Back to Multiple platform build/check report for BioC 3.22: simplified long |
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This page was generated on 2025-10-17 12:07 -0400 (Fri, 17 Oct 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" | 4887 |
lconway | macOS 12.7.6 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4677 |
kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4622 |
taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4632 |
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 196/2353 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
BioCor 1.33.1 (landing page) Lluís Revilla Sancho
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | ERROR | |||||||||
lconway | macOS 12.7.6 Monterey / x86_64 | OK | OK | ERROR | OK | |||||||||
kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | ERROR | OK | |||||||||
taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | ERROR | ||||||||||
To the developers/maintainers of the BioCor package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/BioCor.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: BioCor |
Version: 1.33.1 |
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:BioCor.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings BioCor_1.33.1.tar.gz |
StartedAt: 2025-10-17 06:28:11 -0000 (Fri, 17 Oct 2025) |
EndedAt: 2025-10-17 06:31:34 -0000 (Fri, 17 Oct 2025) |
EllapsedTime: 202.3 seconds |
RetCode: 1 |
Status: ERROR |
CheckDir: BioCor.Rcheck |
Warnings: NA |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD check --install=check:BioCor.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings BioCor_1.33.1.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/BioCor.Rcheck’ * using R version 4.5.0 (2025-04-11) * 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 ‘BioCor/DESCRIPTION’ ... OK * this is package ‘BioCor’ version ‘1.33.1’ * 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 ‘BioCor’ 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 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 files in ‘vignettes’ ... OK * checking examples ... ERROR Running examples in ‘BioCor-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: plot_data > ### Title: The position of the nodes is based on the similarity between > ### them. > ### Aliases: plot_data plot_similarity > > ### ** Examples > > if (require("org.Hs.eg.db") & require("reactome.db")) { + # Extract the paths of all genes of org.Hs.eg.db from KEGG + # (last update in data of June 31st 2011) + genes.kegg <- as.list(org.Hs.egPATH) + # Extracts the paths of all genes of org.Hs.eg.db from reactome + genes.react <- as.list(reactomeEXTID2PATHID) + + sim <- mgeneSim(c("81", "18", "10"), genes.react) + pd <- plot_data(sim, top = 0.25) + if (requireNamespace("ggplot2", quietly = TRUE)){ + plot_similarity(pd) + } + } Loading required package: org.Hs.eg.db Loading required package: AnnotationDbi Loading required package: stats4 Loading required package: BiocGenerics Loading required package: generics Attaching package: ‘generics’ The following objects are masked from ‘package:base’: as.difftime, as.factor, as.ordered, intersect, is.element, setdiff, setequal, union Attaching package: ‘BiocGenerics’ The following objects are masked from ‘package:stats’: IQR, mad, sd, var, xtabs The following objects are masked from ‘package:base’: Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append, as.data.frame, basename, cbind, colnames, dirname, do.call, duplicated, eval, evalq, get, grep, grepl, is.unsorted, lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply, saveRDS, table, tapply, unique, unsplit, which.max, which.min Loading required package: Biobase Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. Loading required package: IRanges Loading required package: S4Vectors Attaching package: ‘S4Vectors’ The following object is masked from ‘package:utils’: findMatches The following objects are masked from ‘package:base’: I, expand.grid, unname Loading required package: reactome.db Warning in mgeneSim(c("81", "18", "10"), genes.react) : Some genes are not in the list provided. Error in quantile.default(x[upper.tri(x)], probs = 1 - top) : missing values and NaN's not allowed if 'na.rm' is FALSE Calls: plot_data -> quantile -> quantile.default Execution halted * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘spelling.R’ 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: 1 ERROR See ‘/home/biocbuild/bbs-3.22-bioc/meat/BioCor.Rcheck/00check.log’ for details.
BioCor.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL BioCor ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.5.0/site-library’ * installing *source* package ‘BioCor’ ... ** this is package ‘BioCor’ version ‘1.33.1’ ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading Creating a generic function from function ‘clusterGeneSim’ in package ‘BioCor’ Creating a generic function from function ‘clusterSim’ in package ‘BioCor’ Creating a generic function from function ‘geneSim’ in package ‘BioCor’ Creating a generic function from function ‘mclusterGeneSim’ in package ‘BioCor’ Creating a generic function from function ‘mclusterSim’ in package ‘BioCor’ Creating a generic function from function ‘mgeneSim’ in package ‘BioCor’ Creating a generic function from function ‘mpathSim’ in package ‘BioCor’ Creating a generic function from function ‘pathSim’ in package ‘BioCor’ ** 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 (BioCor)
BioCor.Rcheck/tests/spelling.Rout
R version 4.5.0 (2025-04-11) -- "How About a Twenty-Six" Copyright (C) 2025 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. > if(requireNamespace('spelling', quietly = TRUE)) + spelling::spell_check_test(vignettes = TRUE, error = FALSE, + skip_on_cran = TRUE) All Done! > > proc.time() user system elapsed 0.187 0.030 0.200
BioCor.Rcheck/tests/testthat.Rout
R version 4.5.0 (2025-04-11) -- "How About a Twenty-Six" Copyright (C) 2025 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("BioCor") > > if (requireNamespace("testthat", quietly = TRUE)) { + library("testthat") + test_check("BioCor") + } Loading required package: AnnotationDbi Loading required package: stats4 Loading required package: BiocGenerics Loading required package: generics Attaching package: 'generics' The following objects are masked from 'package:base': as.difftime, as.factor, as.ordered, intersect, is.element, setdiff, setequal, union Attaching package: 'BiocGenerics' The following objects are masked from 'package:stats': IQR, mad, sd, var, xtabs The following objects are masked from 'package:base': Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append, as.data.frame, basename, cbind, colnames, dirname, do.call, duplicated, eval, evalq, get, grep, grepl, is.unsorted, lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply, saveRDS, table, tapply, unique, unsplit, which.max, which.min Loading required package: Biobase Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. Loading required package: IRanges Loading required package: S4Vectors Attaching package: 'S4Vectors' The following object is masked from 'package:utils': findMatches The following objects are masked from 'package:base': I, expand.grid, unname [ FAIL 0 | WARN 14 | SKIP 0 | PASS 314 ] [ FAIL 0 | WARN 14 | SKIP 0 | PASS 314 ] > > proc.time() user system elapsed 15.550 0.604 16.184
BioCor.Rcheck/BioCor-Ex.timings
name | user | system | elapsed | |
AintoB | 0.002 | 0.000 | 0.001 | |
addSimilarities | 0.005 | 0.004 | 0.008 | |
clusterGeneSim | 3.391 | 0.200 | 3.598 | |
clusterSim | 2.517 | 0.064 | 2.587 | |
combinadic | 0.001 | 0.000 | 0.000 | |
combineScores | 0.009 | 0.000 | 0.008 | |
combineSources | 0.003 | 0.000 | 0.003 | |
conversions | 0.000 | 0.000 | 0.001 | |
diceSim | 0.000 | 0.000 | 0.001 | |
duplicateIndices | 0.000 | 0.000 | 0.001 | |
geneSim | 4.122 | 0.096 | 4.229 | |
mclusterGeneSim | 2.946 | 0.067 | 3.020 | |
mclusterSim | 2.360 | 0.024 | 2.389 | |
mgeneSim | 4.621 | 0.068 | 4.698 | |
mpathSim | 4.276 | 0.048 | 4.331 | |
pathSim | 2.713 | 0.004 | 2.723 | |