/packages/GeDi |
| git_branch: devel |
| git_last_commit: 3edc9b7 |
| git_last_commit_date: 2024-04-30 11:56:08 -0400 (Tue, 30 Apr 2024) |
| Back to Mac ARM64 build report for BioC 3.20 |
|
This page was generated on 2024-05-20 11:32:11 -0400 (Mon, 20 May 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4381 |
| 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 765/2233 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| GeDi 1.1.0 (landing page) Annekathrin Nedwed
| kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | | |||||||
|
To the developers/maintainers of the GeDi package: - 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: 1.1.0 |
| 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_1.1.0.tar.gz |
| StartedAt: 2024-05-19 13:57:38 -0400 (Sun, 19 May 2024) |
| EndedAt: 2024-05-19 14:09:38 -0400 (Sun, 19 May 2024) |
| EllapsedTime: 719.9 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_1.1.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.20-bioc-mac-arm64/meat/GeDi.Rcheck’
* using R version 4.4.0 Patched (2024-04-24 r86482)
* 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 13.6.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GeDi/DESCRIPTION’ ... OK
* this is package ‘GeDi’ version ‘1.1.0’
* 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 138.959 3.623 147.148
getPPI 87.849 2.261 90.956
goSimilarity 7.050 0.536 7.630
scaleGO 5.666 0.398 6.099
* 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-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 version 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup"
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.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
167.562 5.569 177.902
GeDi.Rcheck/GeDi-Ex.timings
| name | user | system | elapsed | |
| GeDi | 0.009 | 0.001 | 0.011 | |
| buildClusterGraph | 0.123 | 0.009 | 0.133 | |
| buildGraph | 0.007 | 0.001 | 0.008 | |
| buildHistogramData | 0.011 | 0.001 | 0.012 | |
| calculateJaccard | 0.009 | 0.001 | 0.011 | |
| calculateKappa | 0.037 | 0.001 | 0.039 | |
| calculateSorensenDice | 0.010 | 0.002 | 0.011 | |
| checkInclusion | 0.009 | 0.002 | 0.010 | |
| clustering | 0.144 | 0.006 | 0.152 | |
| distanceDendro | 0.112 | 0.003 | 0.116 | |
| distanceHeatmap | 0.089 | 0.011 | 0.102 | |
| enrichmentWordcloud | 0.182 | 0.008 | 0.194 | |
| fuzzyClustering | 0.005 | 0.001 | 0.006 | |
| getAdjacencyMatrix | 0.052 | 0.001 | 0.053 | |
| getAnnotation | 138.959 | 3.623 | 147.148 | |
| getBipartiteGraph | 0.008 | 0.000 | 0.008 | |
| getClusterAdjacencyMatrix | 0.060 | 0.001 | 0.063 | |
| getGenes | 0.011 | 0.001 | 0.012 | |
| getGraphTitle | 0.005 | 0.000 | 0.005 | |
| getId | 0.159 | 0.011 | 0.749 | |
| getInteractionScore | 0.016 | 0.002 | 0.018 | |
| getJaccardMatrix | 0.367 | 0.011 | 0.383 | |
| getKappaMatrix | 1.277 | 0.121 | 1.414 | |
| getMeetMinMatrix | 0.769 | 0.070 | 0.843 | |
| getPPI | 87.849 | 2.261 | 90.956 | |
| getSorensenDiceMatrix | 0.513 | 0.004 | 0.520 | |
| getStringDB | 0.128 | 0.010 | 0.685 | |
| getpMMMatrix | 0.494 | 0.019 | 0.520 | |
| goSimilarity | 7.050 | 0.536 | 7.630 | |
| gsHistogram | 0.026 | 0.005 | 0.031 | |
| kNN_clustering | 0.042 | 0.003 | 0.045 | |
| pMMlocal | 0.038 | 0.006 | 0.044 | |
| scaleGO | 5.666 | 0.398 | 6.099 | |
| seedFinding | 0.006 | 0.003 | 0.009 | |