Back to Multiple platform build/check report for BioC 3.22: simplified long |
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This page was generated on 2025-10-18 12:03 -0400 (Sat, 18 Oct 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
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 182/2353 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
bioCancer 1.37.0 (landing page) Karim Mezhoud
| 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 bioCancer package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/bioCancer.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: bioCancer |
Version: 1.37.0 |
Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:bioCancer.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings bioCancer_1.37.0.tar.gz |
StartedAt: 2025-10-17 21:27:09 -0400 (Fri, 17 Oct 2025) |
EndedAt: 2025-10-17 21:33:34 -0400 (Fri, 17 Oct 2025) |
EllapsedTime: 385.5 seconds |
RetCode: 1 |
Status: ERROR |
CheckDir: bioCancer.Rcheck |
Warnings: NA |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:bioCancer.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings bioCancer_1.37.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/bioCancer.Rcheck’ * using R version 4.5.1 Patched (2025-08-23 r88802) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0 GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0 * running under: Ubuntu 24.04.3 LTS * using session charset: UTF-8 * checking for file ‘bioCancer/DESCRIPTION’ ... OK * this is package ‘bioCancer’ version ‘1.37.0’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... INFO Imports includes 24 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 ‘bioCancer’ can be installed ... OK * checking installed package size ... INFO installed size is 6.6Mb sub-directories of 1Mb or more: app 3.4Mb extdata 2.6Mb * 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 ... NOTE Invalid package aliases in Rd file 'bioCancer.Rd': ‘-package’ * 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 LazyData ... OK * checking data for ASCII and uncompressed saves ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ ERROR Running the tests in ‘tests/testthat.R’ failed. Last 13 lines of output: 6. │ └─base::is.data.frame(x) 7. └─cBioPortalData::clinicalData(x, "gbm_tcga_pub") 8. └─cBioPortalData:::.invoke_bind(...) 9. ├─cBioPortalData:::.bind_content(.invoke_fun(api, name, ...)) 10. │ ├─dplyr::bind_rows(httr::content(x)) 11. │ │ └─rlang::list2(...) 12. │ └─httr::content(x) 13. │ ├─base::stopifnot(is.response(x)) 14. │ └─httr:::is.response(x) 15. └─cBioPortalData:::.invoke_fun(api, name, ...) 16. └─httr::stop_for_status(res) [ FAIL 1 | WARN 0 | SKIP 1 | PASS 0 ] Error: Test failures Execution halted * 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: 1 ERROR, 1 NOTE See ‘/home/biocbuild/bbs-3.22-bioc/meat/bioCancer.Rcheck/00check.log’ for details.
bioCancer.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL bioCancer ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’ * installing *source* package ‘bioCancer’ ... ** this is package ‘bioCancer’ version ‘1.37.0’ ** using staged installation ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** 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 (bioCancer)
bioCancer.Rcheck/tests/testthat.Rout.fail
R version 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" Copyright (C) 2025 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(bioCancer) Loading required package: radiant.data Loading required package: magrittr Attaching package: 'magrittr' The following objects are masked from 'package:testthat': equals, is_less_than, not Loading required package: ggplot2 Loading required package: lubridate Attaching package: 'lubridate' The following objects are masked from 'package:base': date, intersect, setdiff, union Loading required package: tidyr Attaching package: 'tidyr' The following object is masked from 'package:magrittr': extract The following object is masked from 'package:testthat': matches Loading required package: dplyr Attaching package: 'dplyr' The following object is masked from 'package:testthat': matches The following objects are masked from 'package:stats': filter, lag The following objects are masked from 'package:base': intersect, setdiff, setequal, union Attaching package: 'radiant.data' The following objects are masked from 'package:lubridate': month, wday The following object is masked from 'package:ggplot2': diamonds The following object is masked from 'package:magrittr': set_attr The following object is masked from 'package:testthat': describe The following object is masked from 'package:base': date Loading required package: cBioPortalData Loading required package: AnVIL Loading required package: AnVILBase Loading required package: MultiAssayExperiment Loading required package: SummarizedExperiment Loading required package: MatrixGenerics Loading required package: matrixStats Attaching package: 'matrixStats' The following object is masked from 'package:dplyr': count Attaching package: 'MatrixGenerics' The following objects are masked from 'package:matrixStats': colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse, colCounts, colCummaxs, colCummins, colCumprods, colCumsums, colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs, colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats, colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds, colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads, colWeightedMeans, colWeightedMedians, colWeightedSds, colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet, rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods, rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps, rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins, rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks, rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars, rowWeightedMads, rowWeightedMeans, rowWeightedMedians, rowWeightedSds, rowWeightedVars Loading required package: GenomicRanges Loading required package: stats4 Loading required package: BiocGenerics Loading required package: generics Attaching package: 'generics' The following objects are masked from 'package:radiant.data': explore, visualize The following object is masked from 'package:dplyr': explain The following object is masked from 'package:lubridate': as.difftime 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 object is masked from 'package:radiant.data': normalize The following object is masked from 'package:dplyr': combine 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: S4Vectors Attaching package: 'S4Vectors' The following objects are masked from 'package:dplyr': first, rename The following object is masked from 'package:tidyr': expand The following objects are masked from 'package:lubridate': second, second<- The following object is masked from 'package:utils': findMatches The following objects are masked from 'package:base': I, expand.grid, unname Loading required package: IRanges Attaching package: 'IRanges' The following objects are masked from 'package:dplyr': collapse, desc, slice The following object is masked from 'package:lubridate': %within% Loading required package: Seqinfo Attaching package: 'GenomicRanges' The following object is masked from 'package:magrittr': subtract 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")'. Attaching package: 'Biobase' The following object is masked from 'package:MatrixGenerics': rowMedians The following objects are masked from 'package:matrixStats': anyMissing, rowMedians Loading required package: XML > > test_check("bioCancer") getCancerStudies... OK getCaseLists (1/1) ... OK ReactomeFI connection... OK [ FAIL 1 | WARN 0 | SKIP 1 | PASS 0 ] ══ Skipped tests (1) ═══════════════════════════════════════════════════════════ • empty test (1): 'test_funs.R:20:1' ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test_funs.R:17:23'): cBioPortal connection ────────────────────────── <http_404/http_400/http_error/error/condition> Error in `.invoke_fun(api, name, ...)`: Not Found (HTTP 404). Backtrace: ▆ 1. └─bioCancer::test.CGDS(cgds) at test_funs.R:17:23 2. ├─base::cat(...) 3. ├─bioCancer (local) checkTrue(...) 4. ├─"DFS_MONTHS" %in% ... 5. ├─base::colnames(cBioPortalData::clinicalData(x, "gbm_tcga_pub")) 6. │ └─base::is.data.frame(x) 7. └─cBioPortalData::clinicalData(x, "gbm_tcga_pub") 8. └─cBioPortalData:::.invoke_bind(...) 9. ├─cBioPortalData:::.bind_content(.invoke_fun(api, name, ...)) 10. │ ├─dplyr::bind_rows(httr::content(x)) 11. │ │ └─rlang::list2(...) 12. │ └─httr::content(x) 13. │ ├─base::stopifnot(is.response(x)) 14. │ └─httr:::is.response(x) 15. └─cBioPortalData:::.invoke_fun(api, name, ...) 16. └─httr::stop_for_status(res) [ FAIL 1 | WARN 0 | SKIP 1 | PASS 0 ] Error: Test failures Execution halted
bioCancer.Rcheck/bioCancer-Ex.timings
name | user | system | elapsed | |
AnnotationFuncs | 0.155 | 0.005 | 0.162 | |
Edges_Diseases_obj | 0.001 | 0.001 | 0.002 | |
Mutation_obj | 0.127 | 0.010 | 0.362 | |
Node_Diseases_obj | 0.002 | 0.000 | 0.001 | |
Node_df_FreqIn | 0.001 | 0.000 | 0.000 | |
Node_obj_CNA_ProfData | 0.062 | 0.012 | 0.094 | |
Node_obj_FreqIn | 0.001 | 0.000 | 0.000 | |
Node_obj_Met_ProfData | 0.061 | 0.011 | 0.088 | |
Node_obj_mRNA_Classifier | 0.001 | 0.000 | 0.001 | |
Studies_obj | 0.006 | 0.000 | 0.006 | |
UnifyRowNames | 0.058 | 0.014 | 0.087 | |
attriColorGene | 0.057 | 0.014 | 0.089 | |
attriColorValue | 0.056 | 0.015 | 0.087 | |
attriColorVector | 0.199 | 0.027 | 0.242 | |
attriShape2Gene | 0 | 0 | 0 | |
attriShape2Node | 0 | 0 | 0 | |
bioCancer | 0 | 0 | 0 | |
checkDimensions | 0.059 | 0.005 | 0.079 | |
coffeewheel | 0 | 0 | 0 | |
coffeewheelOutput | 0.000 | 0.000 | 0.001 | |
displayTable | 0.056 | 0.005 | 0.078 | |
findPhantom | 0 | 0 | 0 | |
getEvidenceCodes | 0 | 0 | 0 | |
getFreqMutData | 0.059 | 0.001 | 0.075 | |
getGenesClassification | 0.059 | 0.000 | 0.074 | |
getListProfData | 0.060 | 0.000 | 0.076 | |
getList_Cases | 0.058 | 0.001 | 0.076 | |
getList_GenProfs | 0.058 | 0.001 | 0.076 | |
getOrthologs | 0 | 0 | 0 | |
getProfData | 0.069 | 0.000 | 0.085 | |
getSequensed_SampleSize | 0.000 | 0.000 | 0.001 | |
mapLists | 0.000 | 0.001 | 0.000 | |
metabologram | 0 | 0 | 0 | |
metabologramOutput | 0 | 0 | 0 | |
pickGO | 0.089 | 0.002 | 0.093 | |
pickRefSeq | 0.053 | 0.002 | 0.055 | |
reStrColorGene | 0.058 | 0.002 | 0.076 | |
reStrDimension | 0.061 | 0.000 | 0.078 | |
reStrDisease | 0.056 | 0.016 | 0.088 | |
removeNAs | 0 | 0 | 0 | |
renderCoffeewheel | 0 | 0 | 0 | |
renderMetabologram | 0 | 0 | 0 | |
returnTextAreaInput | 0 | 0 | 0 | |
translate | 0.104 | 0.006 | 0.109 | |
whichGeneList | 0 | 0 | 0 | |
widgetThumbnail | 0 | 0 | 0 | |