############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD check --install=check:metaseqR2.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings metaseqR2_1.18.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/metaseqR2.Rcheck’ * using R version 4.4.1 (2024-06-14) * using platform: aarch64-unknown-linux-gnu * R was compiled by gcc (GCC) 12.2.1 20220819 (openEuler 12.2.1-14) GNU Fortran (GCC) 10.3.1 * running under: openEuler 22.03 (LTS-SP1) * 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: ‘gcc (conda-forge gcc 14.2.0-1) 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 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 ... 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... 2024-11-20 09:49:09: 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: /home/biocbuild/tmp/RtmppHlu52/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 /home/biocbuild/tmp/RtmppHlu52/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... Importing mds... Writing plot database in /home/biocbuild/tmp/RtmppHlu52/test1/data/reportdb.js Creating HTML report... Compressing figures... adding: home/biocbuild/tmp/RtmppHlu52/test1/plots/qc/mds.png (deflated 42%) 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 272 KB trying URL 'https://code.highcharts.com/highcharts-more.js' downloaded 95 KB trying URL 'https://code.highcharts.com/modules/exporting.js' downloaded 19 KB trying URL 'https://code.highcharts.com/modules/offline-exporting.js' downloaded 9865 bytes trying URL 'https://code.highcharts.com/modules/export-data.js' downloaded 12 KB trying URL 'http://jvenn.toulouse.inrae.fr/app/js/canvas2svg.js' Content type 'application/javascript' length 35122 bytes (34 KB) ================================================== downloaded 34 KB trying URL 'http://jvenn.toulouse.inrae.fr/app/js/jvenn.min.js' Content type 'application/javascript' length 100524 bytes (98 KB) ================================================== downloaded 98 KB trying URL 'https://unpkg.com/dexie@2.0.4/dist/dexie.min.js' Warning in download.file("https://unpkg.com/dexie@2.0.4/dist/dexie.min.js", : cannot open URL 'https://unpkg.com/dexie@2.0.4/dist/dexie.min.js': HTTP status was '520 Unknown Error' Error in download.file("https://unpkg.com/dexie@2.0.4/dist/dexie.min.js", : cannot open URL 'https://unpkg.com/dexie@2.0.4/dist/dexie.min.js' Calls: metaseqr2 -> .downloadJsLibs -> download.file Execution halted * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘runTests.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, 2 NOTEs See ‘/home/biocbuild/bbs-3.20-bioc/meat/metaseqR2.Rcheck/00check.log’ for details.