############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:BeadArrayUseCases.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings BeadArrayUseCases_1.45.1.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.21-data-experiment/meat/BeadArrayUseCases.Rcheck’ * using R Under development (unstable) (2025-03-13 r87965) * 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 24.04.2 LTS * using session charset: UTF-8 * checking for file ‘BeadArrayUseCases/DESCRIPTION’ ... OK * this is package ‘BeadArrayUseCases’ version ‘1.45.1’ * 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 ‘BeadArrayUseCases’ can be installed ... OK * checking installed package size ... INFO installed size is 249.8Mb sub-directories of 1Mb or more: extdata 249.7Mb * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... NOTE Malformed Description field: should contain one or more complete sentences. * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... 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 files in ‘vignettes’ ... OK * checking examples ... NONE * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... ERROR Error(s) in re-building vignettes: --- re-building ‘BeadArrayUseCases.rnw’ using Sweave 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: hexbin Welcome to beadarray version 2.57.0 Setting options('download.file.method.GEOquery'='auto') Setting options('GEOquery.inmemory.gpl'=FALSE) Loading required package: AnnotationDbi Loading required package: stats4 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: org.Hs.eg.db Sample Sheet /home/biocbuild/bbs-3.21-bioc/R/site-library/BeadArrayUseCases/extdata/Chips/sampleSheet.csv will be used to read the data Processing section 4613710017_B Processing section 4613710052_B Processing section 4613710054_B Processing section 4616443079_B Processing section 4616443093_B Processing section 4616443115_B Processing section 4616443081_B Processing section 4616443081_H Processing section 4616443092_B Processing section 4616443107_A Processing section 4616443136_A Processing section 4616494005_A HULKing section 4613710017_B Calculating Neighbourhood Using locs file to generate neighbours matrix Loading required package: illuminaHumanv3.db Annotating control probes using package illuminaHumanv3.db Version:1.26.0 Annotating control probes using package illuminaHumanv3.db Version:1.26.0 Annotating control probes using package illuminaHumanv3.db Version:1.26.0 Annotating control probes using package illuminaHumanv3.db Version:1.26.0 Annotating control probes using package illuminaHumanv3.db Version:1.26.0 Annotating control probes using package illuminaHumanv3.db Version:1.26.0 Loading required package: Biostrings Loading required package: XVector Loading required package: GenomeInfoDb Attaching package: ‘Biostrings’ The following object is masked from ‘package:base’: strsplit Loading required package: GenomicRanges Attaching package: ‘limma’ The following object is masked from ‘package:beadarray’: imageplot The following object is masked from ‘package:BiocGenerics’: plotMA Found 0 file(s) NA Error: processing vignette 'BeadArrayUseCases.rnw' failed with diagnostics: chunk 48 (label = readFromGEO) Error in httr2::req_perform(req) : HTTP 404 Not Found. --- failed re-building ‘BeadArrayUseCases.rnw’ SUMMARY: processing the following file failed: ‘BeadArrayUseCases.rnw’ Error: Vignette re-building failed. Execution halted * checking PDF version of manual ... OK * DONE Status: 1 ERROR, 1 NOTE See ‘/home/biocbuild/bbs-3.21-data-experiment/meat/BeadArrayUseCases.Rcheck/00check.log’ for details.