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> 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> on behalf of Zhu, > Jack (NIH/NCI) [E] via Bioc-devel <bioc-devel@r-project.org> > Sent: Tuesday, December 3, 2024 10:20 AM > To: bioc-devel@r-project.org <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 <bbs-nore...@bioconductor.org> > Date: Tuesday, November 26, 2024 at 12:02 PM > To: Zhu, Jack (NIH/NCI) [E] <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 > > Notes: > > * This was the status of your package at the time this email was sent to > you. > Given that the online report is updated daily (in normal conditions) > you > could see something different when you visit the URL(s) above, > especially if > you do so several days after you received this email. > > * It is possible that the problems reported in this report are false > positives, > either because another package (from CRAN or Bioconductor) breaks your > package (if yours depends on it) or because of a Build System problem. > If this is the case, then you can ignore this email. > > * Please check the report again 24h after you've committed your changes > to the > package and make sure that all the problems have gone. > > * If you have questions about this report or need help with the > maintenance of your package, please use the Bioc-devel mailing list: > > https://bioconductor.org/help/mailing-list/< > https://secure-web.cisco.com/13ShfWUilJ7HSUJJNxhvdff22zE5_XmjO_2QCpkqfTBSByH9dEez9DqMIFyK1_2iwGwalvz95hRGjr3HkgE2LhTtkN873R3RUb899FqzdozKq1jkWiUOXk0NyF4VsVoO44oIYwzGzr4gf5H_im36jyzQs0nrHsW4DJS_e-ret7bTQmLN-S62P4Pz73cGDbZWhcXyCQFwcJBG3xZnNbp_Cc6hooFH2W9C_Yk5YVErSOwXZ4cLJ-9rHK1R53MlwcVtyRIjCxXXB-YXLg2SfJoF7NsexkgaPagQPLB08iyb39E1bxRXA3MwpRvWdBmjEW1-b/https%3A%2F%2Fbioconductor.org%2Fhelp%2Fmailing-list%2F > > > > (all package maintainers are requested to subscribe to this list) > > For immediate notification of package build status, please > subscribe to your package's RSS feed. 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