I am able to reproduce this locally
* checking for unstated dependencies in examples ... OK * checking installed files from 'inst/doc' ... OK * checking files in 'vignettes' ... OK * checking examples ... ERROR Running examples in 'uncoverappLib-Ex.R' failed The error most likely occurred in: > ### Name: buildInput > ### Title: Build input file > ### Aliases: buildInput > > ### ** Examples > > gene.list<- system.file("extdata", "mygene.txt", package = "uncoverappLib") > > bam_example <- system.file("extdata", "example_POLG.bam", + package = "uncoverappLib") > cat(bam_example, file = "bam.list", sep = "\n") > temp_dir=tempdir() > buildInput(geneList= gene.list, genome= "hg19", type_bam= "chr", + bamList= "bam.list",type_input="genes", outDir= temp_dir) Reading gene name started at: 2022-11-10 12:53:21.140608 Read 1 item 'select()' returned 1:many mapping between keys and columns Error in buildInput(geneList = gene.list, genome = "hg19", type_bam = "chr", : ERROR: unrecognized GENE NAME. Please remove genes stored in preprocessing_log1.txt Execution halted * checking for unstated dependencies in vignettes ... OK * checking package vignettes in 'inst/doc' ... OK * checking running R code from vignettes ... What version of R and Bioc are you using to test? You should be using R 4.2.2 and Bioc 3.16 Have you run a BiocManager::install() and BiocManager::valid() to ensure you are using the latest versions of all packages? Lori Shepherd - Kern Bioconductor Core Team Roswell Park Comprehensive Cancer Center Department of Biostatistics & Bioinformatics Elm & Carlton Streets Buffalo, New York 14263 ________________________________ From: Bioc-devel <bioc-devel-boun...@r-project.org> on behalf of Emanuela Iovino <emanuela.iov...@unibo.it> Sent: Tuesday, November 8, 2022 8:42 AM To: bioc-devel@r-project.org <bioc-devel@r-project.org> Subject: [Bioc-devel] R: uncoverappLib problems reported in the Multiple platform build/check report for BioC 3.16 Hi, I keep getting to receive an error in my package during check process, I tried to reproduce the error in my environment, but I cannot understand what it is going wrong, because devtools::check() and BiocCheck do not return any error, I guess that something's wrong in a file stored as example (mygene.txt) and despite I have modified it I receive the same error. Could you please help me to handle this? Thanks ________________________________ Da: bbs-nore...@bioconductor.org <bbs-nore...@bioconductor.org> Inviato: luned� novembre 2022 18:00 A: Emanuela Iovino <emanuela.iov...@unibo.it> Oggetto: uncoverappLib problems reported in the Multiple platform build/check report for BioC 3.16 [This is an automatically generated email. Please don't reply.] Hi uncoverappLib maintainer, According to the Multiple platform build/check report for BioC 3.16, the uncoverappLib package has the following problem(s): o ERROR for 'R CMD check' on nebbiolo2. See the details here: https://secure-web.cisco.com/1ye23e6VILCo8EGm_FZohksBP40u7sJ3WQpoPakwn0933iJny1qcPU7XRyU6P0dZnVrboE-a-vAnunNzohAlhsTPQ4nLnNVREHlrN2OrleZFQtDXV8x89Xc75R-sbHaEtaDT05samq7NVk8rwhF3zxdSA0gh2JkktsHmP2TllJPXGUmBD70gR-FPvSP46-Im5qOExaUKiesueZ2fFJbnnPaGVtAn9yl4nu7_WlJ7eGYQFZRW8219icQjwb5QLkQLvimXYCBrKrSuLonVGPHzXujRWJwhnSVDEAmEthQPbpssmWrriWihf2Gd10CMTIDRV/https%3A%2F%2Fmaster.bioconductor.org%2FcheckResults%2F3.16%2Fbioc-LATEST%2FuncoverappLib%2Fnebbiolo2-checksrc.html Please take the time to address this by committing and pushing changes to your package at git.bioconductor.org Notes: * This was the status of your package at the time this email was sent to you. 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