Back to Multiple platform build/check report for BioC 3.21: simplified long |
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This page was generated on 2025-03-22 11:42 -0400 (Sat, 22 Mar 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2025-03-13 r87965) -- "Unsuffered Consequences" | 4777 |
palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2025-03-01 r87860 ucrt) -- "Unsuffered Consequences" | 4547 |
lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences" | 4576 |
kjohnson3 | macOS 13.7.1 Ventura | arm64 | R Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences" | 4528 |
kunpeng2 | Linux (openEuler 24.03 LTS) | aarch64 | R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" | 4458 |
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 1228/2313 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
metaseqR2 1.19.1 (landing page) Panagiotis Moulos
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | ERROR | |||||||||
palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | ERROR | 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 24.03 LTS) / aarch64 | OK | ERROR | skipped | ||||||||||
To the developers/maintainers of the metaseqR2 package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/metaseqR2.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: metaseqR2 |
Version: 1.19.1 |
Command: E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:metaseqR2.install-out.txt --library=E:\biocbuild\bbs-3.21-bioc\R\library --no-vignettes --timings metaseqR2_1.19.1.tar.gz |
StartedAt: 2025-03-22 03:11:12 -0400 (Sat, 22 Mar 2025) |
EndedAt: 2025-03-22 03:24:12 -0400 (Sat, 22 Mar 2025) |
EllapsedTime: 780.4 seconds |
RetCode: 1 |
Status: ERROR |
CheckDir: metaseqR2.Rcheck |
Warnings: NA |
############################################################################## ############################################################################## ### ### Running command: ### ### E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:metaseqR2.install-out.txt --library=E:\biocbuild\bbs-3.21-bioc\R\library --no-vignettes --timings metaseqR2_1.19.1.tar.gz ### ############################################################################## ############################################################################## * using log directory 'E:/biocbuild/bbs-3.21-bioc/meat/metaseqR2.Rcheck' * using R Under development (unstable) (2025-03-01 r87860 ucrt) * using platform: x86_64-w64-mingw32 * R was compiled by gcc.exe (GCC) 13.3.0 GNU Fortran (GCC) 13.3.0 * running under: Windows Server 2022 x64 (build 20348) * using session charset: UTF-8 * using option '--no-vignettes' * checking for file 'metaseqR2/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'metaseqR2' version '1.19.1' * 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 whether package 'metaseqR2' can be installed ... OK * used C compiler: 'gcc.exe (GCC) 14.2.0' * 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 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 ... NOTE getUcscUtr: no visible binding for global variable 'customDir' Undefined global functions or variables: customDir * 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: metaseqr2.Rd: render Please provide package anchors for all Rd \link{} targets not in the package itself and the base packages. * 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 line endings in C/C++/Fortran sources/headers ... OK * checking compiled code ... NOTE Note: information on .o files for x64 is not available * checking files in 'vignettes' ... OK * checking examples ... ERROR Running examples in 'metaseqR2-Ex.R' failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: getAnnotation > ### Title: Annotation downloader > ### Aliases: getAnnotation > > ### ** Examples > > mm10Genes <- getAnnotation("mm10","gene") Using Ensembl host https://jan2024.archive.ensembl.org Error in `req_perform()`: ! HTTP 500 Internal Server Error. Backtrace: ▆ 1. └─metaseqR2::getAnnotation("mm10", "gene") 2. └─metaseqR2:::getEnsemblAnnotation(org, type, ver) 3. └─biomaRt::useMart(biomart = dat, host = host, dataset = getDataset(org)) 4. └─biomaRt:::.useMart(...) 5. └─biomaRt:::.listMarts(...) 6. └─biomaRt:::bmRequest(...) 7. └─httr2::req_perform(request) 8. └─httr2:::handle_resp(req, resp, error_call = error_call) 9. └─httr2:::resp_failure_cnd(req, resp, error_call = error_call) 10. ├─rlang::catch_cnd(...) 11. │ ├─rlang::eval_bare(...) 12. │ ├─base::tryCatch(...) 13. │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers) 14. │ │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]]) 15. │ │ └─base (local) doTryCatch(return(expr), name, parentenv, handler) 16. │ └─base::force(expr) 17. └─rlang::abort(...) Execution halted * checking for unstated dependencies in 'tests' ... OK * checking tests ... Running 'runTests.R' ERROR Running the tests in 'tests/runTests.R' failed. Last 13 lines of output: 1 Test Suite : metaseqR2 RUnit Tests - 2 test functions, 1 error, 0 failures ERROR in test_estimate_aufc_weights: Error in req_perform(request) : HTTP 500 Internal Server Error. Test files with failing tests test_estimate_aufc_weights.R test_estimate_aufc_weights Error in BiocGenerics:::testPackage("metaseqR2") : unit tests failed for package metaseqR2 In addition: Warning message: The column that contains the gene biotypes ("embedCols$btCol") is missing with embedded annotation! Biotype filters and certain plots will not be available... Execution halted * 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: 2 ERRORs, 3 NOTEs See 'E:/biocbuild/bbs-3.21-bioc/meat/metaseqR2.Rcheck/00check.log' for details.
metaseqR2.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD INSTALL metaseqR2 ### ############################################################################## ############################################################################## * installing to library 'E:/biocbuild/bbs-3.21-bioc/R/library' * installing *source* package 'metaseqR2' ... ** this is package 'metaseqR2' version '1.19.1' ** using staged installation ** libs using C compiler: 'gcc.exe (GCC) 14.2.0' gcc -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -c pval.c -o pval.o pval.c: In function 'add_from_both_sides': pval.c:26:11: warning: unused variable 'esttotalperlength' [-Wunused-variable] 26 | double esttotalperlength = total/2; | ^~~~~~~~~~~~~~~~~ gcc -shared -s -static-libgcc -o metaseqR2.dll tmp.def pval.o -LC:/rtools45/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools45/x86_64-w64-mingw32.static.posix/lib -LE:/biocbuild/bbs-3.21-bioc/R/bin/x64 -lR installing to E:/biocbuild/bbs-3.21-bioc/R/library/00LOCK-metaseqR2/00new/metaseqR2/libs/x64 ** R ** data ** 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 (metaseqR2)
metaseqR2.Rcheck/tests/runTests.Rout.fail
R Under development (unstable) (2025-03-01 r87860 ucrt) -- "Unsuffered Consequences" Copyright (C) 2025 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 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. > BiocGenerics:::testPackage("metaseqR2") 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 Attaching package: 'S4Vectors' The following object is masked from 'package:utils': findMatches The following objects are masked from 'package:base': I, expand.grid, unname Attaching package: 'IRanges' The following object is masked from 'package:grDevices': windows 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 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 Attaching package: 'limma' The following object is masked from 'package:DESeq2': plotMA The following object is masked from 'package:BiocGenerics': plotMA locfit 1.5-9.12 2025-03-05 Attaching package: 'metaseqR2' The following object is masked from 'package:limma': readTargets Downsampling counts... Estimating initial dispersion population... Estimating dispersions using log-likelihood... Running simulations... This procedure requires time... Please wait...Using Ensembl host https://jan2024.archive.ensembl.org Timing stopped at: 3.35 0.16 117.4 Error in req_perform(request) : HTTP 500 Internal Server Error. In addition: There were 50 or more warnings (use warnings() to see the first 50) 2025-03-22 03:23:35: Data processing started... Read counts file: imported custom data frame Conditions: e14.5, adult_8_weeks Samples to include: e14.5_1, e14.5_2, a8w_1, a8w_2 Samples to exclude: none Requested contrasts: adult_8_weeks_vs_e14.5 Library sizes: e14.5_1: 3102907 e14.5_2: 2067905 a8w_1: 3742059 a8w_2: 4403954 Annotation: embedded Organism: mm9 Reference source: ensembl Count type: gene Analysis preset: medium_basic Transcriptional level: gene Exon filters: minActiveExons minActiveExons: exonsPerGene: 5 minExons: 2 frac: 0.2 Gene filters: length, avgReads, expression, biotype length: length: 500 avgReads: averagePerBp: 100 quantile: 0.25 expression: median: TRUE mean: FALSE quantile: NA known: NA custom: NA biotype: pseudogene: FALSE snRNA: FALSE protein_coding: FALSE antisense: FALSE miRNA: FALSE lincRNA: FALSE snoRNA: FALSE processed_transcript: FALSE misc_RNA: FALSE rRNA: TRUE sense_overlapping: FALSE sense_intronic: FALSE polymorphic_pseudogene: FALSE non_coding: FALSE three_prime_overlapping_ncrna: FALSE IG_C_gene: FALSE IG_J_gene: FALSE IG_D_gene: FALSE IG_V_gene: FALSE ncrna_host: FALSE Filter application: postnorm Normalization algorithm: edger Normalization arguments: method: TMM logratioTrim: 0.3 sumTrim: 0.05 doWeighting: TRUE Acutoff: -1e+10 p: 0.75 Statistical algorithm(s): edger, limma Statistical arguments: edger: classic, 5, 10, movingave, NULL, grid, 11, c(-6, 6), NULL, CoxReid, 10000, NULL, auto, NULL, NULL, NULL, NULL, 0.125, NULL, auto, chisq, TRUE, FALSE, c(0.05, 0.1) limma: none Meta-analysis method: simes Multiple testing correction: BH p-value threshold: 0.05 Logarithmic transformation offset: 1 Analysis preset: medium_basic Quality control plots: mds Figure format: png Output directory: E:\biocbuild\bbs-3.21-bioc\tmpdir\RtmpctXcux Output data: annotation, p_value, adj_p_value, meta_p_value, adj_meta_p_value, fold_change Output scale(s): natural, log2 Output values: normalized Loading gene annotation... Saving gene model to E:\biocbuild\bbs-3.21-bioc\tmpdir\RtmpctXcux/data/gene_model.RData Removing genes with zero counts in all samples... Normalizing with: edger Applying gene filter length... Threshold below which ignored: 500 Applying gene filter avgReads... Threshold below which ignored: 0.0659629215631332 Applying gene filter expression... Threshold below which ignored: 68 Applying gene filter biotype... Biotypes ignored: rRNA 2106 genes filtered out 1681 genes remain after filtering Running statistical tests with: edger Contrast: adult_8_weeks_vs_e14.5 Contrast adult_8_weeks_vs_e14.5: found 906 genes Running statistical tests with: limma Contrast: adult_8_weeks_vs_e14.5 Contrast adult_8_weeks_vs_e14.5: found 911 genes Performing meta-analysis with simes Building output files... Contrast: adult_8_weeks_vs_e14.5 Adding non-filtered data... binding annotation... binding p-values... binding FDRs... binding meta p-values... binding adjusted meta p-values... binding natural normalized fold changes... binding log2 normalized fold changes... Writing output... Adding filtered data... binding annotation... binding p-values... binding FDRs... binding meta p-values... binding adjusted meta p-values... binding natural normalized fold changes... binding log2 normalized fold changes... Writing output... Adding report data... binding annotation... binding meta p-values... binding adjusted meta p-values... binding log2 normalized fold changes... binding normalized mean counts... binding normalized mean counts... Creating quality control graphs... Plotting in png format... Plotting mds... Importing mds... Writing plot database in E:\biocbuild\bbs-3.21-bioc\tmpdir\RtmpctXcux/data/reportdb.js Creating HTML report... Compressing figures... adding: biocbuild/bbs-3.21-bioc/tmpdir/RtmpctXcux/plots/qc/mds.png (deflated 49%) Downloading required JavaScript libraries...trying URL 'https://raw.github.com/HubSpot/pace/v1.0.0/pace.min.js' Content type 'text/plain; charset=utf-8' length 12363 bytes (12 KB) ================================================== downloaded 12 KB trying URL 'https://code.highcharts.com/highcharts.js' downloaded 268 KB trying URL 'https://code.highcharts.com/highcharts-more.js' downloaded 92 KB trying URL 'https://code.highcharts.com/modules/exporting.js' downloaded 19 KB trying URL 'https://code.highcharts.com/modules/offline-exporting.js' downloaded 26 KB trying URL 'https://code.highcharts.com/modules/export-data.js' downloaded 12 KB trying URL 'https://unpkg.com/dexie@2.0.4/dist/dexie.min.js' Content type 'text/javascript' length 56670 bytes (55 KB) ================================================== downloaded 55 KB processing file: metaseqr2_report.Rmd output file: metaseqr2_report.knit.md "C:/PROGRA~1/Pandoc/pandoc" +RTS -K512m -RTS metaseqr2_report.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output pandoc154304b7a7c41.html --lua-filter "E:\biocbuild\bbs-3.21-bioc\R\library\rmarkdown\rmarkdown\lua\pagebreak.lua" --lua-filter "E:\biocbuild\bbs-3.21-bioc\R\library\rmarkdown\rmarkdown\lua\latex-div.lua" +RTS -K2048m -RTS --variable "material:true" --variable "lightbox:true" --variable "thumbnails:true" --variable "gallery:true" --variable "cards:true" --variable bs3=TRUE --standalone --section-divs --table-of-contents --toc-depth 1 --template "E:\biocbuild\bbs-3.21-bioc\R\library\rmdformats\templates\material\material.html" --highlight-style kate --variable theme=bootstrap --include-in-header "E:\biocbuild\bbs-3.21-bioc\tmpdir\RtmpctXcux\rmarkdown-str1543027d93bcf.html" Output created: E:/biocbuild/bbs-3.21-bioc/tmpdir/RtmpctXcux/index.html 2025-03-22 03:23:58: Data processing finished! Total processing time: 23 seconds RUNIT TEST PROTOCOL -- Sat Mar 22 03:23:58 2025 *********************************************** Number of test functions: 2 Number of errors: 1 Number of failures: 0 1 Test Suite : metaseqR2 RUnit Tests - 2 test functions, 1 error, 0 failures ERROR in test_estimate_aufc_weights: Error in req_perform(request) : HTTP 500 Internal Server Error. Test files with failing tests test_estimate_aufc_weights.R test_estimate_aufc_weights Error in BiocGenerics:::testPackage("metaseqR2") : unit tests failed for package metaseqR2 In addition: Warning message: The column that contains the gene biotypes ("embedCols$btCol") is missing with embedded annotation! Biotype filters and certain plots will not be available... Execution halted
metaseqR2.Rcheck/metaseqR2-Ex.timings
name | user | system | elapsed | |
buildAnnotationDatabase | 0 | 0 | 0 | |
buildCustomAnnotation | 0 | 0 | 0 | |
combineBonferroni | 0 | 0 | 0 | |
combineHarmonic | 0.00 | 0.00 | 0.05 | |
combineMaxp | 0 | 0 | 0 | |
combineMinp | 0 | 0 | 0 | |
combineSimes | 0 | 0 | 0 | |
combineWeight | 0 | 0 | 0 | |
createSignalTracks | 0.01 | 0.00 | 0.01 | |
diagplotAvgFtd | 0.16 | 0.04 | 0.19 | |
diagplotBoxplot | 1.04 | 0.11 | 1.16 | |
diagplotCor | 0.16 | 0.07 | 0.23 | |
diagplotDeHeatmap | 2.56 | 0.02 | 2.58 | |
diagplotEdaseq | 0.60 | 0.08 | 0.69 | |
diagplotFiltered | 0.06 | 0.01 | 0.07 | |
diagplotFtd | 0.05 | 0.02 | 0.07 | |
diagplotMds | 0.17 | 0.03 | 0.20 | |
diagplotNoiseq | 0.56 | 0.12 | 0.69 | |
diagplotPairs | 0.59 | 0.05 | 0.64 | |
diagplotRoc | 0.05 | 0.02 | 0.06 | |
diagplotVenn | 0.24 | 0.03 | 0.39 | |
diagplotVolcano | 2.03 | 0.06 | 2.09 | |
downsampleCounts | 0.23 | 0.00 | 0.24 | |
estimateAufcWeights | 1.02 | 0.08 | 1.09 | |
estimateSimParams | 0.98 | 0.05 | 1.03 | |