Back to Multiple platform build/check report for BioC 3.19: simplified long |
|
This page was generated on 2024-06-21 17:38 -0400 (Fri, 21 Jun 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" | 4758 |
palomino3 | Windows Server 2022 Datacenter | x64 | 4.4.0 (2024-04-24 ucrt) -- "Puppy Cup" | 4492 |
merida1 | macOS 12.7.4 Monterey | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4506 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4464 |
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 | ![]() | ||||||||
palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | ![]() | ||||||||
merida1 | macOS 12.7.4 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kjohnson1 | macOS 13.6.6 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: 1.0.0 |
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_1.0.0.tar.gz |
StartedAt: 2024-06-19 23:24:56 -0400 (Wed, 19 Jun 2024) |
EndedAt: 2024-06-19 23:39:16 -0400 (Wed, 19 Jun 2024) |
EllapsedTime: 859.8 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_1.0.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/GeDi.Rcheck’ * using R version 4.4.0 (2024-04-24) * 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 ‘1.0.0’ * 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 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 88.792 8.322 177.919 getPPI 65.907 4.008 70.493 goSimilarity 5.009 0.696 5.705 scaleGO 4.845 0.527 5.373 getId 0.429 0.032 5.855 * 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 4.4.0 (2024-04-24) -- "Puppy Cup" 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.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 132.887 9.708 231.074
GeDi.Rcheck/GeDi-Ex.timings
name | user | system | elapsed | |
GeDi | 0.007 | 0.000 | 0.007 | |
buildClusterGraph | 0.157 | 0.037 | 0.192 | |
buildGraph | 0.007 | 0.000 | 0.007 | |
buildHistogramData | 0.009 | 0.000 | 0.009 | |
calculateJaccard | 0.008 | 0.000 | 0.008 | |
calculateKappa | 0.020 | 0.000 | 0.019 | |
calculateSorensenDice | 0.009 | 0.000 | 0.009 | |
checkInclusion | 0.005 | 0.003 | 0.009 | |
clustering | 0.111 | 0.000 | 0.112 | |
distanceDendro | 0.132 | 0.016 | 0.148 | |
distanceHeatmap | 0.241 | 0.008 | 0.249 | |
enrichmentWordcloud | 0.245 | 0.004 | 0.250 | |
fuzzyClustering | 0.006 | 0.000 | 0.006 | |
getAdjacencyMatrix | 0.063 | 0.003 | 0.067 | |
getAnnotation | 88.792 | 8.322 | 177.919 | |
getBipartiteGraph | 0.005 | 0.004 | 0.009 | |
getClusterAdjacencyMatrix | 0.03 | 0.02 | 0.05 | |
getGenes | 0.011 | 0.000 | 0.011 | |
getGraphTitle | 0.005 | 0.000 | 0.005 | |
getId | 0.429 | 0.032 | 5.855 | |
getInteractionScore | 0.030 | 0.004 | 0.035 | |
getJaccardMatrix | 0.495 | 0.052 | 0.546 | |
getKappaMatrix | 2.002 | 0.284 | 2.287 | |
getMeetMinMatrix | 0.671 | 0.056 | 0.726 | |
getPPI | 65.907 | 4.008 | 70.493 | |
getSorensenDiceMatrix | 0.421 | 0.024 | 0.444 | |
getStringDB | 0.337 | 0.041 | 3.305 | |
getpMMMatrix | 0.674 | 0.072 | 0.747 | |
goSimilarity | 5.009 | 0.696 | 5.705 | |
gsHistogram | 0.031 | 0.000 | 0.031 | |
kNN_clustering | 0.038 | 0.012 | 0.051 | |
pMMlocal | 0.027 | 0.004 | 0.032 | |
scaleGO | 4.845 | 0.527 | 5.373 | |
seedFinding | 0.005 | 0.000 | 0.006 | |