Thanks, Sean and all, for the fix. I have updated both devel and release versions. Hopefully, the error will be gone in the next build process.
Best, Jack Zhu From: Sean Davis <seand...@gmail.com> Date: Tuesday, December 3, 2024 at 11:36 AM To: Kern, Lori <lori.sheph...@roswellpark.org> Cc: bioc-devel@r-project.org <bioc-devel@r-project.org>, Zhu, Jack (NIH/NCI) [E] <zhuj...@mail.nih.gov> Subject: Re: [Bioc-devel] [EXTERNAL] SRAdb problems reported in the Multiple platform build/check report for BioC 3.21 Sorry, all, for not getting to this sooner. R.utils::gunzip() is a replacement. I created PRs for those changes, but I didn't test them. Let me know how it goes. Sean On Tue, Dec 3, 2024 at 10:31 AM Kern, Lori via Bioc-devel <bioc-devel@r-project.org<mailto:bioc-devel@r-project.org>> wrote: gunzip function was removed from GEOquery. See https://code.bioconductor.org/browse/GEOquery/commit/b3f81349f937870ae030757b454a02fa759b4da7 So you will either have to find a replacement function or implement your own. 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<mailto:bioc-devel-boun...@r-project.org>> on behalf of Zhu, Jack (NIH/NCI) [E] via Bioc-devel <bioc-devel@r-project.org<mailto:bioc-devel@r-project.org>> Sent: Tuesday, December 3, 2024 10:20 AM To: bioc-devel@r-project.org<mailto:bioc-devel@r-project.org> <bioc-devel@r-project.org<mailto:bioc-devel@r-project.org>> Subject: [Bioc-devel] FW: [EXTERNAL] SRAdb problems reported in the Multiple platform build/check report for BioC 3.21 Hi, I have been trying to fix the following error from the SRAdb building process at Bioconductor servers: * installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-library’ * installing *source* package ‘SRAdb’ ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading Error: object ‘gunzip’ is not exported by 'namespace:GEOquery' Execution halted ERROR: lazy loading failed for package ‘SRAdb’ * removing ‘/home/biocbuild/bbs-3.21-bioc/R/site-library/SRAdb’ Can you give me some suggestions? Best, Jack Zhu From: bbs-nore...@bioconductor.org<mailto:bbs-nore...@bioconductor.org> <bbs-nore...@bioconductor.org<mailto:bbs-nore...@bioconductor.org>> Date: Tuesday, November 26, 2024 at 12:02 PM To: Zhu, Jack (NIH/NCI) [E] <zhuj...@mail.nih.gov<mailto:zhuj...@mail.nih.gov>> Subject: [EXTERNAL] SRAdb problems reported in the Multiple platform build/check report for BioC 3.21 [This is an automatically generated email. Please don't reply.] Hi SRAdb maintainer, According to the Multiple platform build/check report for BioC 3.21, the SRAdb package has the following problem(s): o ERROR for 'R CMD INSTALL' on nebbiolo1. See the details here: https://bioconductor.org/checkResults/3.21/bioc-LATEST/SRAdb/nebbiolo1-install.html<https://secure-web.cisco.com/1AN4ZyYCv_R-nyMNRb7vc_mJo0zHixK_bK89bZoIGXUAYVJSMhCNMSqX0qp4BYFJm9jJU8tmYI_opDMRrCYAhuuAsrjF7tcY7kMmVGmPFKZLKGnfRIqYZX921k4VYbNH0nN4aBhMt7gH4FcYIuNeDNgmXPYbyhhHHSTq4Exo-Uo5XaMuoxQbXqnE-Ut7FEYHo03myzvwIBUAKmznyQeGeBoBlpn5dpnDfnMhB9_n1tkTpzTIP9b4uv7pi2A-pq0gh28ullTZC6B7e2JABv3FeDbC5_3MPOutDdrl4sS-Ok6-fyC79NziGX9VYqpIW4d9b/https%3A%2F%2Fbioconductor.org%2FcheckResults%2F3.21%2Fbioc-LATEST%2FSRAdb%2Fnebbiolo1-install.html> o ERROR for 'R CMD build' on nebbiolo1. See the details here: https://bioconductor.org/checkResults/3.21/bioc-LATEST/SRAdb/nebbiolo1-buildsrc.html<https://secure-web.cisco.com/1ZzGNu4CautDm4WowVnXhIbwiejsZcZQAdhkTVxt6M5TFsYtpqwUyyRbEZ1Hqdey_3HRbb2xjbjYG9orwW6xHV59kVvYuF_Q1Fz5Dj7iHHwGXcbOewrQHpaUrQFB3dzYKlYljBEVr-n3cAzyw4WfjQKU1Gq1GhnbXOMZ7zoH_pVxl4LsfuM7d0MhdXxbzeBj6koYRY8qnqN7AV4YtvE2b8Rs_2pRQeoSqYNJ1nh8787JPKk3_GT1P9l0mr9YwFqx_W6YqtI-Qj4kelqZpupiUevxG9YSgkD348eUSlBJBE7d1E7EXCu41DjEC-gFaV0hP/https%3A%2F%2Fbioconductor.org%2FcheckResults%2F3.21%2Fbioc-LATEST%2FSRAdb%2Fnebbiolo1-buildsrc.html> Please take the time to address this by committing and pushing changes to your package at git.bioconductor.org<http://git.bioconductor.org/> Notes: * This was the status of your package at the time this email was sent to you. 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