Back to Multiple platform build/check report for BioC 3.19: simplified long |
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This page was generated on 2024-09-10 17:33 -0400 (Tue, 10 Sep 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4758 |
palomino7 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4495 |
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 1.0.1 (landing page) Annekathrin Nedwed
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino7 | Windows Server 2022 Datacenter / x64 | 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: 1.0.1 |
Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:GeDi.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings GeDi_1.0.1.tar.gz |
StartedAt: 2024-09-08 23:18:01 -0400 (Sun, 08 Sep 2024) |
EndedAt: 2024-09-08 23:32:34 -0400 (Sun, 08 Sep 2024) |
EllapsedTime: 873.0 seconds |
RetCode: 0 |
Status: OK |
CheckDir: GeDi.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:GeDi.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings GeDi_1.0.1.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.19-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 ‘1.0.1’ * 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 99.166 9.405 196.384 getPPI 65.862 3.789 70.063 goSimilarity 5.174 0.592 5.767 scaleGO 5.014 0.558 5.572 getId 0.324 0.048 5.258 * 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-3.19-bioc/R/bin/R CMD INSTALL GeDi ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.19-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 122.629 9.315 226.092
GeDi.Rcheck/GeDi-Ex.timings
name | user | system | elapsed | |
GeDi | 0.004 | 0.004 | 0.007 | |
buildClusterGraph | 0.123 | 0.000 | 0.123 | |
buildGraph | 0.007 | 0.000 | 0.007 | |
buildHistogramData | 0.009 | 0.000 | 0.009 | |
calculateJaccard | 0.008 | 0.000 | 0.008 | |
calculateKappa | 0.019 | 0.000 | 0.019 | |
calculateSorensenDice | 0.008 | 0.000 | 0.008 | |
checkInclusion | 0.007 | 0.000 | 0.008 | |
clustering | 0.111 | 0.003 | 0.116 | |
distanceDendro | 0.179 | 0.021 | 0.199 | |
distanceHeatmap | 0.132 | 0.004 | 0.136 | |
enrichmentWordcloud | 0.217 | 0.024 | 0.241 | |
fuzzyClustering | 0.005 | 0.000 | 0.006 | |
getAdjacencyMatrix | 0.196 | 0.008 | 0.205 | |
getAnnotation | 99.166 | 9.405 | 196.384 | |
getBipartiteGraph | 0.009 | 0.000 | 0.009 | |
getClusterAdjacencyMatrix | 0.040 | 0.004 | 0.043 | |
getGenes | 0.01 | 0.00 | 0.01 | |
getGraphTitle | 0.004 | 0.000 | 0.004 | |
getId | 0.324 | 0.048 | 5.258 | |
getInteractionScore | 0.025 | 0.007 | 0.031 | |
getJaccardMatrix | 0.447 | 0.048 | 0.496 | |
getKappaMatrix | 1.174 | 0.260 | 1.433 | |
getMeetMinMatrix | 0.622 | 0.138 | 0.760 | |
getPPI | 65.862 | 3.789 | 70.063 | |
getSorensenDiceMatrix | 0.429 | 0.008 | 0.436 | |
getStringDB | 0.312 | 0.040 | 3.041 | |
getpMMMatrix | 0.675 | 0.056 | 0.731 | |
goSimilarity | 5.174 | 0.592 | 5.767 | |
gsHistogram | 0.020 | 0.008 | 0.027 | |
kNN_clustering | 0.034 | 0.008 | 0.041 | |
pMMlocal | 0.025 | 0.005 | 0.030 | |
scaleGO | 5.014 | 0.558 | 5.572 | |
seedFinding | 0.006 | 0.000 | 0.006 | |