Back to Multiple platform build/check report for BioC 3.21: simplified long |
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This page was generated on 2024-12-24 11:46 -0500 (Tue, 24 Dec 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" | 4754 |
palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" | 4472 |
lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4426 |
kjohnson3 | macOS 13.7.1 Ventura | arm64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4381 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" | 4373 |
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 778/2274 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
GeDi 1.3.0 (landing page) Annekathrin Nedwed
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | OK | OK | OK | |||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | WARNINGS | ||||||||||
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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
Package: GeDi |
Version: 1.3.0 |
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:GeDi.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings GeDi_1.3.0.tar.gz |
StartedAt: 2024-12-24 06:55:52 -0000 (Tue, 24 Dec 2024) |
EndedAt: 2024-12-24 07:23:40 -0000 (Tue, 24 Dec 2024) |
EllapsedTime: 1668.1 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: GeDi.Rcheck |
Warnings: 5 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD check --install=check:GeDi.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings GeDi_1.3.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/GeDi.Rcheck’ * using R Under development (unstable) (2024-11-24 r87369) * using platform: aarch64-unknown-linux-gnu * R was compiled by aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0 GNU Fortran (GCC) 14.2.0 * running under: openEuler 24.03 (LTS) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘GeDi/DESCRIPTION’ ... OK * this is package ‘GeDi’ version ‘1.3.0’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... INFO Imports includes 29 non-default packages. Importing from so many packages makes the package vulnerable to any of them becoming unavailable. Move as many as possible to Suggests and use conditionally. * 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 ... WARNING Found the following significant warnings: Warning: program compiled against libxml 212 using older 211 See ‘/home/biocbuild/bbs-3.21-bioc/meat/GeDi.Rcheck/00install.out’ for details. * 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 ...Warning: program compiled against libxml 212 using older 211 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 ... NOTE Warning: program compiled against libxml 212 using older 211 A namespace must be able to be loaded with just the base namespace loaded: otherwise if the namespace gets loaded by a saved object, the session will be unable to start. Probably some imports need to be declared in the NAMESPACE file. * 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 ... NOTE Warning: program compiled against libxml 212 using older 211 It looks like this package (or a package it requires) has a startup message which cannot be suppressed: see ?packageStartupMessage. * checking dependencies in R code ... NOTE Warning: program compiled against libxml 212 using older 211 * checking S3 generic/method consistency ... WARNING Warning: program compiled against libxml 212 using older 211 See section ‘Generic functions and methods’ in the ‘Writing R Extensions’ manual. * checking replacement functions ... WARNING Warning: program compiled against libxml 212 using older 211 The argument of a replacement function which corresponds to the right hand side must be named ‘value’. * checking foreign function calls ... NOTE Warning: program compiled against libxml 212 using older 211 See chapter ‘System and foreign language interfaces’ in the ‘Writing R Extensions’ manual. * checking R code for possible problems ... NOTE Warning: program compiled against libxml 212 using older 211 * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... NOTE Found the following Rd file(s) with Rd \link{} targets missing package anchors: buildClusterGraph.Rd: igraph dot-graphMetricsGenesetsDT.Rd: igraph getAnnotation.Rd: STRINGdb getId.Rd: STRINGdb getPPI.Rd: STRINGdb getStringDB.Rd: STRINGdb Please provide package anchors for all Rd \link{} targets not in the package itself and the base packages. * checking for missing documentation entries ... WARNING Warning: program compiled against libxml 212 using older 211 All user-level objects in a package should have documentation entries. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. * checking for code/documentation mismatches ... WARNING Warning: program compiled against libxml 212 using older 211 Warning: program compiled against libxml 212 using older 211 Warning: program compiled against libxml 212 using older 211 * checking Rd \usage sections ... NOTE Warning: program compiled against libxml 212 using older 211 The \usage entries for S3 methods should use the \method markup and not their full name. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. * 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 120.855 5.214 250.373 getPPI 79.597 2.471 83.343 goDistance 7.423 0.332 7.769 scaleGO 6.326 0.331 6.670 getId 0.209 0.127 7.631 getStringDB 0.193 0.071 18.277 * 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: 5 WARNINGs, 7 NOTEs See ‘/home/biocbuild/bbs-3.21-bioc/meat/GeDi.Rcheck/00check.log’ for details.
GeDi.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL GeDi ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library’ * installing *source* package ‘GeDi’ ... ** using staged installation ** R ** data ** inst ** byte-compile and prepare package for lazy loading Warning: program compiled against libxml 212 using older 211 ** help *** installing help indices *** copying figures ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location Warning: program compiled against libxml 212 using older 211 ** testing if installed package can be loaded from final location Warning: program compiled against libxml 212 using older 211 ** testing if installed package keeps a record of temporary installation path * DONE (GeDi)
GeDi.Rcheck/tests/testthat.Rout
R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: aarch64-unknown-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) Warning: program compiled against libxml 212 using older 211 > > 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 9 | SKIP 0 | PASS 185 ] [ FAIL 0 | WARN 9 | SKIP 0 | PASS 185 ] > > proc.time() user system elapsed 157.200 6.000 831.249
GeDi.Rcheck/GeDi-Ex.timings
name | user | system | elapsed | |
GeDi | 0.007 | 0.000 | 0.007 | |
buildClusterGraph | 0.208 | 0.016 | 0.226 | |
buildGraph | 0.008 | 0.000 | 0.008 | |
buildHistogramData | 0.01 | 0.00 | 0.01 | |
calculateJaccard | 0.009 | 0.000 | 0.010 | |
calculateKappa | 0.013 | 0.004 | 0.017 | |
calculateSorensenDice | 0.009 | 0.000 | 0.009 | |
checkInclusion | 0.009 | 0.000 | 0.009 | |
clustering | 0.250 | 0.004 | 0.255 | |
deprecated | 0 | 0 | 0 | |
distanceDendro | 0.164 | 0.004 | 0.167 | |
distanceHeatmap | 0.19 | 0.00 | 0.19 | |
enrichmentWordcloud | 0.305 | 0.000 | 0.306 | |
fuzzyClustering | 0.007 | 0.000 | 0.007 | |
getAdjacencyMatrix | 0.080 | 0.012 | 0.092 | |
getAnnotation | 120.855 | 5.214 | 250.373 | |
getBipartiteGraph | 0.012 | 0.000 | 0.012 | |
getClusterAdjacencyMatrix | 0.064 | 0.000 | 0.065 | |
getGraphTitle | 0.003 | 0.003 | 0.007 | |
getId | 0.209 | 0.127 | 7.631 | |
getInteractionScore | 0.037 | 0.008 | 0.045 | |
getJaccardMatrix | 3.500 | 0.878 | 4.387 | |
getKappaMatrix | 1.021 | 0.036 | 1.060 | |
getMeetMinMatrix | 4.245 | 0.587 | 4.842 | |
getPPI | 79.597 | 2.471 | 83.343 | |
getSorensenDiceMatrix | 0.660 | 0.024 | 0.686 | |
getStringDB | 0.193 | 0.071 | 18.277 | |
getpMMMatrix | 1.108 | 0.059 | 1.170 | |
goDistance | 7.423 | 0.332 | 7.769 | |
gsHistogram | 0.025 | 0.004 | 0.029 | |
kMeansClustering | 0.018 | 0.000 | 0.018 | |
kNN_clustering | 0.01 | 0.00 | 0.01 | |
louvainClustering | 0.076 | 0.012 | 0.088 | |
markovClustering | 0.094 | 0.004 | 0.098 | |
pMMlocal | 0.037 | 0.000 | 0.037 | |
pamClustering | 0.008 | 0.000 | 0.008 | |
prepareGenesetData | 0.01 | 0.00 | 0.01 | |
scaleGO | 6.326 | 0.331 | 6.670 | |
seedFinding | 0.004 | 0.004 | 0.008 | |