[Bioc-devel] [EXTERNAL] SRAdb problems reported in the Multiple platform build/check report for BioC 3.21

Tue Dec 3 17:35:31 CET 2024

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 using 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-bounces using r-project.org> on behalf of Zhu,
> Jack (NIH/NCI) [E] via Bioc-devel <bioc-devel using r-project.org>
> Sent: Tuesday, December 3, 2024 10:20 AM
> To: bioc-devel using r-project.org <bioc-devel using 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-noreply using bioconductor.org <BBS-noreply using bioconductor.org>
> Date: Tuesday, November 26, 2024 at 12:02 PM
> To: Zhu, Jack (NIH/NCI) [E] <zhujack using 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:
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