############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:metaseqR2.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings metaseqR2_1.18.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/metaseqR2.Rcheck’ * using R version 4.4.2 (2024-10-31) * using platform: aarch64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0 * running under: macOS Ventura 13.7.1 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘metaseqR2/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘metaseqR2’ version ‘1.18.0’ * 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 ‘metaseqR2’ can be installed ... OK * used C compiler: ‘Apple clang version 15.0.0 (clang-1500.0.40.1)’ * used SDK: ‘MacOSX11.3.sdk’ * 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 ... 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 line endings in C/C++/Fortran sources/headers ... OK * checking compiled code ... NOTE Note: information on .o files 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: metaseqr2 > ### Title: The main metaseqr2 pipeline > ### Aliases: metaseqr2 > > ### ** Examples > > # An example pipeline with gene counts > data("mm9GeneData",package="metaseqR2") > > result <- metaseqr2( + counts=mm9GeneCounts, + sampleList=sampleListMm9, + contrast=c("adult_8_weeks_vs_e14.5"), + libsizeList=libsizeListMm9, + annotation="embedded", + org="mm9", + countType="gene", + normalization="edger", + statistics="edger", + pcut=0.05, + figFormat="png", + qcPlots="mds", + exportWhat=c("annotation","p_value","adj_p_value","fold_change"), + exportScale="natural", + exportValues="normalized", + exportStats="mean", + exportWhere=file.path(tempdir(),"test1"), + restrictCores=0.01, + geneFilters=list( + length=list( + length=500 + ), + avgReads=list( + averagePerBp=100, + quantile=0.25 + ), + expression=list( + median=TRUE, + mean=FALSE, + quantile=NA, + known=NA, + custom=NA + ), + biotype=getDefaults("biotypeFilter","mm9") + ), + outList=TRUE + ) Warning: The column that contains the gene biotypes ("embedCols$btCol") is missing with embedded annotation! Biotype filters and certain plots will not be available... 2025-03-01 00:38:40: 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 Transcriptional level: gene Exon filters: minActiveExons minActiveExons: exonsPerGene: 5 minExons: 2 frac: 0.2 Gene filters: length, avgReads, expression length: length: 500 avgReads: averagePerBp: 100 quantile: 0.25 expression: median: TRUE mean: FALSE quantile: NA known: NA custom: NA 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 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) Meta-analysis method: none Multiple testing correction: BH p-value threshold: 0.05 Logarithmic transformation offset: 1 Quality control plots: mds Figure format: png Output directory: /tmp/RtmpIUWxQE/test1 Output data: annotation, p_value, adj_p_value, fold_change Output scale(s): natural Output values: normalized Loading gene annotation... Saving gene model to /tmp/RtmpIUWxQE/test1/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 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 Building output files... Contrast: adult_8_weeks_vs_e14.5 Adding non-filtered data... binding annotation... binding p-values... binding FDRs... binding natural normalized fold changes... Writing output... Adding filtered data... binding annotation... binding p-values... binding FDRs... binding natural normalized fold changes... Writing output... Adding report data... binding annotation... binding p-values... binding FDRs... binding log2 normalized fold changes... binding normalized mean counts... binding normalized mean counts... Creating quality control graphs... Plotting in png format... Plotting mds...2025-03-01 00:38:40.792 R[4189:256360678] XType: Using static font registry. Importing mds... Writing plot database in /tmp/RtmpIUWxQE/test1/data/reportdb.js Creating HTML report... Compressing figures... adding: tmp/RtmpIUWxQE/test1/plots/qc/mds.png (deflated 39%) 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 'http://jvenn.toulouse.inrae.fr/app/js/canvas2svg.js' Warning in download.file("http://jvenn.toulouse.inrae.fr/app/js/canvas2svg.js", : downloaded length 0 != reported length 299 Warning in download.file("http://jvenn.toulouse.inrae.fr/app/js/canvas2svg.js", : cannot open URL 'https://jvenn.toulouse.inrae.fr/app/js/canvas2svg.js': HTTP status was '503 Service Unavailable' Error in download.file("http://jvenn.toulouse.inrae.fr/app/js/canvas2svg.js", : cannot open URL 'http://jvenn.toulouse.inrae.fr/app/js/canvas2svg.js' Calls: metaseqr2 -> .downloadJsLibs -> download.file 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_metaseqr: Error in download.file("http://jvenn.toulouse.inrae.fr/app/js/canvas2svg.js", : cannot open URL 'http://jvenn.toulouse.inrae.fr/app/js/canvas2svg.js' Test files with failing tests test_metaseqr.R test_metaseqr Error in BiocGenerics:::testPackage("metaseqR2") : unit tests failed for package metaseqR2 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, 2 NOTEs See ‘/Users/biocbuild/bbs-3.20-bioc/meat/metaseqR2.Rcheck/00check.log’ for details.