Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-08-21 11:41 -0400 (Wed, 21 Aug 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" | 4703 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4440 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4472 |
kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4421 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4414 |
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 774/2255 | 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 | OK | OK | OK | OK | ![]() | ||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | ERROR | OK | |||||||||
kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | OK | OK | ![]() | ||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | 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: F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:GeDi.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings GeDi_1.1.1.tar.gz |
StartedAt: 2024-08-21 01:01:24 -0400 (Wed, 21 Aug 2024) |
EndedAt: 2024-08-21 01:14:29 -0400 (Wed, 21 Aug 2024) |
EllapsedTime: 785.4 seconds |
RetCode: 0 |
Status: OK |
CheckDir: GeDi.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:GeDi.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings GeDi_1.1.1.tar.gz ### ############################################################################## ############################################################################## * using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/GeDi.Rcheck' * using R version 4.4.1 (2024-06-14 ucrt) * using platform: x86_64-w64-mingw32 * R was compiled by gcc.exe (GCC) 13.2.0 GNU Fortran (GCC) 13.2.0 * running under: Windows Server 2022 x64 (build 20348) * using session charset: UTF-8 * using option '--no-vignettes' * 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 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 137.55 5.60 149.51 getPPI 98.03 3.78 102.55 goSimilarity 7.08 0.82 8.16 scaleGO 6.06 0.56 6.63 * 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: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL GeDi ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.20-bioc/R/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 ucrt) -- "Race for Your Life" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 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 167.76 8.75 185.40
GeDi.Rcheck/GeDi-Ex.timings
name | user | system | elapsed | |
GeDi | 0.00 | 0.02 | 0.01 | |
buildClusterGraph | 0.14 | 0.00 | 0.14 | |
buildGraph | 0 | 0 | 0 | |
buildHistogramData | 0.02 | 0.00 | 0.02 | |
calculateJaccard | 0 | 0 | 0 | |
calculateKappa | 0.03 | 0.02 | 0.05 | |
calculateSorensenDice | 0.00 | 0.01 | 0.01 | |
checkInclusion | 0.01 | 0.00 | 0.02 | |
clustering | 0.13 | 0.02 | 0.23 | |
distanceDendro | 0.12 | 0.02 | 0.14 | |
distanceHeatmap | 0.28 | 0.09 | 0.38 | |
enrichmentWordcloud | 0.65 | 0.36 | 0.56 | |
fuzzyClustering | 0 | 0 | 0 | |
getAdjacencyMatrix | 0.08 | 0.05 | 0.06 | |
getAnnotation | 137.55 | 5.60 | 149.51 | |
getBipartiteGraph | 0.01 | 0.00 | 0.02 | |
getClusterAdjacencyMatrix | 0.03 | 0.00 | 0.03 | |
getGenes | 0 | 0 | 0 | |
getGraphTitle | 0 | 0 | 0 | |
getId | 0.17 | 0.01 | 1.77 | |
getInteractionScore | 0.05 | 0.00 | 0.04 | |
getJaccardMatrix | 0.55 | 0.02 | 0.57 | |
getKappaMatrix | 2.00 | 0.17 | 2.17 | |
getMeetMinMatrix | 1.86 | 0.03 | 1.89 | |
getPPI | 98.03 | 3.78 | 102.55 | |
getSorensenDiceMatrix | 0.44 | 0.03 | 0.47 | |
getStringDB | 0.14 | 0.00 | 1.29 | |
getpMMMatrix | 1.03 | 0.03 | 1.06 | |
goSimilarity | 7.08 | 0.82 | 8.16 | |
gsHistogram | 0.01 | 0.02 | 0.03 | |
kNN_clustering | 0.05 | 0.00 | 0.04 | |
pMMlocal | 0.04 | 0.00 | 0.03 | |
scaleGO | 6.06 | 0.56 | 6.63 | |
seedFinding | 0.00 | 0.02 | 0.01 | |