If the microbiome package is needed for functionality in your package, it should be listed as a dependency of your package DESCRIPTION. It currently is not listed as a Depend, Import, or Suggest. Linux will check that all needed dependencies are declared in the DESCRIPTION so that packages can have a clean independent install. I'm assuming since its only a suggest of ANCOMBC it does not do this automatically. Please consider adding microbiome as a Suggest to your package and I think the error would resolve.
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 Cao <caoyang.n...@gmail.com> Sent: Thursday, February 13, 2025 8:15 PM To: bioc-devel@r-project.org <bioc-devel@r-project.org> Subject: [Bioc-devel] Bioconductor checking error: example failed due to a suggest package of a dependecy package of my package Dear, I have addressed the checking error of my package *microbiomeMarker* and pushed the commit to the bioconductor repository. As shown in the checkResults package (https://secure-web.cisco.com/1HQJa5oZzllcg3nbwms_UbxNkzkfvBzTGOkc3X6h3mXVI60pEFVQrJmAkA--Mz8cMbQseMKWmKhkxu_OGlVgtk10zfK5BPqFtLJlHBYbwUjBKvL445hgAExPE53sRuN-OGrGy5-ldCuPpqlaRDZ6tDvKGG7v0g-F3E1SoB_7FlD2a3RUdrOQTvspa3TJtqtUM4LYUocU8X3uac7fzBQ4_xxD-kvgZTul3nhnxaVrTXjA8G3gE_-5IWv-0m6NZNZVQ1eE7xllrfVFDvGf3ss2Dr3aFAI5aSK030jmSCdikAuHkg9eHJI5iZ6bIT4rXIjSGT4ATmUd7opfiToc6BWGkCw/https%3A%2F%2Fbioconductor.org%2FcheckResults%2Frelease%2Fbioc-LATEST%2FmicrobiomeMarker%2F), all checks passed for windows and mac os. But for Linux (Ubuntu), an error occurred while checking the example in function /run_ancombc/: Running examples in ‘microbiomeMarker-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: run_ancombc > ### Title: Differential analysis of compositions of microbiomes with bias > ### correction (ANCOM-BC). > ### Aliases: run_ancombc > > ### ** Examples > > data(enterotypes_arumugam) > ps <- phyloseq::subset_samples( + enterotypes_arumugam, + Enterotype %in% c("Enterotype 3", "Enterotype 2") + ) > run_ancombc(ps, group = "Enterotype") 'ancombc' has been fully evolved to 'ancombc2'. Explore the enhanced capabilities of our refined method! Checking the input data type ... The input data is of type: phyloseq Error in data_sanity_check(data = data, taxa_are_rows = taxa_are_rows, : The 'microbiome' package is needed to process the imported data but is not installed. Please install the package to continue. Calls: run_ancombc -> <Anonymous> -> data_sanity_check Execution halted The package *microbiome *is in the Suggests list of *ANCOMBC *packge, and ANCOMBC is in the Import list of *microbiomeMarker*. Why is the *microbiome* package not installed automatically on Linux，how can I fix this checking error? Thanks for your attention! Sincerely, Yang Cao [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://secure-web.cisco.com/12K7YkPT2UeDPD77h5Kxk0cWbi6CFzGE8GhWaRWQGN-mpIDmgz9y0IqsUJFArGwf7ElKTFeHuL4M9-r8jCYX02l6LZAGQQsC8Qi8KHYVrdoajSjrDbcUbSd-xG1cjdHz8yU1Jy2WiQovWeMmE5S5bLjdAG3cke5zJq7_NvalWZX6DdBztaMngeAv4wDTisyKbP6PDSq2IvlgZ48cUpRXndAVeBkYp_RMoG02DKhmB4_0la8zBiwDhKkcsXKd6K5p58sYhFyWvdLSCuEvTgvCPZgU8Dvcw-kGWUt2y4v4whvT0hTjaIPB1BLT5pXK6k7FkikRsywaLSuohlI2uYohUGg/https%3A%2F%2Fstat.ethz.ch%2Fmailman%2Flistinfo%2Fbioc-devel This email message may contain legally privileged and/or confidential information. If you are not the intended recipient(s), or the employee or agent responsible for the delivery of this message to the intended recipient(s), you are hereby notified that any disclosure, copying, distribution, or use of this email message is prohibited. If you have received this message in error, please notify the sender immediately by e-mail and delete this email message from your computer. Thank you. [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
