Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-07-24 11:38 -0400 (Wed, 24 Jul 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4688 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4284 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4455 |
kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4404 |
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 772/2248 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
GeDi 1.1.1 (landing page) Annekathrin Nedwed
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | ERROR | ERROR | skipped | skipped | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | OK | OK | ![]() | ||||||||
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: 1.1.1 |
Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:GeDi.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings GeDi_1.1.1.tar.gz |
StartedAt: 2024-07-23 23:41:30 -0400 (Tue, 23 Jul 2024) |
EndedAt: 2024-07-23 23:56:01 -0400 (Tue, 23 Jul 2024) |
EllapsedTime: 871.6 seconds |
RetCode: 0 |
Status: OK |
CheckDir: GeDi.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:GeDi.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings GeDi_1.1.1.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/GeDi.Rcheck’ * using R version 4.4.1 (2024-06-14) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 * running under: Ubuntu 22.04.4 LTS * using session charset: UTF-8 * checking for file ‘GeDi/DESCRIPTION’ ... OK * this is package ‘GeDi’ version ‘1.1.1’ * 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 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 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 104.599 9.091 199.388 getPPI 68.887 2.055 71.426 goSimilarity 6.705 0.256 6.966 getId 0.327 0.020 5.109 * 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: OK
GeDi.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL GeDi ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-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 4.4.1 (2024-06-14) -- "Race for Your Life" 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. > 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 0 | SKIP 0 | PASS 182 ] > > proc.time() user system elapsed 125.451 7.586 223.715
GeDi.Rcheck/GeDi-Ex.timings
name | user | system | elapsed | |
GeDi | 0.008 | 0.000 | 0.007 | |
buildClusterGraph | 0.186 | 0.028 | 0.214 | |
buildGraph | 0.008 | 0.000 | 0.009 | |
buildHistogramData | 0.010 | 0.000 | 0.009 | |
calculateJaccard | 0.009 | 0.000 | 0.008 | |
calculateKappa | 0.011 | 0.008 | 0.019 | |
calculateSorensenDice | 0.008 | 0.000 | 0.008 | |
checkInclusion | 0.007 | 0.000 | 0.008 | |
clustering | 0.123 | 0.000 | 0.123 | |
distanceDendro | 0.158 | 0.016 | 0.174 | |
distanceHeatmap | 0.176 | 0.012 | 0.188 | |
enrichmentWordcloud | 0.242 | 0.012 | 0.253 | |
fuzzyClustering | 0.006 | 0.000 | 0.006 | |
getAdjacencyMatrix | 0.066 | 0.000 | 0.066 | |
getAnnotation | 104.599 | 9.091 | 199.388 | |
getBipartiteGraph | 0.005 | 0.003 | 0.009 | |
getClusterAdjacencyMatrix | 0.036 | 0.000 | 0.037 | |
getGenes | 0.004 | 0.006 | 0.010 | |
getGraphTitle | 0.003 | 0.001 | 0.004 | |
getId | 0.327 | 0.020 | 5.109 | |
getInteractionScore | 0.054 | 0.004 | 0.059 | |
getJaccardMatrix | 0.463 | 0.040 | 0.504 | |
getKappaMatrix | 1.222 | 0.163 | 1.386 | |
getMeetMinMatrix | 0.701 | 0.091 | 0.793 | |
getPPI | 68.887 | 2.055 | 71.426 | |
getSorensenDiceMatrix | 0.417 | 0.000 | 0.417 | |
getStringDB | 0.264 | 0.011 | 3.070 | |
getpMMMatrix | 1.039 | 0.044 | 1.083 | |
goSimilarity | 6.705 | 0.256 | 6.966 | |
gsHistogram | 0.02 | 0.00 | 0.02 | |
kNN_clustering | 0.034 | 0.000 | 0.034 | |
pMMlocal | 0.023 | 0.004 | 0.028 | |
scaleGO | 4.326 | 0.124 | 4.451 | |
seedFinding | 0.004 | 0.000 | 0.005 | |